HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation

Abstract

APOBEC3 (A3) family proteins are DNA cytosine deaminases recognized for contributing to HIV-1 restriction and mutation. Prior studies have demonstrated that A3D, A3F, and A3G enzymes elicit a robust anti-HIV-1 effect in cell cultures and in humanized mouse models. Human A3H is polymorphic and can be categorized into three phenotypes: stable, intermediate, and unstable. However, the anti-viral effect of endogenous A3H in vivo has yet to be examined. Here we utilize a hematopoietic stem cell-transplanted humanized mouse model and demonstrate that stable A3H robustly affects HIV-1 fitness in vivo. In contrast, the selection pressure mediated by intermediate A3H is relaxed. Intriguingly, viral genomic RNA sequencing reveled that HIV-1 frequently adapts to better counteract stable A3H during replication in humanized mice. Molecular phylogenetic analyses and mathematical modeling suggest that stable A3H may be a critical factor in human-to-human viral transmission. Taken together, this study provides evidence that stable variants of A3H impose selective pressure on HIV-1.

Experimental Adaptive Evolution of Simian Immunodeficiency Virus SIVcpz to Pandemic Human Immunodeficiency Virus Type 1 by Using a Humanized Mouse Model

“…To elucidate the replication kinetics of these viruses in vivo, equal amounts of each virus supernatant were used to inoculate five humanized mice in an in vivo competition assay ( Fig. 6A) (37). After 6 weeks, the five infected mice were euthanized and the sequence of vRNA in the plasma was directly analyzed.…”

“…The in vivo competition assay ( Fig. 6) was performed as previously described (37). Briefly, four SIVcpzPtt MB897-related viruses (the parental virus MB897, MB897 MA M30R, MB897 NLvpuTM, and MB897 gp120 G413R) in preparations containing 1.25 ng of Gag antigen were mixed and were intraperitoneally inoculated into NOG hCD34 mice.…”

“…To recapitulate and characterize HIV-1 replication and pathogenesis that occurs naturally in humans, we have established an in vivo model of human hematopoietic stem cell-transplanted humanized mice (34)(35)(36)(37). The humanized mice are able to reproduce the characteristics of HIV-1 pathogenesis in humans, such as the gradual decrease of peripheral human CD4 ϩ T cells (34)(35)(36)(37). Moreover, we previously investigated the interplay between viral and host proteins involved with viral replication in this mouse model (37)(38)(39)(40)(41)(42).…”

“…The humanized mice are able to reproduce the characteristics of HIV-1 pathogenesis in humans, such as the gradual decrease of peripheral human CD4 ϩ T cells (34)(35)(36)(37). Moreover, we previously investigated the interplay between viral and host proteins involved with viral replication in this mouse model (37)(38)(39)(40)(41)(42). Here, we further employ this humanized-mouse model to experimentally reproduce the adaptive evolutionary process of SIVcpzPtt to infect humans.…”

The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism

“…Third, despite strict copy number conservation, A3H is the most polymorphic family member in humans with 7 reported haplotypes due to variations at 5 amino acid positions and 4 reported splice variants (Harari et al, 2009; OhAinle et al, 2008; Wang et al, 2011). These naturally occurring A3H variations are known to influence protein stability, antiviral activity, and subcellular localization, with at least two stable variants capable of potently suppressing Vif-deficient HIV-1 replication (Harari et al, 2009; Hultquist et al, 2011; Nakano et al, 2017; OhAinle et al, 2008; Ooms et al, 2013; Refsland et al, 2014; Wang et al, 2011). A3H is also implicated in restricting the replication of multiple other viruses and transposons (Bouzidi et al, 2016; Hultquist et al, 2011; Kock and Blum, 2008; Ooms et al, 2012; Tan et al, 2009).…”