Gene P. Siegal, M.D., Ph.D. Editor-in-Chief, Laboratory Investigation November 20, 2013 Dear Dr. Siegal: Thank you very much for your interest in reviewing our revised manuscript entitled “Modulation of PI3K-LXR-dependent lipogenesis mediated by oxidative/nitrosative stress contributes to inhibition of HCV replication by quercetin“, by Sandra Pisonero-Vaquero et al, with reference 13-0320-RA. We appreciate the comments made by the two reviewers, which we find very reasonable. Consequently, we have made the appropriate changes in a revised version of the manuscript, underlining the text that has been modified, and providing a point-by-point response to each of the reviewer comments as follows: POINT BY POINT RESPONSE TO THE COMMENTS OF REVIEWER 1 1. As reviewer rightly stated, HCV replication inhibitory effect of quercetin at very low concentrations are surprising. In the present research, doses of selected flavonoids were chosen based on our previous experience with these compounds. In this regard, we have observed that at doses higher than 10 M flavonoids, including quercetin, did not inhibit replication in HCV replicon systems, as showed by Gonzalez O et al. in line with the findings of our study (Hepatology, 2009, ref 21 in the revised manuscript). These results can be explained by its antioxidant capacity itself, given that it has been described that high rates of lipid peroxidation led to reduced HCV replication which can be blocked by antioxidants (Huang H et al., Proc Natl Acad Sci U.S.A., 2007, ref 30 in the revised manuscript). Moreover, it has been described that several flavonoids are able to suppress the replication in both non-infectious replicon cells and in HCV-JFH1 cell culture system at doses below 5 M (Sekine-Osajima Y et al., Hepatol Res, 2009; Liu MM, Eur J Med Chem et al., 2012), supporting the effect of treatment with flavonoids on HCV replication efficiency showed in our in vitro model. Sekine-Osajima Y, Sakamoto N, Nakagawa M, Itsui Y, Tasaka M, Nishimura-Sakurai Y, Chen CH, Suda G, Mishima K, Onuki Y, Yamamoto M, Maekawa S, Enomoto N, Kanai T, Tsuchiya K, Watanabe M. Two flavonoids extracts from Glycyrrhizae radix inhibit in vitro hepatitis C virus replication. Hepatol Res. 2009. 39(1):60-9. Liu MM, Zhou L, He PL, Zhang YN, Zhou JY, Shen Q, Chen XW, Zuo JP, Li W, Ye DY. Discovery of flavonoid derivatives as anti-HCV agents via pharmacophore search combining molecular docking strategy. Eur J Med Chem. 2012. 52:33-43. 2. As indicated in the revised manuscript, the vehicle used for all treatments was DMSO (0.05%). HCV-G1 control cells were incubated with the same DMSO concentration alone (vehicle-treated cells) (2nd paragraph, page 7). Therefore, as requested by the reviewer, solvent controls are now indicated in the revised manuscript and supplementary figure 1. 3. While the molecular mechanisms involved in quercetin-mediated impairment of HCV replication seem to be very complex, in our HCV replicon system we proposed that quercetin might exert its inhibitory effect on HCV replication at least in part through oxidative/nitrosative stress blockage and lipid accumulation reduction, which in turn contributes to the efficient replication of HCV (García-Mediavilla MV et al., Lab Invest, 2012, ref 15 in the revised manuscript). As indicated in the manuscript, quercetin also may inhibit HCV replication by increasing the antiviral gene expression regulated by the IFN-activated JAK-STAT pathway, by reducing the NS5A-driven augmentation of IRES-mediated translation and by inhibiting both NS3 and heat shock proteins essential for HCV replication. In addition to these molecular mechanisms, and on the basis of experimental findings obtained in the present study, we argue that oxidative/nitrosative stress inhibition and subsequent lipid metabolism modulation might contribute to the indirect blockage of HCV replication and protein expression by quercetin. Along this line, similar mechanisms have been proposed for curcumin which decrease HCV gene expression via suppression of the AKT-SREBP-1 activation (Kim et al., FEBS Lett, 2010, ref 34 in the revised manuscript). However, we agree with the reviewer and the conclusions have been tempered as suggested (see abstract and the discussion section of the revised version of the manuscript). 