DEVELOPMENT OF A PRIMATE GENOMICS RESOURCE

University Of Washington, Seattle WA

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Abstract

This competitive renewal of an R24 Resource-Related Research Grant is focused on creating proteomic resources that can be applied to research using nonhuman primates. The proposal builds upon resources constructed under the original application in which we developed extensive rhesus macaque (Macaca mulatta)-specific genomic tools and bioinformatics systems. Through the construction of complementary proteomic resources, we intend to provide the research community with the full spectrum of species-specific genomic and proteomic tools needed to apply the technologies of functional genomics to nonhuman primate research. To build these resources, we have teamed with the Biological Systems Analysis and Mass Spectrometry group headed by Dr. Richard D. Smith at Pacific Northwest National Laboratory. This group brings to the effort unrivaled mass spectrometry instrumentation and cutting-edge proteomics expertise. In Aim 1, we will use Fourier transform ion cyclotron resonance mass spectrometry to build accurate mass and time (AMT)-tag databases for use in identifying proteins present in various rhesus macaque tissues. These databases will be used in Aim 2 to characterize the changes in cellular protein profiles that occur in response to simian immunodeficiency virus (SIV) infection. We will begin by analyzing peripheral blood mononuclear cells (PBMCs) infected in vitro with SIVmac239. We will then infect the same animals from which the PBMCs were derived and analyze blood, gut-associated lymphoid tissue, and lymph nodes at multiple time points after infection. Quantitative proteomic analyses will be performed using stable isotope labeling and a labelfree comparative absolute quantification method in combination with the AMT-tag approach. These studies will allow us to evaluate the resources we construct in an experimental system that will enhance our understanding of the use of macaques as models for AIDS research. In Aim 3, we will develop the bioinformatics resources needed for the storage, interpretation, and dissemination of proteomics data. This will include the development and implementation of a proteomics laboratory information management system, species-specific database resources, proteomics data analysis tools, and Web-based resources for data dissemination. The development of macaque-specific proteomic resources will enable researchers to maximize the .types and amounts of information that can be obtained from these valuable research animals.