A new path forward: A potential route to effective HIV vaccines

From the Overbaugh Lab, Human Biology Division

Vaccines to provide protection against the variety of HIV strains found around the globe have proven elusive.  Circulating HIV-1 strains can be divided into four groups and the most common of these, Group M, further subdivided into more than ten subgroups.  In addition to the extensive genetic diversity that is the basis of this classification, HIV is a highly mutable virus capable of evading therapies designed to eradicate it.  Patients infected by HIV generate antibody responses specific to the infecting strain.  In rare cases, long-term infected individuals generate antibodies that are capable of recognizing and neutralizing a wide variety of viral strains.  These broadly neutralizing antibodies (bnAbs) have long been thought to be the golden ticket for vaccine efforts, however because they arise through extensive maturation and optimization of germline immunoglobulin genes, eliciting these bnAbs via vaccination has proven difficult.  New research published in the journal eLife from the Overbaugh Lab in the Human Biology Division, Bloom Lab in the Basic Sciences Division and Cancer Consortium collaborator Erick Matsen suggests that bnAbs may yet hold the key to unraveling the effective HIV vaccine problem.

Vaccines elicit immune responses by presenting epitopes to the immune system in the absence of that actual pathogen.  The challenge for developers of HIV vaccines lies in the ability to identify epitopes that are present in most if not all circulating viral strains and are resistant to antigenic escape through mutation.  One approach to discover effective strategies for vaccine design is to mimic nature’s way.  The Overbaugh lab analyzed a bnAb that was isolated from a Kenyan woman who was infected with HIV not once but twice.  Such cases, termed superinfection (SI), illuminate how the immune system responds to sequential challenge by two related but not identical pathogens.  

Broadly neutralizing antibody from a multiply HIV infected patient may hold the answer.
Broadly neutralizing antibody from a multiply HIV infected patient may hold the answer. Image provided by the authors.

The antibody, QA013.2, binds to a previously identified site on the HIV envelope (Env) protein, named V3.  The V3 region of the SI virus contains a glycan modification that is absent in the initial/first virus. The bnAb QA013.2 arose in response to the SI virus yet retained the ability to bind the original virus.  To determine the likely evolutionary path for developing QA013.2, the researchers used deep sequencing of blood samples obtained from the patient over a 2-year period coupled with computational inference to identify germline heavy (VH) and light chain (VL) B-cell receptor sequences that likely served as the starting point for antibody optimization.  The likely path for development of mature VH and VL sequences was reconstructed computationally and identified a statistically probable route involving eight VH and six VL intermediates arising from specific V, D and J genes followed by extensive somatic hypermutation (SMH) to arrive at the mature sequences.

The researchers then expressed selected intermediate VH and VL sequences as monoclonal antibodies and tested them for binding to Env proteins representing the initial infecting HIV strain as well as the SI strain.  While the inferred naive VH and VL sequences showed weak (SI) or no binding (initial), the bnAb QA013.2 sequence showed strong binding to both. 

Cryoelectron microscopy (cryo-EM) was used to determine the structure of QA013.2 Fab bound to HIV Env protein.  The structure revealed recognition of a conformational epitope in the variable loop 3 (V3) region of Env, in which two glycan moieties together are required to achieve bnAb neutralization. Combining the structural data with functional studies, the authors determined that bnAb neutralization was mediated by a unique combination of VH complementarity determining region 1 (CDRH1) and framework region 1 (FWRH1), with less contribution from the CDRH3.  This is somewhat unusual in that the CDRH3 loop is often critical for achieving broad neutralization in many other HIV bnAbs that target this same epitope.  In addition to the unique paratope that this bnAb possesses, researchers also determined that viral escape from this antibody required mutation of sites on Env both within and outside of the conformational epitope. These findings suggest that features outside of V3 may also be important for vaccine immunogen design aimed at eliciting bnAbs against this conserved region.  Post-doctoral fellow and lead author Mackenzie Shipley said: “These findings are significant because they highlight the multitude of ways in which bnAbs evolve to target the core V3 epitope on Env. Having at least one demonstrable route to an immune response achieving bnAb breadth is a prerequisite for vaccine immunogen design.”

This research was supported by grants from the National Institutes of Health, the Howard Hughes Medical Institute and Simons Foundation

Fred Hutch/UW Cancer Consortium members Julie Overbaugh and Erick Matsen contributed to this study.

Shipley MM, Mangala Prasad V, Doepker LE, Dingens AS, Ralph DK, Harkins E, Dhar A, Arenz D, Chohan V, Weight H, Mandaliya K, Bloom JD, Matsen Iv F, Lee KK, Overbaugh JM. Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection. Elife. 2021 Jul 15;10:e68110. doi: 10.7554/eLife.68110. Epub ahead of print. PMID: 34263727.