Control of mRNA translation is increasingly recognized as a central regulatory step in numerous dynamic processes ranging from embryonic development to stress responses. Whether regulation of mRNA translation plays a role in HIV-1 life cycle, in particular in establishment of antiviral host defenses against HIV-1 is unknown. If true, such a regulatory mechanism would provide a much faster response to HIV-1, in particular in the immune cell subsets that are direct targets of HIV-1 and whose function is to fight infections. Efforts to better understand the innate host responses against HIV-1 have primarily focused on identification and functional characterization of a set of genes, referred to as interferon-stimulated genes (ISGs). The expression of ISGs is induced by type I interferons (IFNs), which get synthesized and secreted upon detection of virus replication intermediates in infected cells. IFN binding to cell surface receptors initiates a signaling cascade and culminates in the transcriptional upregulation of hundreds of ISGs that collectively establish a crudely defined antiviral state. Seminal studies in the past two decades have identified a handful of ISGs that potently block HIV-1 replication and play key roles in its cross-species transmission. However, the known antiviral factors together cannot account for the total inhibitory effects of IFNs on HIV-1 replication, suggesting that many other ISGs or IFN-induced antiviral mechanisms exist. Many groups have attempted to identify novel antiviral factors by screening the activities of a highly curated set of ISGs. In these studies, selection of ISGs was largely based on transcriptional upregulation in microarray- based experiments, which are limited in their ability to detect transcript abundance and do not provide information about post-transcriptional regulatory events including mRNA translation. For example, if there were a set of preexisting mRNAs that get translated in response IFN stimulation, they would be completely missed in the studies to date. To test the hypothesis that regulation of mRNA translation contributes to the diversity of IFN-mediated as well as HIV-1-induced antiviral responses, we propose to conduct in-depth ribosome profiling experiments in IFN-treated and HIV-1-infected primary CD4+ T-cells and macrophages. In preliminary studies, we have adapted this cutting-edge methodology and generated key data sets demonstrating the potential role of translational regulation in expression of numerous host genes in response to IFNs and HIV-1 infection. Identification and functional characterization of such ?paradigm shifting? mechanisms at the HIV-1-host interface will greatly advance our understanding of the innate resistance to HIV-1. Ultimately, these findings can have an impact on the development of new therapeutic strategies against HIV-1/AIDS and better animal models. Lastly, the implications of this work reach far beyond HIV-1, impacting other viral and non-viral pathogens.
Control of mRNA translation is increasingly recognized as a central regulatory mechanism in diverse biological processes ranging from embryonic development to cellular stress responses. Whether translational regulation plays a role in HIV-1 life cycle and in induction of antiviral defense mechanisms against HIV-1 is unknown. By profiling the mRNAs being next generation sequencing-based approaches, we propose to determine the role of mRNA translation in induction of intrinsic and innate antiviral responses against HIV-1, and antagonism of these responses by HIV-1.