Functional analysis of microRNA-122 binding sequences of hepatitis C virus and identification of variants with high resistance against a specific antagomir

Abstract

MicroRNA 122 (miR-122) stimulates the replication and translation of hepatitis C virus (HCV) RNA by binding to two adjacent sites, S1 and S2, within the HCV 5¢UTR. We demonstrated previously that the miR-122 antagomir miravirsen (SPC3649) suppresses the infection of HCV strain JFH1-based recombinants with HCV genotypes 1-6 5¢UTR-NS2 in human hepatoma Huh7.5 cells. However, specific S1 mutations were permitted and conferred virus resistance to miravirsen treatment. Here, using the J6 (genotype 2a) 5¢UTR-NS2 JFH1-based recombinant, we performed reverse-genetics analysis of S1 (ACACUCCG, corresponding to miR-122 seed nucleotide positions 8-1), S2 (CACUCC, positions 7-2), and ACCC (positions 1-4) at the 5¢ end of the HCV genome (5¢E); the CC at positions 2-3 of 5¢E is involved in miR-122 binding. We demonstrated that the 5¢E required four nucleotides for optimal function, and that G or A at position 3 or combined GA at positions 2-3 of 5¢E was permitted. In S1 and S2, several single mutations were allowed at specific positions. A UCC fi CGA change at positions 4-3-2 of S1, S2, or both S1 and S2 (S1/S2), as well as a C fi G change at position 2 of S1/S2 were permitted. We found that 5¢E mutations did not confer virus resistance to miravirsen treatment. However, mutations in S1 and S2 induced virus resistance, and combined S1 and/or S2 mutations conferred higher resistance than single mutations. Identification of miR-122 antagomir resistance-associated mutations will facilitate the study of additional functions of miR-122 in the HCV life cycle and the mechanism of virus escape to host-targeting antiviral approaches.

microRNA Therapeutics in Cancer — An Emerging Concept

“…Importantly, the administration of Miravirsen in patients with chronic HCV-1 displayed extended dose-dependent diminutions in HCV RNA levels without any manifestation of viral resistance (Janssen et al, 2013). However, it was found that long term treatment with Miravirsen in vitro induces resistance due to mutations in the viral genome (Ottosen et al, 2015, Li et al, 2016). …”

Host Defence RNases as Antiviral Agents against Enveloped Single Stranded RNA Viruses

“…For example, miR122 can modify the viral RNA base pairing and increase its half-life, promoting translation and protection of HCV RNA [138,282]. The emergence of resistant virus strains to miR-122 inhibitors with enhanced genome stability and protection against host RNases has recently been reported [283]. Therefore, the ability of host RNases to target viral RNA might be hindered by the presence of a diversity of ncRNAs.…”

MicroRNA regulation of viral replication in teleost fish: a review

“…Traditionally, miRNA binds to the 3 0 untranslated region (3 0 UTR) of the target RNAs (Chen et al 2016;Riess et al 2016;Zuo et al 2016;Zhang et al 2016a;Zhang et al 2016c;Hazra et al 2017;Yu et al 2017;Yang et al 2017b;Trobaugh et al 2019). However, growing evidences have showed that miRNA can also bind to the 5 0 UTR and coding region of target RNAs (Akhtar et al 2015;Li et al 2016;Niederr€ ohrmann et al 2016;Gerresheim et al 2017;Gutkoska et al 2017). miRNA participates in various biological processes of eukaryotes, including cell proliferation, development, differentiation, metabolism, tumorigenesis and apoptosis (Contreras et al 2015;Hajarnis et al 2017;Li et al 2017;Zhao et al 2017;Liu et al 2017a;Gomez et al 2020;Farina et al 2020), Moreover, it also plays an extremely important role in the regulation of viral replication.…”