Abstract Highly homologous putative GTPase-activating proteins IQGAP1 and IQGAP2 are multidomain scaffolding proteins that juxtapose Rho GTPases Rac1 and Cdc42, Ca2+/calmodulin signals and cytoskeletal reorganization events. Previously, we found that IQGAP2 deficiency in mice leads to the development of hepatocellular carcinoma (HCC), identifying IQGAP2 as a potential tumor suppressor gene (Schmidt VA, et al. MCB 2008; 28:1489-502). Moreover, mice deficient in both Iqgap1 and Iqgap2 genes displayed relative protection against HCC and enhanced long-term survival, indicating opposing roles for IQGAP2 and IQGAP1 in hepatic carcinogenesis. We hypothesized that diminished levels of hepatic IQGAP2 expression, along with subsequent upregulation of IQGAP1, may have a causative effect in the development of HCC in humans. To test this, we first evaluated mRNA transcript and protein expression in an array of liver samples from patients with HCC of different etiologies using qRT-PCR and immunohistochemistry (IHC). qPCR TissueScan Array™ containing 23 individual cDNAs from patients with primary HCC of different stages and non-malignant adjacent tissue controls demonstrated decreased expression of IQGAP2 transcript in HCC tumors compared to normal tissue, and the magnitude of the decrease in expression correlated with progression of disease. The lowest IQGAP2 transcript expression was observed at the most advanced stage IV HCC, a 4-fold decrease compared to the non-malignant controls. At the protein level, lack of IQGAP2 expression was confirmed in 100% (36/36) of formalin-fixed paraffin-embedded human HCC livers studied by IHC. All samples also showed a significant overexpression of IQGAP1. Normal livers (13/13), cirrhotic livers (23/23), and benign hepatic adenomas (4/4) showed the reverse, i.e. a high level of IQGAP2 expression and very low levels of IQGAP1. Next, functional studies using RNAi technology showed that knockdown of IQGAP2 expression in HepG2 cells leads to a 50% increase in their migratory capacity, while IQGAP1 siRNA has the opposite effect. Finally, the gene expression profile of Iqgap2−/− mouse liver using the Mouse Genome 430 2.0 Array chip (Affymetrix) identified 294 genes which were expressed differentially in Iqgap2−/− HCC livers compared to age-matched disease-free wild-type controls (N=3 in each group). The differentially expressed genes (at least 2-fold change, p<0.05) included those encoding proteins associated with Wnt/beta-catenin signaling pathway activation (Igf2r, Sp5, Ccnb2, Ccnd1, Wif1 and Ctnnbip1) and tumor metastasis (Cdh1, Ctsl, Hgf, Fn1, Hpse and Timp2). Collectively, these findings validate the relevance of the Iqgap2−/− mouse model to human disease and identify a novel IQGAP-dependent pathway regulating HCC development. Modulation of both IQGAP1 and IQGAP2 expression represents a new potential therapeutic strategy for liver cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4996.