The focus of this proposal is to dissect the early innate immune response to HIV infection using a systems biology approach. The paradigm for these studies is that HIV infection elicits an immediate innate response involving antiviral factors that are either constitutively expressed or are induced by innate signaling pathways. The activities of some of these factors are in turn blocked by HIV countermeasures including the actions of viral accessory proteins. The ensuing battle between the host innate response and these viral countermeasures is crucial for determining whether the virus establishes a foothold, inducing replication and eliciting subsequent adaptive immune responses. Therefore, a comprehensive systems-level understanding of these immediate virus-host responses is critical for devising strategies to interfere with the initial establishment of HIV infection. This proposal describes a multidisciplinary and highly integrated approach that is designed to obtain this critically important information. The foundation for the proposal is a unique dataset that we have obtained by combining cutting-edge experimental and computational technologies to obtain a systems-level view of the immediate innate response to HIV-1 infection. The team assembled in the program consists of thirteen research groups arranged into six scientific projects and a scientific core. The program will exploit systems-based approaches to understand the complete repertoire of cellular sensors and effectors involved in the innate signaling pathways that respond to HIV-1 infection (Project 1);the rate-limiting components, pathway modules, and emergent properties of these viral-host circuits (Project 6);the kinetic regulation of different steps of HIV-1 infection by these circuits (Project 3);the role of these circuits in regulating primary myeloid and lymphoid cell activities that are relevant during HIV-1 infection (Projects 2 and 4);and the relationship between these circuits and the clinical outcome of infection (Project 5). These projects are supported by the Administrative and Data Management Core (Core A) and the Molecular Virology and Systems Biology Screening Core (Core B). Identifying novel genetic and proteomic networks involved in innate responses to HIV infection, combined with iterative modeling and testing of the relative roles of these networks and their molecular components in shaping innate immune responses will likely identify unique features of the HlV-specific response, revealing ways to develop successful therapeutic and vaccine strategies for HIV infections. PROJECT 1: Global Analysis of Cellular Networks Involved In Restriction of HIV Replication (CHANDA, S) PROJECT 1 DESCRIPTION (provided by applicant): We hypothesize that the host-pathogen interface that mediate the innate immune response to HIV infection is comprised of three fundamental components: (i) recognition and induction of signaling by innate immune receptors, (ii) cellular antiviral responses, and (iii) viral evasion of innate restriction mechanisms. Aspects of these viral-host circuits are beginning to be uncovered, and include innate immune recognition of HIV RNA by the TLR7 pattern recognition receptor, restriction of HIV replication by interferon inducible HIV restriction factors Apobec3G and BST2, and inactivation of the latter two molecules by the HIV-encoded proteins Vif and Vpu, respectively. However, comprehensive insight towards the molecular circuitries that underlies these host and viral responses has yet to be established. Towards this end, we propose to employ a systems based strategy to map signaling networks and host-pathogen interactions that form the basis of innate immune responses to HIV infection. This approach will leverage existing functional genomics and proteomics datasets, and also will rely on novel systems-based studies, including RNAi and protein interaction analysis, to comprehensively delineate these innate and host-pathogen networks. For this purpose, we have assembled a team of two co-PIs with significant experience in the field of systems biology. Dr. Chanda has over 10 years experience in functional genomics and genetic analysis in mammalian cells, and Dr. Krogan brings over 10 years of experience in the areas of large-scale proteomic and network analysis. These studies are expected to provide global molecular insight into cellular and viral processes that regulate early immune responses to HIV infection.
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