New strategy targets rare B cells for effective HIV vaccine development

By Tarun Sai LomteReviewed by Lily Ramsey, LLMJun 3 2024

A recent study published in Nature Immunology showed that germline-targeting epitope scaffold nanoparticles elicit rare broadly neutralizing antibody (bnAb) precursors against human immunodeficiency virus (HIV).

​​​​​​​Study: Vaccination induces broadly neutralizing antibody precursors to HIV gp41. Image Credit: Salov Evgeniy/Shutterstock.com

Background

Broad vaccination protection against antigenically diverse viruses, such as beta coronaviruses, hepatitis C virus, HIV, and influenza virus, requires bnAbs against the conserved epitopes on variable membrane glycoproteins. While monoclonal bnAbs have been identified for these viruses, strategies to elicit bnAbs with predefined binding specificities and genetic features are needed.

In germline-targeting vaccine design, the priming immunogen elicits responses from rare bnAb-precursor B cells with the required genetic features for bnAb development. After priming, sequential boosting with immunogens similar to native glycoproteins can guide B cell maturation to produce bnAbs against the target epitope.

This approach has been demonstrated for VRC01 class bnAbs for the HIV envelope CD4-binding site in humans. However, most VRC01-class bnAbs exhibit heavy chain complementarity determining region 3 (HCDR3)-dominant interactions.

HCDR3-dominant bnAbs against the HIV envelop protein’s (Env) membrane-proximal external region (MPER) will be crucial as such bnAbs (e.g., DH511, LN01, and 10E8) have high neutralization breadth.

The study and findings

In the present study, researchers developed germline-targeting epitope scaffold nanoparticles to induce 10E8-class HCDR3-dominant bnAb-precursor responses. First, they selected one of the epitope scaffolds in MPER, i.e., T117v2, for optimization.

The scaffold exhibited robust binding to mature 10E8 but failed to bind to other 10E8-class precursors identified in next-generation sequencing (NGS) database search (NGS precursors).

Next, the team sought to develop immunogens based on T117v2 having the following features – ≥ 10 μM affinity towards 10E8 unmutated common ancestor (UCA) and NGS precursors, affinity gradient for 10E8-class antibodies, multivalent display on self-assembling single-component nanoparticles, and N-linked glycosylation sites.

Accordingly, iterative optimization of T117v2 binding to 10E8 inferred germline, NGS precursors, and UCA yielded a series of immunogens (10E8-GTs).

These 10E8-GT scaffolds were multimerized through fusion with self-assembling nanoparticles from hyper-thermophilic bacteria. N-linked glycosylation sites were added to scaffold surfaces to mitigate off-target responses.

These scaffolds stabilized MPER in 10E8-bound conformation and engaged 10E8-class HCDR3s resembling 10E8-glycoprotein 41 (gp41) interactions. Next, the team assessed the ability of a naïve B cell receptor (BCR) repertoire to respond to 10E8-GT immunogens.

 On average, 10E8-GT12, 10E8-GT10.1, and 10E8-GT9.2 bound to 0.7%, 0.8%, and 0.05% of naïve B cells (from HIV-seronegative donors).

Of these epitope scaffold-binding cells, 97%, 94%, and 81% did not bind to 10E8 epitope-knockout (KO) versions of the corresponding 10E8-GT constructs and were termed epitope-specific BCRs.

BCR sequencing showed that epitope-specific BCRs were enriched for long HCDR3s and the binding motif (YxFW) in HCDR3 compared to unsorted control datasets.

In total, 16%, 23%, and 18% of epitope-specific BCRs sorted with 10E8-GT12, 10E8-GT10.1, and 10E8-GT9.2, respectively, fulfilling the criteria for 10E8-class HCDR3s.

Next, the researchers synthesized monoclonal antibodies (mAbs) from B cells that sorted with 10E8-GT12, 10E8-GT10.1, or 10E8-GT9.2 and had 10E8-class or non-10E8-class HCDR3s. They found that 60 (out of 70) 10E8-like mAbs had an affinity for their respective sorting probe.

Additional experiments indicated that 10E8-GT scaffolds selectively engaged with naïve BCRs with 10E8-class HCDR3s and bound them with affinities that enable efficient in vivo B cell activation.

Next, the team examined whether 10E8-GT immunogens elicit 10E8-class responses in mice with diverse 10E8-class precursors. To this end, hD3-3/J_H6 mice were developed, in which mouse JH1-JH4 and DQ52 segments were replaced with human J_H6 and D_H3-3 segments, respectively.

These mice were immunized with adjuvanted proteins 10E8-GT10.2 12mer, 10E8-GT12 24mer, 10E8-GT12 12mer, mRNA lipid nanoparticle (LNP)-encoded 10E8-GT12 24mer, or control 10E8-GT9-KO 12mer.

Six weeks later, immunogen-specific BCRs of immunoglobulin D (IgD^-) IgM^- B cells were sequenced. All immunogens, except the control, elicited 10E8-class HCDR3s and were enriched for the YxFw motif and long HCDR3s.

All mice immunized with 10E8-GT12 12mer or 10E8-GT10.2 12mer and 11 immunized with 10E8-GT12 24mer had detectable LN01-class HCDR3s.

Thus, 10E8-GT12 was delivered as protein or LNP-induced responses from diverse and rate 10E8- and LN01-class precursors in vivo.

Next, the researchers immunized rhesus macaques with 10E8-GT10.2 12mer and saponin/mono-phosphoryl A lipid A nanoparticle (SMNP) adjuvant through a dose escalation regimen for 14 days.

Control macaques received stabilized HIV-1 Env trimer lacking MPER. Strong CD71⁺CD38^- B cell responses were observed in the germinal centers (GCs) through week 10. Notably, 10E8-GT10.2 12mer elicited robust epitope-specific GC responses.

Macaques immunized with 10E8-GT10.2 12mer had detectable 10E8-class HCDR3s in CD71⁺CD38^- GCs and IgD^-CD20⁺ memory B cells in peripheral blood. In contrast, a single 10E8-like HCDR3 was detected in over 9000 BCRs from controls.

Finally, the researchers evaluated the binding of post-prime antibodies to 10E8-B1, a fully native epitope scaffold with one mutation (for solubility). 10E8-B1 lacked affinity for early 10E8 lineage members but had an ultrahigh affinity for mature 10E8.

10E8-B1 bound to 10% of 10E8-class antibodies induced by 10E8-GT nanoparticles and 25% of those primed by 10E8-GT10 12mer.

Conclusions

The researchers developed immunogens through germline targeting, epitope scaffolding, and nanoparticles. The immunogens consistently elicited 10E8-class HIV bnAb precursors in two mouse models and rhesus macaques. Thus, the findings illustrate that epitope scaffolds could be designed to trigger responses from rare bnAb precursors and select for favorable maturation.

Taken together, the researchers posit 10E8-GT nanoparticles as MPER vaccine priming immunogens. The epitope scaffolds bound to and isolated naïve bnAb precursors from human peripheral blood.

Besides, mRNA-LNP delivery of 10E8-GT12 24mer induced similar responses as SMNP-adjuvanted protein immunization, supporting the potential for rapid clinical testing.