Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans

Abstract

Viral glycoproteins are a primary target for host antibody responses. However, glycans on viral glycoproteins can hinder antibody recognition since they are self glycans derived from the host biosynthesis pathway. During natural HIV-1 infection, neutralizing antibodies are made against glycans on HIV-1 envelope glycoprotein (Env). However, such antibodies are rarely elicited with vaccination. Previously, the vaccine-induced, macaque antibody DH501 was isolated and shown to bind to high mannose glycans on HIV-1 Env. Understanding how DH501 underwent affinity maturation to recognize glycans could inform vaccine induction of HIV-1 glycan antibodies. Here, we show that DH501 Env glycan reactivity is mediated by both germline-encoded residues that contact glycans, and somatic mutations that increase antibody paratope flexibility. Only somatic mutations in the heavy chain were required for glycan reactivity. The paratope conformation was fragile as single mutations within the immunoglobulin fold or complementarity determining regions were sufficient for eliminating antibody function. Taken together, the initial germline VHDJH rearrangement generated contact residues capable of binding glycans, and somatic mutations were required to form a flexible paratope with a cavity conducive to HIV-1 envelope glycan binding. The requirement for the presence of most somatic mutations across the heavy chain variable region provides one explanation for the difficulty in inducing anti-Env glycan antibodies with HIV-1 Env vaccination.

Conformational diversity facilitates antibody mutation trajectories and discrimination between foreign and self-antigens

“…A second key question is: Does hypermutation-induced acquisition of antibody conformational diversity increase self-reactivity ( 4 – 9 )? In the results here, the quadruple mutant antibody became dramatically more specific for foreign over self, through 19-fold loss of self-affinity and 67-fold gain of foreign affinity.…”

“…While monospecificity is often sought for diagnostic and therapeutic uses, broader reactivity is preferred when mounting broadly neutralizing antibodies (bnAbs) against viruses that rapidly mutate, exemplified by the HIV Env protein and the influenza virus hemagglutinin protein. These rare bnAbs are only observed in a small subset of individuals, often after several years of infection; such antibodies tend to be characterized by noncanonical structures, high mutational loads in antibody variable genes, conformational diversity ( 2 – 5 ), and polyspecificity for many other antigens including binding to self-antigens ( 6 – 9 ).…”

The Impact of Sustained Immunization Regimens on the Antibody Response to Oligomannose Glycans

“…71,72 DH501, which binds oligomannose but neutralizes only kifunensinetreated virus (bearing exclusively Man 8/9 glycans), is also highly mutated (23% of amino acids in the heavy chain). 73 DH501 arose during a four-year course of 17 immunizations using both Env protein and Env DNA in monkeys, which is the only vaccine regimen to date that has definitively elicited antibodies that bind to the Manα1→2Man motif. 64 To recapitulate and improve on those findings with a more practical immunization regimen remains an important goal.…”

“…This includes the high-mannose-patch antibodies, which generally bear ∼20% nucleotide mutation in the heavy chain . In contrast, antibodies from vaccination have been reported to average ∼6% nucleotide mutation. , DH501, which binds oligomannose but neutralizes only kifunensine-treated virus (bearing exclusively Man 8/9 glycans), is also highly mutated (23% of amino acids in the heavy chain) . DH501 arose during a four-year course of 17 immunizations using both Env protein and Env DNA in monkeys, which is the only vaccine regimen to date that has definitively elicited antibodies that bind to the Manα1→2Man motif .…”

Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates

“…Soluble HIV-1 Env trimers were expressed, purified and characterized as previously described [ 11 , 84 ]. The soluble CON-S envelope trimer was designed as a stabilized CON-S SOSIP gp140 and was expressed in Freestyle293 cells (ThermoFisher Cat No.…”