Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8

• Published in: PloS one 2016-06, Vol.11 (6), p.e0157409
• Main Authors: Soto, Cinque, Ofek, Gilad, Joyce, M Gordon, Zhang, Baoshan, McKee, Krisha, Longo, Nancy S, Yang, Yongping, Huang, Jinghe, Parks, Robert, Eudailey, Joshua, Lloyd, Krissey E, Alam, S Munir, Haynes, Barton F, Mullikin, James C, Connors, Mark, Mascola, John R, Shapiro, Lawrence, Kwong, Peter D
• Format: Article
• Language: English
• Subjects: 60 APPLIED LIFE SCIENCES; Amino Acid Sequence; Antibodies; Antibodies, Neutralizing - chemistry; Antibodies, Neutralizing - genetics; Antibodies, Neutralizing - immunology; Binding sites; Biology and Life Sciences; Cell Line; Complementarity Determining Regions - chemistry; Complementarity Determining Regions - genetics; Complementarity Determining Regions - immunology; Crystallography, X-Ray; Enzyme-linked immunoassays; Epitopes; Genomes; HIV; HIV Antibodies - chemistry; HIV Antibodies - genetics; HIV Antibodies - immunology; HIV Envelope Protein gp41 - chemistry; HIV Envelope Protein gp41 - immunology; HIV Infections - genetics; HIV Infections - immunology; HIV-1; HIV-1 - chemistry; HIV-1 - immunology; Human immunodeficiency virus; Human immunodeficiency virus 1; Humans; Immunoglobulins; Infections; Infectious diseases; Laboratories; Medicine and Health Sciences; Models, Molecular; Multiple alignment calculation; Mutagenesis; Phylogenetic analysis; Research and Analysis Methods; Sequence alignment; Sequence analysis; Sequence motif analysis; Vaccines
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0157409

Antibody 10E8 targets the membrane-proximal external region (MPER) of HIV-1 gp41, neutralizes >97% of HIV-1 isolates, and lacks the auto-reactivity often associated with MPER-directed antibodies. The developmental pathway of 10E8 might therefore serve as a promising template for vaccine design, but samples from time-of-infection-often used to infer the B cell record-are unavailable. In this study, we used crystallography, next-generation sequencing (NGS), and functional assessments to infer the 10E8 developmental pathway from a single time point. Mutational analysis indicated somatic hypermutation of the 2nd-heavy chain-complementarity determining region (CDR H2) to be critical for neutralization, and structures of 10E8 variants with V-gene regions reverted to genomic origin for heavy-and-light chains or heavy chain-only showed structural differences >2 Å relative to mature 10E8 in the CDR H2 and H3. To understand these developmental changes, we used bioinformatic sieving, maximum likelihood, and parsimony analyses of immunoglobulin transcripts to identify 10E8-lineage members, to infer the 10E8-unmutated common ancestor (UCA), and to calculate 10E8-developmental intermediates. We were assisted in this analysis by the preservation of a critical D-gene segment, which was unmutated in most 10E8-lineage sequences. UCA and early intermediates weakly bound a 26-residue-MPER peptide, whereas HIV-1 neutralization and epitope recognition in liposomes were only observed with late intermediates. Antibody 10E8 thus develops from a UCA with weak MPER affinity and substantial differences in CDR H2 and H3 from the mature 10E8; only after extensive somatic hypermutation do 10E8-lineage members gain recognition in the context of membrane and HIV-1 neutralization.