Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies

Abstract

Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population “arms” that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.

Atypical B cells consist of subsets with distinct functional profiles

“…To determine whether atypical B cells that arise in other inflammatory conditions also consist of subpopulations with different functional profiles, we reanalyzed scRNA-seq data from SLE patients 36 and HIV-infected individuals. 37 Atypical B cells were extracted from these datasets (n = 3,487 for SLE and n = 55,179 for HIV) and clustered into 5 and 8 clusters, respectively ( Figures S11 and S12 ). Among these were clusters with similar gene expression patterns as observed for the malaria-associated atypical B cells analyzed in this study ( Figure 3 E).…”

“…(2020) 36 GEO: GSE135779 scRNA-seq data for class-switched memory B cells from HIV-infected patients Joyce et al. (2023) 37 GEO: GSE229232 Experimental models: Cell lines Human: Expi293F cell line Thermo Cat# A14527; RRID:CVCL_D615 Mouse: CD40L-expressing 3T3 cells Dr. Mark Connors, NIH RRID:CVCL_1H10 Recombinant DNA Plasmid MSP1-bio Addgene Cat# 47709; RRID:Addgene_47709 Plasmid AMA1-bio Addgene Cat# 47741; RRID:Addgene_47741 Plasmid secretedBirA-8his Addgene Cat# 32408; RRID:Addgene_32408 Software and algorithms Cell Ranger v3.1.0 10x Genomics https://www.10xgenomics.com/ Seurat v3.2.3 Stuart et al. (2019) 58 https://satijalab.org/seurat/ Reactome pathway analysis Jassal et al.…”

“…The HIV scRNA-seq data (CellRanger output feature barcoded matrix) of memory B cells (n = 70 samples) and memory B cell-depleted samples (n = 3 samples) were downloaded from GEO: GSE229232 . 37 First, we ran Scrublet 61 for doublet detection. Then we used Seurat 58 to process individual samples and retain only those cells which are not doublets, have nFeature_RNA > 200, percent.mt < 10 and percent.ribo > 4.…”

Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4+decline

“…It has been speculated that the shifts in variant proportion in early infection are immune-driven, with minor variants cyclically out-competing the dominant variant due to a non-negligible selective advantage 31 . Given that multiple variant infections lead to earlier presence of broadly neutralising antibodies, it may follow in trying to mount a sufficiently broad immune response, initial efficacy is attenuated and leads to increased sequestration and higher viral loads during the acute phase 35,36 .…”