Only genes for which expression was significantly altered in Sirt

Only genes for which expression was significantly altered in Sirt6-null hepatocytes (signal log ratio >1 and filtered for absent calls) were included as part of the Sirt6 signature. The resulting Sirt6

signature contained 1,615 probe IDs representing 1,241 genes (Supporting Table 1). Eighteen of the most deregulated targets were further validated using qRT-PCR (Supporting Fig. 1) overall demonstrating a high concordance (P < 0.001; r = 0.85). Next, we investigated in more detail the functional enrichment of these genes in Ku-0059436 different networks and signaling pathways by using ingenuity pathway analysis and the GeneGo microarray analysis tools. The two most significant pathway map folders were related to cell cycle and its regulation and cholesterol/bile acid homeostasis (Table 1). Dysregulated pathways also included tissue remodeling and wound repair, lipid biosynthesis, and immune system response as well as nuclear GSI-IX molecular weight receptor signaling. Additional map folders with a significant number of genes affected by the loss of Sirt6 were involved in mitogenic signaling, cell differentiation, DNA damage response, and apoptosis. Furthermore, canonical pathways and signaling resembling NF-κB and insulin-like growth factor (IGF) signaling were consistently activated in Sirt6-deficient hepatocytes (Supporting Fig. 2). The analyses suggested that loss of Sirt6 predisposes

hepatocytes for oncogenic transformation. To validate the results, we performed qRT-PCR and western blot analyses of selected HCC marker genes in serum samples and isolated hepatocytes from WT and Sirt6-deficient animals (Fig. 2). For these

studies, we examined Afp, Igf2, H19, and glypican-3 as well-established HCC biomarkers that we found to be up-regulated in our microarray analysis. Consistently, these genes were more abundantly expressed in Sirt6 KO hepatocytes compared with WT littermates. Afp and Igf2 were readily detectable on western blots of serum, and in the case of Afp, in hepatocytes from Sirt6 KO mice (Fig. 2B). Also, the recently reported H19-derived miRNA-675 was elevated in hepatocytes of KO animals (Fig. 2B, right panel). These results confirm that key oncogenic molecules associated with hepatocarcinogenesis are affected by the loss of Sirt6 signaling, thus strengthening the validity of the results from the microarrays. We next characterized a series of human hepatoma selleck chemicals llc cell lines for SIRT6 expression in comparison with that of the series of HCC biomarkers (Fig. 3). SIRT6 was consistently down-regulated in comparison to primary human hepatocytes in all hepatoma cell lines examined. AFP was up-regulated in all cell lines compared with primary hepatocytes. IGF2 was up-regulated in all cell lines except PLC/PRF/5 cells. H19 was increased in Hep3B only. Taken together, these results suggest that the deregulation of SIRT6 and genes in the SIRT6 signature can at least in part be recapitulated in established hepatoma lines.

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