Proteomics and phosphoproteomics analysis in HIV-1 infection

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Abstract Infection with HIV-1 elicits complex, fine-tuned immune responses that involve virtually all components of the innate and adaptive immune system. Yet, this immune response fails in most cases to control the infection, and there are reasons to believe that in many cases, immune responses to HIV contribute to disease pathogenesis by increasing abnormal immune activation and facilitating the establishment of a long-lasting reservoir of HIV-1 infected cells, thus propagating a disease they are meant to restrict. While innate and adaptive effector cell responses against HIV-1 have been analyzed in detail in the last years, there is still a remarkable knowledge gap in the understanding of molecular events and host-pathogen interactions inside CD4 T cells that determine the efficacy of the HIV-1 life cycle and influence the fate and survival of HIV-1 infected cells. However, immune responses to HIV-1 within the actual viral target cells arguably represent one of the most active and one of the most effective antiviral immune defense mechanisms that may have a profound effect on the dynamics of clinical HIV-1 disease progression. Here, we propose to take advantage of recent methodological advances for high- throughput, ultra-sensitive protein and phosphoprotein profiling to analyze molecular events and cell-intrinsic immune responses to HIV-1 inside the main target cells for HIV-1. In Specific Aim 1, we will focus on phosphorylation of HIV-1 gene products by host kinases. We hypothesize that specific sequence motifs within the HIV-1 proteome are susceptible to phosphorylation by host kinases in vivo, and represent sites of extraordinary viral vulnerability that have a profound impact on viral fitness; identifying such sites may have important implications for generating a comprehensive view of the HIV-1 fitness landscape and for selecting viral sequences to be included in vaccines and immunogens. In Specific Aim 2, we will analyze proteomic and phosphoproteomic responses to productive HIV-1 infection, and test the hypothesis that HIV-1 infection induces specific molecular pathways that maintain survival and homeostasis of infected cells. These studies build on a substantial set of provocative preliminary data indicating that proteomic signatures of HIV-1 infected cells show selective activation of cell survival programs, and hold promise for identifying molecular targets for reducing viability and persistence of virally infected cells. In Specific Aim 3, we will focus on analyzing the proteomic and phosphoproteomic signatures of latently-infected CD4 T cells, which are regarded as the main reason for our current insufficiency to eradicate and cure HIV-1 infection. These studies have the potential to discover novel functional pathways that are involved in regulation of viral latency and persistence, and will provide data that may significantly enhance our ability to detect, monitor and therapeutically eliminate latently-infected cells.