br Materials and methods br Results

Materials and methods
Results
Discussion Cdc42 has been implicated in mediating the entry of HCV into hepatocytes, but how Cdc42 affects the response of HCV patients to IFN therapy is unknown. This study therefore examined the genetic association between Cdc42-related genes and efficacy of IFN therapy and identified the ACK1 gene at chromosome 3q29 as a new candidate susceptibility gene. Association analysis revealed that HCV-infected Japanese carriers of the homozygous ACK1 rs2278034 GG genotype were more likely to achieve sustained viral response with IFN monotherapy (Table 2, Table 3). Using Bonferroni correction in the analysis of two independent patient data sets strongly supports an association of this ACK1 locus with the outcome of IFN therapy. Detailed re-sequencing failed to identify further non-synonymous allelic variants in ACK1, implicating the rs2278034 G allele as the sole susceptible allele for IFN response. On the other hand, the most effective standard therapy in hepatitis C patients is considered to be a combination of pegylated IFNα and ribavirin [5]. Our association analysis revealed that the ACK1 variant was not associated with treatment outcome in subjects treated with PEG-IFN and ribavirin therapy but the reason is unclear. One possible explanation for the lack of an association between the ACK1 rs2278034 polymorphism and SVR in treatment with PEG-IFN and ribavirin combination therapy is that the effect of rs2278034 is rather modest and does not influence treatment outcome when a more effective therapy is used. The ACK1 SNP associated with the IFN therapy is located in the genomic intron, thus confirmation was sought as to whether variants of this SNP affect the PHA-793887 of ACK1. The results of ACK1 variant and ISG gene expression analysis seem to support the hypothesis that genetic variants in ACK1 affect the expression of ACK1 and might additionally explain the association between the SNP genotype and the effect of IFN therapy for HCV infection. However, the present study did not analyze the functional effect of the intronic SNP on gene transcription, and further functional studies are needed to clarify such an association. Expression analysis using publicly available HapMap data revealed that ACK1 expression apparently correlate with ISGs levels. These data suggest that ACK1 might play a role in IFN-signaling pathways, and support, albeit indirect, the physiological relevance of our in vitro findings. Interestingly, in other ethnic groups, the rs2278034 variant affects neither ACK1 nor ISG expression. These findings may suggest that rs2278034 is not directly causal but instead serves as a marker variant within Asian populations. Additionally more intensive re-sequencing is needed to explore if a true causal variant exists. The activity of many protein kinases is controlled by reversible phosphorylation in the activation loop of the catalytic domain. Tyr416 and Tyr284 are the main phosphorylation sites in ACK1. Yokoyama and Miller [35] mapped the major autophosphorylation site of ACK1 to Tyr284, and mutation of Tyr284 decreased phosphorylation dramatically in mammalian cells. It was proposed that Cdc42-GTP targets ACK1 but plays no role in modulating kinase function [23]. Based on this assumption, two expression vectors were constructed in the present study: full-length ACK1 for wild-type ACK1 and the Y284F mutant of ACK1 for its inactive form. It was subsequently demonstrated that ACK1 could induce the IFN-susceptible genes (ISGs) through the ISRE or GAS element present within the ISG promoters, although ACK1-m did not induce ISG activity. Finally, the results also demonstrated for the first time that ACK1 could suppress viral replication of HCV replicons. The JAK-STAT signaling pathway plays an important role in IFN biological activity, and STAT1 and STAT2 are required for this signal [37]. It was reported previously that ACKs translocate into the nucleus after binding to Cdc42 [38], suggesting that ACKs alter the transcription of ACK-specific genes. This hypothesis was tested in the current study by examining the STAT-related signaling. ACK1 induced the tyrosine phosphorylation of STAT1, indicating that ACK1 might have induced ISGs via this mechanism.