FULL MANUSCRIPT Three Gene Signature for Predicting the Development of Hepatocellular Carcinoma in Chronically Infected Hepatitis C Virus Patients Marwa K. Ibrahim, 1 Hosny Salama, 2 Mohamad Abd El Rahman, 3 Reham M. Dawood, 1 Noha G. Bader El Din, 1 Heba F. Salem, 4 Mohamed E.A. Abdelrahim, 5 Dalia Omran, 2 Moataza H. Omran, 1 Khaled Helmi El-Wakeel, 6 Tawfeek H. Abdelhafez, 1 Ahmed Khedr, 1 and Mostafa K. El Awady 1 Hepatitis C virus (HCV) is the leading cause of liver fibrosis and hepatocellular carcinoma (HCC). At present, there is no predictive biomarker for the patients at high risk of developing HCC. In this study, we examined the association between single-nucleotide polymorphisms (SNPs) in 3 innate immunity genes [2¢-5¢oligoadenylate synthetase 1 (OAS1) rs10774671, interleukin 28B (IL28B) rs12979860, and low molecular mass polypeptide 7 (LMP-7) at codon 49] besides cytomegalovirus (CMV) coinfection and susceptibility to HCC in genotype 4 (GT4) chronically infected Egyptian patients. SNPs were determined using restriction fragment length poly- morphism analysis in DNA from HCC patients (n = 34) and compared with either controls (n = 70) or patients with early grades of liver fibrosis (n = 49). Our results demonstrated that patients bearing the genetic combi- nation consisting of LMP-7 CA/AA [OR 4.75, 95% confidence interval (CI) 1.443–15.631, P = 0.007] and IL28B rs12979860 CT/TT (OR 6.00, 95% CI 1.603–22.455, P = 0.004) and positive for CMV viremia (OR 3.11, 95% CI 1.151–8.412, P = 0.02) were more likely to have HCC. However, OAS1 rs10774671 does not seem to contribute to the development of HCC. Binary regression analysis indicated that HCC risk significantly in- creases with the presence of each unfavorable genotype (LMP-7 CA/AA, IL28B rs12979860 CT/TT), when accompanied by the existence of CMV coinfection (probability of HCC risk is 0.8 for combined factors versus 0.14, 0.07, and 0.07 for individual factor IL28B, LMP-7, and CMV; respectively). These data suggest that the 2 SNPs and the coinfection in concert have potential in predicting the risk of HCC development in patients infected with HCV GT4. Keywords: LMP7, OAS1, IL28B, liver fibrosis, HCV, HCC Introduction H epatitis C virus (HCV) infection is a serious health problem with more than 150 million infected people all over the world (Mohd Hanafiah and others 2013; WHO 2014). The chronic HCV infection gives rise to liver diseases that ends up with cirrhosis and hepatocellular carcinoma (HCC) in 27% and 25% of the patients, respectively. HCC is ranked as the fifth commonest cancer and the third cause of cancer death in the world (Li and others 2011). HCV is the leading etiology for the development of HCC (Goossens and Hoshida 2015), with HCC being the main cause of death in patients with chronic HCV (Andrade and others 2009). Despite the current progress in HCV therapies with the resulting increase in sustained viro- logical response to 68%–74% (Thompson and others 2009), HCV-initially induced liver injury is still likely to progress to cirrhosis and HCC at different rates. Several etiologies, including viral, environmental, and ge- netic factors, interplay to determine the rate of disease pro- gression in HCV infection (Tolmane and others 2012), of those, host genetic factors represent the major determinants for the risk of HCC development. Single-nucleotide polymorphisms 1 Genetic Engineering Division, Department of Microbial Biotechnology, National Research Centre, Dokki, Giza, Egypt. 2 Endemic Medicine Department, Faculty of Medicine, Cairo University, Egypt. 3 Clinical Pharmacy Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt. 4 Department of Pharmaceutics and Industrial Pharmacy and 5 Clinical Pharmacy Department, Faculty of Pharmacy, Beni-Suef Uni- versity, Beni-Suef, Egypt. 6 Medical Research Division, Biological Anthropology Department, National Research Centre, Dokki, Giza, Egypt. JOURNAL OF INTERFERON & CYTOKINE RESEARCH Volume 00, Number 00, 2016 ª Mary Ann Liebert, Inc. DOI: 10.1089/jir.2016.0042 1