Analyzing CD4 binding site-directed broadly neutralizing HIV-1 antibodies by 454 pyrosequencing and computational bioinformatics
HIV-1 has evolved to evade the antibody-mediated immune response. However, after several years of infection, 10-25% of HIV-1-infected individuals develop antibodies that neutralize diverse strains of HIV-1. Identification and characterization of such antibodies could form a critical step in an antibody-based vaccine strategy. Recently, several groups identified broadly neutralizing antibodies directed against a range of epitopes on the functional HIV-1 viral spike. Among these antibodies, those precisely targeting the CD4 binding site on the HIV-1 gp120 envelope glycoprotein are promising vaccine templates due to their remarkable breadth and potency. For example, human antibody VRC01 neutralizes ~90% of circulating HIV-1 strains and protects against S/HIV challenge in non-human primates. Crystal structures of three VRC01-like antibodies in complex with gp120 reveal a convergent mode of binding to the CD4 binding site. To understand how these antibodies evolve to achieve precise epitope targeting and broad neutralization, we used 454 pyrosequencing to probe the antibodyome (repertoire of expressed antibodies) of HIV-1-infected individuals and to identify additional VRC01-like antibodies. By using unusual features of VRC01-like antibodies as filters in the sequencing analysis, we discovered a universe of VRC01-like antibodies. To assess the biological function of 454-identified antibodies, we selected a set of representative sequences for synthesis and tests of neutralization: 24 heavy-chain sequences showed HIV-1 neutralizing activity. Phylogenetic analysis further revealed a focused maturation pathway for VRC01-like antibodies: specifically, the neutralizing VRC01-like antibodies from different donors segregate on a distinct branch in a phylogenetic tree rooted at their genomic precursor, providing a computational method for identifying new VRC01-like antibodies. Genome-wide CDR H3 analysis showed that multiple antibody lineages evolve in parallel to target the same site of viral vulnerability. Maturation intermediates inferred by either phylogenetic analysis or obtained directly from CDR H3 analysis provide pathway for eliciting such VRC01-like antibodies in vaccination.
Dr. Jiang Zhu is a Staff Scientist and co-head of the Structural Bioinformatics Core Section of the Vaccine Research Center, NIAID/NIH. For more information, please visit: http://www.niaid.nih.gov/labsandresources/labs/aboutlabs/vrc/structuralbioinform/Pages/default.aspx