Scientific Core: Structural Proteomics

Project Summary/Abstract Rational, structure-based immunogen design for HIV vaccine development has begun to deliver promising results in both, pre-clinical non-human primate (NHP) and clinical studies such as the IAVI G001 phase I trial [NCT03547245]. Moreover, advances in single cell RNAseq and electron microscopy-based polyclonal antibody mapping (EMPEM) have enabled analysis of both vaccine and pathogen-induced antibody responses at unprecedented resolution, further enabling rational vaccine design. EMPEM and single cell B cell analysis deliver fundamentally different data formats that if properly integrated, can illuminate immune responses at unprecedented detail. We recently extended the original negative stain EMPEM method, capable of distinguishing polyclonal antibody epitope specificities and angle of approach, to high resolution cryoEM-based EMPEM to yield molecular details of epitope-paratope interfaces. In the best cases we can derive some sequence information for the complementarity determining regions (CDRs) from structural data, identify Vh/Vl gene usage, and query databases of antibody BCR sequences to directly generate monoclonal antibodies. As such, we can short cut the laborious efforts to generate epitope specific monoclonal antibodies using conventional methods. These molecular details are critical for identifying how bona fide human germline bnAb precursors engage germline targeting immunogens such as the V2 apex targeting Q23 immunogen. EMPEM is also critical for evaluating polyclonal antibody responses in BCR knock-in mice that have been immunized with germline targeting immunogens that are designed to prime and mature antibodies with specific features in CDRs that resemble known broadly neutralizing antibodies (bnAbs). The Structural Proteomics Core will be highly integrated into all both Project 1 and 2 as well as the Animals and Data Cores within this P01 application, providing unique structural data to evaluate, refine, and optimize multi-epitope germline targeting immunogens for development as candidate HIV vaccines.