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Host Mrna Decay Proteins Influence HIV-1 Replication and Viral Gene

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Host Mrna Decay Proteins Influence HIV-1 Replication and Viral Gene Rao et al. Retrovirology (2019) 16:3 https://doi.org/10.1186/s12977-019-0465-2 Retrovirology RESEARCH Open Access Host mRNA decay proteins infuence HIV-1 replication and viral gene expression in primary monocyte-derived macrophages Shringar Rao1,2†, Raquel Amorim1,3†, Meijuan Niu1, Yann Breton4, Michel J. Tremblay4,5 and Andrew J. Mouland1,2,3* Abstract Background: Mammalian cells harbour RNA quality control and degradative machineries such as nonsense-medi- ated mRNA decay that target cellular mRNAs for clearance from the cell to avoid aberrant gene expression. The role of the host mRNA decay pathways in macrophages in the context of human immunodefciency virus type 1 (HIV-1) infection is yet to be elucidated. Macrophages are directly infected by HIV-1, mediate the dissemination of the virus and contribute to the chronic activation of the infammatory response observed in infected individuals. Therefore, we characterized the efects of four host mRNA decay proteins, i.e., UPF1, UPF2, SMG6 and Staufen1, on viral replication in HIV-1-infected primary monocyte-derived macrophages (MDMs). Results: Steady-state expression levels of these host mRNA decay proteins were signifcantly downregulated in HIV-1-infected MDMs. Moreover, UPF2 and SMG6 inhibited HIV-1 gene expression in macrophages to a similar level achieved by SAMHD1, by directly infuencing viral genomic RNA levels. Staufen1, a host protein also involved in UPF1- dependent mRNA decay and that acts at several HIV-1 replication steps, enhanced HIV-1 gene expression in MDMs. Conclusions: These results provide new evidence for roles of host mRNA decay proteins in regulating HIV-1 replica- tion in infected macrophages and can serve as potential targets for broad-spectrum antiviral therapeutics. Keywords: HIV-1, Macrophages, UPF1, UPF2, SMG6, Staufen1 Background Macrophages play multiple roles in human immuno- Macrophages are cells of the myeloid lineage that serve defciency virus type 1 (HIV-1) pathogenesis (reviewed important functions in the host innate immune response. in [4–6]) as they express the host cell surface receptors Tey recognise and phagocytose invading pathogens and CD4 and CCR5 required for HIV-1 entry and thus, can play many roles in tissue development, homeostasis and be directly infected by HIV-1 [7, 8]. Tey promote the repair [1]. Tey are present in most tissues in the body dissemination and cell-to-cell transmission of HIV-1 via and arise from the terminal diferentiation of infltrating virological synapses [9–11] and they can also be infected monocytes [2]. Examples of tissue-resident macrophages in trans by the selective capture and engulfment of HIV- are the alveolar macrophages in the lung, Kupfer cells in 1-infected CD4+ T cells [12]. Furthermore, they directly the liver and the microglial cells of the central nervous contribute to pathogenesis via the activation of infam- system [3]. matory pathways resulting in the cognitive dysfunc- tion, respiratory dysfunction, cardiovascular disease and microbial translocation in the intestine associated with *Correspondence: [email protected] HIV-1 infection (reviewed in [5]). †Shringar Rao and Raquel Amorim contributed equally to this work Te ability of HIV-1 to rapidly form a stable viral res- 1 HIV-1 RNA Trafcking Laboratory, Lady Davis Institute at the Jewish ervoir upon infection is the major obstacle towards an General Hospital, Montréal, Québec, Canada Full list of author information is available at the end of the article HIV-1 cure [13]. Most studies on HIV-1 latency have © The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/ publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Rao et al. Retrovirology (2019) 16:3 Page 2 of 15 focused on CD4+ T cells. However, the contribution of SMG5 and SMG7, resulting in the degradation of aber- cells of the myeloid lineage to the maintenance of HIV-1 rant mRNAs (reviewed in [30, 31]). UPF1 is also involved latency has recently been recognised [14]. Macrophages in the mRNA decay process of SMD that is mediated by have been proposed to represent a long-lived HIV-1 viral the host protein Staufen1 [32]. reservoir [5, 15–17], as they have a longer life-span than In our earlier studies, we demonstrated that the HIV-1 CD4+ T cells and possess self-renewing properties [18]. genomic RNA (vRNA) is able to evade mRNA surveil- During HIV-1 infection, macrophages are more resistant lance in HeLa cells and CD4+ T cells [33–35]. Moreover, to the cytopathic efects of the virus and display increased HIV-1 hijacks UPF1 and Staufen1 to promote vRNA sta- telomerase activity which contributes to their increased bility and ensure viral gene