Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein

Abstract

Hepatitis C virus (HCV) encodes mechanisms to evade the multilayered antiviral actions of the host immune system. Great progress has been made in elucidating the strategies HCV employs to downregulate interferon (IFN) production, impede IFN signaling transduction, and impair IFN-stimulated gene (ISG) expression. However, there is a limited understanding of the mechanisms governing how viral proteins counteract the antiviral functions of downstream IFN effectors due to the lack of an efficient approach to identify such interactions systematically. To study the mechanisms by which HCV antagonizes the IFN responses, we have developed a high-throughput profiling platform that enables mapping of HCV sequences critical for anti-IFN function at high resolution. Genome-wide profiling performed with a 15-nt insertion mutant library of HCV showed that mutations in the p7 region conferred high levels of IFN sensitivity, which could be alleviated by the expression of WT p7 protein. This finding suggests that p7 protein of HCV has an immune evasion function. By screening a liver-specific ISG library, we identified that IFI6-16 significantly inhibits the replication of p7 mutant viruses without affecting WT virus replication. In contrast, knockout of IFI6-16 reversed the IFN hypersensitivity of p7 mutant virus. In addition, p7 was found to be coimmunoprecipitated with IFI6-16 and to counteract the function of IFI6-16 by depolarizing the mitochondria potential. Our data suggest that p7 is a critical immune evasion protein that suppresses the antiviral IFN function by counteracting the function of IFI6-16.HCV | innate immune evasion mechanism | IF6-16 antiviral function | high-throughput mutagenesis | p7 ion channel protein W ith an estimated 170 million people persistently infected worldwide, hepatitis C virus (HCV) has emerged as a major cause of human liver diseases, including chronic hepatitis, cirrhosis, and hepatocellular carcinoma (1, 2). Despite the recent breakthroughs in the development of HCV direct antiviral agents (DAAs) aiming to cure chronic HCV infection, emerging resistant mutations and drug-resistant polymorphisms at the baseline of treatments remain major challenges to eradicate HCV (3-8). In addition, the high cost of these DAAs limits their accessibility to the majority of patients worldwide. Therefore, HCV eradication is still heavily dependent on the development of an effective preventative vaccine (9). Understanding how the virus evades the immune system, which results in a poor immune response of the infected host against the virus, will provide important information for immune therapy and vaccine development.

The role of spatial structure in the evolution of viral innate immunity evasion: A diffusion-reaction cellular automaton model

“…Based on known dynamics [24][25][26], though, we initially assumed that virion release preceded IFN secretion (N Eπ � 0). We also incorporated the observation that uninfected cells respond to IFN in a dose-dependent manner [5,27] and become immunized (N R ), but do not produce IFN themselves [28]. Infection (N S !N E ) and immunization (N S !N R ) were simulated as Poisson stochastic processes occurring with probability…”

Hepatitis C Virus: Evading the Intracellular Innate Immunity

“…After measuring the impact of each liver-specific ISG on HCV replication, they found that p7-mutant HCV was susceptible to IFI16-16 overexpression, an ISG that is highly inducible upon type I IFN treatment of viral infections, but whose function remains to be elucidated. Qi et al furthermore reported that p7 interacts with IFI16-16 and induces depolarization of mitochondrial membrane potential, which they suggest to inhibit IFI16-16 function [114]. Table 1.…”

“…cleaves MAVS, to impair production of IFNs and proinflammatory cytokines [31,37,[52][53][54][55]57] cleaves TRIF, to impair production of IFNs and proinflammatory cytokines [28,58] inactivates Riplet, inhibiting RIG-I and IRF3 activation [62,63] binds to LUBAC, impairing the polyubiquitynation of NEMO required for NF-κB activation [66] induces degradation of STAT1, impairing the expression of antiviral effectors [67] binds to TBK1, impairing IRF3 activation [59][60][61] Core blocks NF-κB, to suppress inflammatory response [98,99] targets JAK/STAT pathway by targeting STAT1 and STAT2, inhibiting the production of ISGs [52,67,[104][105][106][107][108][110][111][112] E2 interacts with PKR, repressing its antiviral effects [89] NS5A interacts with PKR, repressing its antiviral effects [88,90] induces NAP1L1 degradation, inhibiting gene transcription essential for RIG-I-and TLR3-mediated responses [91] impedes RIG-I-and MDA5 activation, impairing IFNs expression [33] NS4B downregulates TRIF protein, inhibiting TLR3 signaling [68] interacts with STING, inhibiting the production of IFNs [69,70] p7 interacts with IFI16-16, inhibiting its antiviral function [114] Growing evidence demonstrates that HCV modifies host microRNA (miRNA) expression to modulate a diverse range of host functions [115]. It was re...…”

Beyond Channel Activity: Protein-Protein Interactions Involving Viroporins

“…Another role, in immune evasion, has been identified recently for p7 (Qi et al 2017). Indeed, HCV acts against the host immune system by downregulating interferon (IFN) production, blocking IFN signaling transduction, and impairing IFNstimulated gene (ISG) expression.…”