Post-transcriptional inhibition of hepatitis C virus replication through small interference RNA

HCV has infected 200 million people worldwide, of which 10 million individuals (6% of the population) have been spotted in Pakistan [1]. In 40-60% of HCV-infected individuals, persistent infection is mainly associated with liver cirrhosis and steatosis, leading to hepatocellular carcinoma (HCC) [2, 3]. About 75% of patients receive no therapeutic benefit from the current combination therapy with PEG-IFN α and the guanosine analog ribavirin because of adverse side effects and high cost [4]. In order to improve treatment outcomes, there is a dire need to develop more effective and better therapeutic options for treating HCV infections.

Currently, RNA interference (RNAi) has been emerged as a potential technique for developing anti-mRNA based therapeutics against different viral diseases such as HPV [5], HIV [6], Yellow fever virus [7, 8]. RNAi is a sequence-specific RNA degradation process in the cytoplasm of eukaryotic cells triggered by double-stranded RNA (dsRNA), widely existing in many species from nematode to human [Fire, 1998, Elbashir, 2001, Leung, 2005,]. Upon introduction into the cells, exogenous dsRNAs are cut into 21-25 nt small interfering RNA (siRNA) by an RNase III-like enzyme called Dicer. The siRNAs form RNA-induced silencing complex (RISC) with other cellular components, and lead to the cleavage of their homologous transcript and eventually the silencing of specific gene [9‐11]. HCV RNA is an attractive target for RNAi, as the single positive-stranded viral transcript functions both as genomic RNA and a replication template, and also because of its localization in the infected liver, an organ that can be readily targeted by nucleic acid molecules and viral vectors. As Dicer and the RISC act in the cytoplasm so the cytoplasmic location of RNAi machinery makes it technically easier than other methods that attempt to silence genes at the nuclear level. Several reports demonstrated that siRNAs against HCV genomic and sub-genomic replicons inhibit HCV replication [12‐16].

HCV was firstly recognized in 1989 [17], comprising a 9.6 kb genome of positive sense. It encodes a single large polyprotein of 3010 amino acids is translated from the long open reading frame (ORF) encoded within the viral RNA genome. This large protein is then cleaved into 10 different individual proteins by the combined action of the cellular and viral proteases. The viral core, E1, E2, and P-7 proteins are called the structural proteins required for the production of infectious virus particles, their secretion and infection. The remaining non-structural proteins (NS2, NS3, NS4A, NS4B, NS5A, NS5B) are essential for replication of HCV positive and negative strand RNA [18]. Among these non-structural proteins, HCV NS3 serine protease and NS5b RNA dependent RNA Polymerase are important targets to develop antiviral drugs against HCV [19, 20]. The present study was devise to study the effect of siRNAs against HCV replication in liver infected cells. The present study demonstrates that the RNAi-mediated silencing of the HCV full length viral particle may be one of the important therapeutic opportunities against HCV 1a genotype.

The ability of siRNAs to inhibit HCV replication were evaluated by designing and constructing siRNAs against different sites of HCV non-structural genes having genotype 1a (NS2, NS3, NS4B and NS5B). siRNA targeting sites were selected in regions conserved among different samples. Selected siRNAs were labeled as NS2si-241, NS3si-229, NS3si-858, NS4Bsi-166, NS5Bsi-241 and NS5Bsi-1065. The negative control siRNA was also included which has the same nucleotide composition as the experimental siRNA, but the sequence has been scrambled so that it does not has the significant sequence homology to with the HCV genes. The DNA olio templates were ordered from Sigma (Sigma Aldrich U.S.A.) (Table 1). We speculated that siRNAs design against HCV non-structural genes has the ability to inhibit the replication of HCV. To test this possibility, Huh-7 serum infected cells were treated with synthetic siRNAs and subsequently incubated for 3 days. Real time results showed that siRNAs targeted against non- structural genes inhibit HCV replication different from each other. siRNAs directed against HCV NS3 serine protease/helicase (NS3si-229 and NS3si-858) resulted in 58% and 82% reduction in viral titer, while siRNA against HCV NS2 gene (NS2si-241) showed 27% reduction in viral titer. siRNAs aginst HCV NS5B RNA dependent RNA polymerase and NS4B genes showed a dramatic reduction in HCV viral RNA, NS4Bsi-166 and NS5Bsi-1064 exhibited maximum inhibition up to 90% at a 20 μM concentration. No significant inhibition was detected in cells transfected with the negative control siRNA (Figure 1). This result was in accordance with Zekri et al. 2009 [21] who also showed best inhibitory effect of siRNAs against 5'UTR on 3rd day of post-transfection. Together, these data suggest that siRNA targeted against HCV non-structural genes inhibit HCV repliction.

With the progress in advanced technologies, RNAi has not only become a powerful tool for studying gene function and development of gene-based therapies, but also been widely used to inhibit viral replication of viruses such as HIV [6], HBV [12], HCV [12], respiratory viruses [23]. Previous reports showed that, at the molecular, cellular and individual levels, RNAi can potentially be used to block viral transmission and thus prevent the viral diseases [24]. With the high efficiency, specificity and low cytotoxicity, RNAi offered a new promise of anti-viral therapy.

Huh-7 and its derived cell lines are the most widely used cell culture systems for liver-associated diseases and the development of antiviral agents against HCV [25‐27]. Guha et al. reported that in-vitro cell culture models can demonstrate the infectivity of the virus and can be used for evaluating drugs for antiviral activity or inhibition of HCV infection [28]. Recently different groups have studied the HCV replication in serum infected liver cell lines which mimics the naturally occurring HCV virions biology and kinetics of HCV infection in human. We infected Huh-7 cells with native viral particles from HCV-1a positive serum using the same protocol as describe by El-Awady et al., and Zekri et al [21, 22].

Previous reports have demonstrated that NS3 and NS5B is essential for viral replication and therefore, provides an attractive target for development of antiviral agents [29‐31]. In this study, we showed that siRNAs can be used as a potent approach to reduce HCV replication in a sequence-specific manner. We screened six siRNAs targeting conserved region of HCV non- structural genes and examined their effect on viral replication. An exciting finding of this study is decline of HCV viral titer to a maximum of 90% with a gene specific siRNAs directed against HCV NS5B RNA dependent RNA polymerase and NS4B. HCV replication in the Huh-7 cells was observed through detection of 5'UTR of viral copies by Real Time PCR in cells 3rd day post infection. HCV NS3si-229 and NS5Bsi-241 showed greater than 50% inhibition in viral titer, while NS2si-241 exhibited only 27% reduction in viral titer. Other investigators have also reported the inhibition of HCV replication by targeting NS5A, NS3, or NS5B sequences [13, 15, 32, 33]. Our data suggest that effect of siRNAs against HCV non- structural genes on HCV viral titer reduction is possibly due to the simultaneous degradation of HCV genomic RNA (as HCV genome contains a positive sense ssRNA).

In summary, these results clearly show that the siRNAs mediated viral gene silencing is a very effective antiviral strategy that has a very strong potential for curing chronic hepatitis C virus infection.

Usman Ali Ashfaq (PhD Molecular Biology), Tariq Javed (M.Phil pharmaceutical chemistry, Sidra Rehman (MSc Chemistry) and Sheikh Riazuddin (PhD molecular Biology and Dean Post graduate study at Allama Iqbal medical college, Lahore