Rabbit Anti-HIV-1 GP120 monoclonal antibody, clone IHA2

The results of the RV144 vaccine clinical trial showed a correlation between high level of anti-V1V2 antibodies (Abs) and a decreased risk of acquiring HIV-1 infection. This turned the focus of HIV vaccine design to the induction of elevated levels of anti-V2 Abs to increase vaccine efficacy. In plasma samples from HIV-1 infected Cameroonian individuals, we observed broad variations in levels of anti-V2 Abs, and 6 of the 79 plasma samples tested longitudinally displayed substantial deficiency of V2 Abs. Sequence analysis of the V2 region from plasma viruses and multivariate analyses of V2 characteristics showed a significant difference in several features between V2-deficient and V2-reactive plasma Abs. These results suggest that HIV vaccine immunogens containing a shorter V2 region with fewer glycosylation sites and higher electrostatic charges can be beneficial for induction of a higher level of anti-V2 Abs and thus contribute to HIV vaccine efficacy.

The repertoires of B cell receptors (BCRs), which can be captured by single cell-resolution sequencing technologies, contain a personal history of a donor's antigen exposure. One of the current challenges in analyzing such BCR sequence data is to assign sequences to groups with similar antigen and epitope binding specificity. This is a non-trivial task given the paucity of experimentally-determined antibody-antigen structures and the fact that different gene combinations in B cells can lead to receptors that target the same antigen and epitope. Here, we describe a method for clustering BCRs based on sequence and predicted structural features in order to predict groups with similar antigen and epitope binding specificity. We show that all known experimentally-determined structures of antibody-antigen complexes can be clustered accurately (AUC 0.981) and that use of predicted structural features improved the accuracy of the epitope classification. We next show that an independent and non-redundant set of 104 anti-HIV antibody sequences could be clustered corresponding to manually-assigned epitopes with a specificity of 99.7% and a sensitivity of 61.93%, with the imbalance in sensitivity due almost entirely to one group of antibodies-those that target the gp120 V3 loop, which do not form a single, well-defined cluster. We next examined a diverse set of anti-hemagglutinin BCR sequences from humans and mice. We observed clusters that included human or mouse sequences with anti-hemagglutinin antibodies of known structure. We also observed clusters that included both human and mouse sequences. Importantly, to the extent that the epitopes have been experimentally characterized, none of the observed clusters erroneously grouped different hemagglutinin binding regions. Taken together, these results demonstrate that the proposed clustering method provides high-throughput prediction of BCRs with common binding specificity across clonal lineages, donors and even species.