4. As reviewer mentioned, total AKT protein levels seem to be suppressed by quercetin in a dose-dependent manner, though AKT/-actin ratio remains constant independently of quercetin concentration. Moreover, we represented pAKT/AKT ratio which decreases indicating a reduction in AKT phosphorylation levels when quercetin concentration is increased. 5. We apologize for these confusing data. In response to the reviewer, we repeated these experiments and included a new experimental group. Figure 7 (B-E) has been modified, substituting results from HCV-G1 cells treated only with LY294002 for 8 h by HCV-G1 cells pretreated for 8 h with LY294002 and then incubated with vehicle for an additional 48 h, as indicated in material and methods in the revised version of the manuscript. POINT BY POINT RESPONSE TO THE COMMENTS OF REVIEWER 2 1. In our study, quercetin inhibits HCV replication and proteins NS5A and core expression. Nonstructural protein 5A (NS5A) has been implicated in regulation of viral genome replication, translation from the viral IRES and viral packaging (Gonzalez O et al., Hepatology, 2009, ref 21 in the revised manuscript) and HCV core protein has been shown to inhibit mitochondrial electron transport and to increase reactive oxygen species in vitro and in vivo, which can be restored by reducing HCV replication (Ando M et al., Liver Int, 2008, ref 41). Thus, we agree with the reviewer that the effects of quercetin on redox status should be mediated by reducing HCV replication and HCV NS5A and core protein expression, as previously suggested (Harris C et al., J Biol Chem, 2011, ref 47 in the revised manuscript). However, our results indicated that quercetin exerts an antioxidant effect which in turn reduces lipogenesis and lipid accumulation, contributing to HCV replication and protein expression inhibition in HCV-replicating cells, as previously indicated (García-Mediavilla MV et al., Lab Invest, 2012, ref 15 in the revised manuscript). Therefore, we suggested that the inhibitory effect of quercetin on HCV replication might be exerted at least in part through these indirect mechanisms involving redox status and lipid accumulation. 2. As reviewer requested, we studied the effect of IFNtreatment on LXR expression in our adenoviral in vitro model. Thus, Figure 6 has been modified, including data from Huh7 Ad-0.5 cells treated with IFN-2b (0.5 and 50 U/ml) (see material and methods, results and discussion sections and figure 6 legend in the revised version of the manuscript). As indicated by the reviewer, unlike quercetin, in HCV-replicating cells IFN-2b treatment inhibited HCV-induced LXR gene expression in a PI3K-AKTindependent manner. Furthermore, in our in vitro model of LXRoverexpression in wild type Huh7 cells IFN treatment did not repress LXR gene expression, suggesting that the effect of IFN on lipogenesis modulation is mediated by its anti-HCV activity, as previously indicated (Toyoda M et al., Int J Mol Med, 2011, ref 49 in the revised manuscript). 3. and 4. As reviewer also suggested, we studied the effect of PI3K pathway inhibition on LXR expression in our adenoviral in vitro model. Similarly, LY294002 (50M) treatment was not able to repress the overexpression of the nuclear receptor LXR in Huh7 cells infected with the adenoviral vector (data not shown). As reviewer rightly mentioned, and on the basis of experimental findings obtained in the present study, we speculated that “In our in vitro model of LXR overexpression, quercetin could exert its inhibitory effect on LXRexpression and lipid accumulation not only through modulation of PI3K pathway but also the expression of a large number of miRNAs involved in cell signaling and metabolism, which could in turn cause down-regulation of CMV-expressed LXR”. Obviously, this is merely a hypothesis which has to be confirmed or not in future experimental studies. Due to the above referred modifications, we are submitting a revised version of the manuscript (reference 13-0320-RAR), in the hope it is now suitable for publication in Laboratory Investigation. Once again we thank you for your interest in reviewing our paper and we look forward to hearing from you at your earliest convenience. Yours sincerely, Sonia Sánchez Campos Ph.D. Department of Biomedical Sciences Institute of Biomedicine University of León, Spain Phone +34 987 291266 Fax +34 987 291267 E-mail ssanc@unileon.es