Expression, potency, and antiviral mechanisms of the interferon-alpha subtypes in retroviral infection

Abstract

More than 30 years after the first recognition of AIDS, HIV-1 infection remains an enormous public health burden globally. Understanding mechanisms of innate immunity to HIV-1 could fulfill the critical needs of novel antivirals, vaccines, or curative therapies. The Type I Interferons (IFN-I), in particular the IFN-alphas (IFN-α), are the first line of defense against HIV-1. The IFNA family in humans consists of 13 genes that all have a common receptor. The expansion of the IFNA family raises important evolutionary questions regarding their expression and potency against specific pathogens. While clinical administration of one subtype, IFN-α2, reduced HIV-1 viremia in infected patients, the potency of other subtypes have not been evaluated, and the downstream effectors are poorly understood. In this dissertation, I evaluated the expression, potency, and antiviral mechanisms of IFN-α subtypes in ex vivo models of HIV-1 infection and a mouse retroviral infection model. IFNA subtype expression was determined in human plasmacytoid dendritic cells (pDCs), the main producers of IFN-α, using a novel next-generation sequencing approach. A distinct signature of IFNA subtype transcripts were detected following HIV-1 exposure, which showed associations with both common promoter elements and relative gene position within the IFNA locus. I then determined the relative potency of each IFN-α subtype in an ex vivo model of gut CD4+ T cell infection. A range of potencies for the IFN-α subtypes were identified, and were related to binding affinity to the IFNAR2 receptor and the induction levels of key HIV-1 restriction factors, with the exception of APOBEC3G (A3G), which was not induced. Despite this, mechanistic investigations of the most potent IFN-α subtypes revealed two signatures of A3G activity: decreased infectivity of progeny virions and increased HIV-1 proviral GG-to-AG mutations. Finally, the relative contribution of mouse Apobec3 (mA3) to the IFN-α treatment effect in the Friend virus (FV) model of retroviral infection was determined. Apobec3 was the primary effector of IFN-α-treatment despite not being transcriptionally induced. The common findings among diverse retroviral model systems highlight APOBEC3 as a critical effector of IFN-α-treatment, and suggest novel approaches to treatment or eradication of HIV-1 infection.