Distinct clonal evolution of B-cells in HIV controllers with neutralizing antibody breadth

Abstract

A minor subset of individuals infected with HIV-1 develop antibody neutralization breadth during the natural course of the infection, often linked to chronic, high level viremia. Despite significant efforts, vaccination strategies have been unable to induce similar neutralization breadth and the mechanisms underlying neutralizing antibody induction remain largely elusive. Broadly neutralizing antibody responses can also be found in individuals who control HIV to low and even undetectable plasma levels in the absence of antiretroviral therapy, suggesting that high antigen exposure is not a strict requirement for neutralization breadth. We therefore performed an analysis of paired heavy and light chain B-cell receptor repertoires in 12,591 HIV-1 Envelope-specific single memory B-cells to determine alterations in the BCR immunoglobulin gene repertoire and B-cell clonal expansions that associate with neutralizing antibody breadth in 22 HIV controllers. We found that the frequency of genomic mutations in IGHV and IGLV was directly correlated with serum neutralization breadth. The repertoire of the most mutated antibodies was dominated by a small number of large clones with evolutionary signatures suggesting that these clones had reached peak affinity maturation. These data demonstrate that even in the setting of low plasma HIV antigenemia, similar to what a vaccine can potentially achieve, BCR selection for extended somatic hypermutation and clonal evolution can occur in some individuals suggesting that host-specific factors might be involved that could be targeted with future vaccine strategies.

Mining HIV controllers for broad and functional antibodies to recognize and eliminate HIV-infected cells

“…Paired IgG heavy and light chains had been sequenced and analyzed for somatic hypermutation (SHM) by calculating mutation frequencies relative to the putative germline sequence. This dataset and the sequence analysis approach have been partially reported by Cizmeci et al (2020) (Kepler, 2013). As high levels of SHM are suggestive of advanced affinity maturation, we hypothesized that highly mutated antibodies would demonstrate superior binding activity to the cell-surface-expressed envelope.…”

“…As previously described by Cizmeci et al, (2020) peripheral blood lymphocytes were isolated from buffy coats by centrifugation on histopaque (Sigma-Aldrich). CD19+ B cells were isolated by negative selection following the manufacturer's instructions (STEMCELL Technologies).…”

“…B cell receptor sequencing, V gene assignment, and somatic hypermutation analysis As previously described by Cizmeci et al, (2020) natively paired variable sequences from heavy-and light-chain pairs were generated by reverse transcription, cDNA barcoding, amplification, and sequencing as described previously (DeFalco et al, 2018;Tan et al, 2014). cDNA sequences were determined by 454 Titanium sequencing.…”

Long-term and low-level envelope C2V3 stimulation from highly diverse virus isolates leads to frequent development of broad and elite antibody neutralization in HIV-1 infected individuals

“…The boost in the quality of the neutralizing response in these patients suggest good restoration of the B cell compartment with ART which is uncommon in chronic HIV-1 infection 88,89,90 . Moreover, the moderate level of plasma viremia (median 11,660 HIV-1 RNA copies /ml, IQR, 380-30,060) found in these patients may have provided the low-level antigenic stimulation needed for the full maturation of memory B cells and bNAb production 31,88,91 . This has precedent in HIV-2 infection where most patients are infected for long periods and produce potent and broadly neutralizing responses in a setting of low plasma viremia 36,92,93 .…”

“…However, the mechanisms underlying the elicitation of such antibodies by B cell populations are still largely unknown 27,28,29,30 . Guiding the immune system to elicit such bNAbs remains a major challenge due to the extremely complex antibody maturation pathways and high levels of somatic hypermutation required by HIV-1 specific antibodies to acquire neutralization breadth 30,31 . An exception is the V3-glycan supersite bNAb lineage that does not require extensive antibody-affinity maturation 32,33 allowing their development in early stages of infection 34 , and explaining their high prevalence in recently infected individuals 3 .…”