Time for HIV to show its hand

From Adam Dingens in the Bloom (Basic Sciences Division) and Overbaugh (Human Biology Division) labs

A prominent feature of infection by the human immunodeficiency virus (HIV) is its ability to evade the host immune system by rapidly mutating. This swift evolution, together with the incredible global diversity of the virus, has made vaccine development a monumental challenge. Nevertheless, there are clues from our immune system on how to target the virus; immune molecules called broadly neutralizing antibodies that can bind to many different HIV variants and prevent infection have been identified. Understanding the mechanisms of how broadly neutralizing antibodies target the virus has the potential to inform how HIV can be targeted by vaccine-elicited immunity. Despite this urgent need, characterizing the functional antibody-HIV interaction has been difficult, given that one-at-a-time experiments involving low-throughput structural studies on individual viral mutations to see how they affect antibody binding, can only screen a small fraction of mutations that mediate viral escape.

Given this obstacle, Dr. Adam Dingens, a recent graduate from the University of Washington Molecular and Cellular Biology program, developed a high-throughput approach that leverages the evolutionary capacity of HIV to obtain a comprehensive view of how these antibodies bind to HIV and prevent infection. This work, published in a recent issue of Immunity, was carried out when he was a graduate student in the laboratories of Drs. Jesse Bloom (Basic Sciences division) and Julie Overbaugh (Human Biology division), both of whom study aspects of viral infection and evolution.

Dr. Jesse Bloom describes the unique approach of this work: "Adam was able to use a new technique originally developed to study HIV evolution to address a very important question: how can HIV escape from antibodies? He did this by defining the set of all mutations that enable the virus to escape from many important antibodies in clinical development.”

This technique, known as mutational antigenic profiling, is a massively parallel experimental approach to quantify the effect of all single amino acid mutations in the HIV envelope (Env) that are the target of broadly neutralizing antibodies, on antibody neutralization. To do this, libraries of HIV that carry all Env amino acid mutations compatible with viral replication were generated. These libraries were incubated with or without an antibody, infected into T cells, and the enrichment of each mutation in the selected versus non-selected libraries was quantified by deep sequencing. In order to generate a comprehensive landscape of viral escape, the authors selected nine broadly neutralizing antibodies targeting the five best-characterized epitopes on Env.  From this, they generated complete maps of viral escape that define the functional epitopes for the panel of broadly neutralizing antibodies, and also found that functionally defined epitopes were distinct from structurally defined epitopes.


This image references the antigenic atlas from this study with the classic imagery of Atlas from Greek mythology. Here, Atlas is depicted as a B lymphocyte bearing the weight of an HIV virion in the figure of a celestial sphere. Antibodies are bound to the Envelope proteins (mountains) that decorate the virion surface. Image by Ryan Nini, "The Illustrative Scientist”

Interestingly, several of the broadly neutralizing antibodies characterized in the study have also been used in human immune therapy studies; there was considerable overlap between sites of escape the authors mapped in vitro and those that occurred in vivo during treatment of infected individuals.  This suggests these maps of viral escape can help interpret viral mutations observed in clinical trials.  Since some immunotherapy studies are starting to use combinations of broadly neutralizing antibodies to treat patients, the authors investigated how escape from a mix of two antibodies compares to escape from each antibody individually. They found that the escape from pooled antibodies is similar to the modeled combination of their independent action; mutations can escape one antibody, but have little effect on the other.  Mutational antigenic profiling was also used to determine the ease of single amino acid mutation escape from each antibody. Similar to influenza antibodies, HIV broadly neutralizing antibodies have distinct measures of breadth and ease of single mutation escape.

Defining how viral mutations modulate the sensitivity of HIV to anti-HIV antibodies is critical to developing effective antibody immunotherapies and vaccines. In this work, the authors mapped all possible single amino-acid viral escape mutations for a panel of HIV broadly neutralizing antibodies that target major sites of vulnerability of the HIV envelope. The creation of these comprehensive maps of viral escape provides an antigenic atlas to guide the development of antibody-based immunotherapies and vaccines.

Dr. Adam Dingens on the significance of this study: “This approach allows us to define a functional epitope, which we show is distinct from the structurally-defined epitope that the field has focused on for so long. Additionally, since these antibodies are being developed as therapeutics, understanding how the virus can escape the antibodies can help to evaluate and improve antibody-based immunotherapies.”  

Dr. Jesse Bloom further expounds on the impact of this work: “From a basic standpoint, Adam’s results show that the set of sites in a virus that physically contact an antibody is not identical to the set of the sites were mutations mediate antibody escape. From a translational perspective, his work shows how mapping escape mutations can help inform anti-HIV immunotherapies."

Dingens AS, Arenz D, Weight H, Overbaugh J, Bloom JD. 2019. An Antigenic Atlas of HIV-1 Escape from Broadly Neutralizing Antibodies Distinguishes Functional and Structural Epitopes. Immunity 50: 520-532

Funding was provided by the National Institutes of Health, Howard Hughes Medical Institute, and the National Science Foundation.