expression and production of longevity [19, 20]. In in vivo studies using humanised the main HIV-1 structural protein, pr55Gag. Te vRNA mouse models, tissue-resident macrophages sustain and assembles into an HIV-1-dependent ribonucleoprotein propagate HIV-1 infection independently of CD4+ T complex (RNP) with UPF1 and Staufen1, resulting in cells [21]. In follow-up studies using the same humanized enhanced vRNA stability, nucleocytoplasmic export and myeloid-only mouse model, HIV-1 infection was rap- translation [33, 36]. UPF2 is excluded from this RNP idly suppressed by combination antiretroviral treatment and is detrimental to the nucleocytoplasmic export of (cART) and viral rebound was observed in a third of the the vRNA, with an overexpression of UPF2 resulting in mice following the discontinuation of cART, thus repre- nuclear sequestration of the vRNA and reduced expres- senting the frst direct evidence of HIV-1 persistence in sion of pr55Gag [34]. UPF1 also has characterised roles in tissue macrophages in vivo [17]. Moreover, macrophages facilitating HIV-1 reverse transcription [37]. In CD4 + T were also demonstrated to function as a latent reservoir cells, both SMG6, the endonuclease involved in the fnal in SIV-infected, ART-treated macaques [22]. step of the degradation of aberrant RNA in NMD, and One of the strategies to cure HIV-1 infection is the UPF2 are detrimental to vRNA expression in a UPF1- “kick and kill” approach. Tis strategy involves the use dependent manner [35]. Staufen1 also plays roles at of latency-reversing agents (LRAs) to stimulate virus various steps of virus replication including pr55 Gag mul- production from latently-infected cells; followed by timerisation, vRNA encapsidation [38–42] and, more their elimination by the host immune system, cytopathic recently, in countering host stress responses [43]. efects of virus production or cART [23]. Tese LRAs In this study, we have characterised the efects of induce viral production in CD4+ T cells [24]. However, UPF1, UPF2, SMG6 and Staufen1 on viral replication in LRA treatment in macrophages resulted in decreased primary monocyte-derived macrophages (MDMs). We viral release due to the activation of autophagy by the observed that these proteins had signifcant efects on LRAs and the degradation of intracellular viral proteins HIV-1 replication in MDMs. Te identifcation of novel [25]. Moreover, in a study evaluating the efcacy of a host proteins capable of restricting HIV-1 replication in combination of two LRAs (i.e. byrostatin and JQ1), latent MDMs will pave the way for novel targets for therapeutic proviruses were more efciently reactivated in monocytic intervention. cells that in lymphoid cells [26]. Tese results highlighted diferential responses to LRAs that exist between T cells Results and macrophages during HIV-1 infection. Terefore, a Relative protein expression levels for UPF1, UPF2 greater understanding for the roles of host cell proteins and SMG6 are decreased in HIV‑1‑infected MDMs that control HIV-1 gene expression in macrophages is Previous work from our group has demonstrated that the needed. NMD proteins UPF1, UPF2 and SMG6 have diferential mRNA surveillance pathways are host quality control efects on vRNA metabolism in cells of the lymphoid lin- mechanisms that degrade aberrant mRNA to prevent eage [33–35]. Terefore, we hypothesized that RNA sur- the accumulation of potentially toxic truncated or mis- veillance proteins can also impact HIV-1 gene expression folded proteins. Examples of these pathways include the in primary MDMs. To determine whether the expression nonsense-mediated mRNA decay (NMD) and Staufen1- of these proteins is modulated during HIV-1 infection, mediated decay (SMD) [27, 28]. Up-frameshift protein 1 we assessed the levels of UPF1, UPF2 and SMG6 expres- (UPF1), the central player in these mechanisms, is a mul- sion in HIV-1-infected primary MDMs using an HIV-1 tifunctional RNA-binding protein that has ATPase and reporter construct called NL4-3-Bal-IRES-HSA [44–46]. RNA helicase activity [29]. During the process of NMD, Tis an infectious molecular clone of HIV-1 that can UPF1 interacts with a family of up-frameshift proteins infect myeloid cells including human monocyte-derived such as UPF2, UPF3A and UPF3B, and its associated macrophages and expresses the gp160 HIV-1 enve- suppressor for morphological defects in genitalia (SMG) lope of the Env gene of the R5-tropic HIV-1 Bal and all proteins such as a kinase SMG1, an endonuclease SMG6, other viral genes of the T-cell tropic HIV-1 isolate NL4.3 Rao et al. Retrovirology (2019) 16:3 Page 3 of 15 [44]. Additionally, this viral construct also expresses a c), with a decrease of 0.71 (± 0.09) log for UPF1, 0.63 murine heat-stable antigen (HSA), a cell surface reporter (± 0.10) log for UPF2 and 0.71 (± 0.15) log for SMG6.
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