Hidden Lineage Complexity of Glycan-Dependent HIV-1 Broadly Neutralizing Antibodies Uncovered by Digital Panning and Native-Like gp140 Trimer.

Linling He,Devin Sok,Ryan Augst,Dennis R Burton,Gabriel Ozorowski,Charles D Morris,Xiaohe Lin,Andrew B Ward,Bin Zhou,Colin J Mann,Parisa Azadnia,Karen L Saye-Francisco,Jiang Zhu,Natalia De Val

doi:10.3389/fimmu.2017.01025

Abstract

Germline precursors and intermediates of broadly neutralizing antibodies (bNAbs) are essential to the understanding of humoral response to HIV-1 infection and B-cell lineage vaccine design. Using a native-like gp140 trimer probe, we examined antibody libraries constructed from donor-17, the source of glycan-dependent PGT121-class bNAbs recognizing the N332 supersite on the HIV-1 envelope glycoprotein. To facilitate this analysis, a digital panning method was devised that combines biopanning of phage-displayed antibody libraries, 900 bp long-read next-generation sequencing, and heavy/light (H/L)-paired antibodyomics. In addition to single-chain variable fragments resembling the wild-type bNAbs, digital panning identified variants of PGT124 (a member of the PGT121 class) with a unique insertion in the heavy chain complementarity-determining region 1, as well as intermediates of PGT124 exhibiting notable affinity for the native-like trimer and broad HIV-1 neutralization. In a competition assay, these bNAb intermediates could effectively compete with mouse sera induced by a scaffolded BG505 gp140.681 trimer for the N332 supersite. Our study thus reveals previously unrecognized lineage complexity of the PGT121-class bNAbs and provides an array of library-derived bNAb intermediates for evaluation of immunogens containing the N332 supersite. Digital panning may prove to be a valuable tool in future studies of bNAb diversity and lineage development.

Highlights

Neutralizing antibodies isolated from a small fraction of infected individuals have provided valuable insights into the humoral response against HIV-1 [1,2,3,4]
Trimer-based HIV-1 vaccine design has long been hampered by the metastable nature of the envelope glycoprotein (Env)
The results suggested that an somatic hypermutation (SHM) level of 10% or lower may be sufficient for the PGT121class bNAb intermediates to achieve effective Env recognition and broad HIV-1 neutralization

Summary

Introduction

Neutralizing antibodies (bNAbs) isolated from a small fraction of infected individuals have provided valuable insights into the humoral response against HIV-1 [1,2,3,4]. Considering the Lineage Complexity of HIV-1 bNAbs extensive somatic hypermutation (SHM) and unusual sequence features of bNAbs, such as long complementarity-determining region (CDR) loops, an in-depth understanding of their ontogeny is imperative to designing sequential immunogens for guided antibody maturation [7]. To this end, next-generation sequencing (NGS) has been utilized to explore details of the antibody repertoire and lineage development for bNAbs of vaccine interest [8,9,10,11,12,13,14,15,16,17,18,19]. Germlinereverted precursors and inferred lineage intermediates have been derived for several bNAbs targeting the CD4-binding site (CD4bs) and the N332 supersite near the base of variable loop 3 (V3) to facilitate immunogen design and in vivo evaluation [18, 23,24,25,26,27,28,29,30,31]

Methods

Results

Conclusion