Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains

• Published in: Proceedings of the National Academy of Sciences - PNAS 2013-04, Vol.110 (16), p.6470-6475
• Main Authors: Zhu, Jiang, Ofek, Gilad, Yang, Yongping, Zhang, Baoshan, Louder, Mark K., Lu, Gabriel, McKee, Krisha, Pancera, Marie, Skinner, Jeff, Zhang, Zhenhai, Parks, Robert, Eudailey, Joshua, Lloyd, Krissey E., Blinn, Julie, Alam, S. Munir, Haynes, Barton F., Simek, Melissa, Burton, Dennis R., Koff, Wayne C., Mullikin, James C., Mascola, John R., Shapiro, Lawrence, Kwong, Peter D.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Antibodies; Antibodies, Neutralizing - chemistry; Antibodies, Neutralizing - genetics; Antigens; B lymphocytes; Bioinformatics; Biological Sciences; Computational Biology; Databases, Genetic; Deoxyribonucleic acid; DNA; Enzyme-Linked Immunosorbent Assay; High-Throughput Nucleotide Sequencing; HIV; HIV 1; HIV-1 - immunology; Human immunodeficiency virus; Humans; Immunoglobulin Heavy Chains - genetics; Immunoglobulin Light Chains - genetics; Immunoglobulins; Immunology; Models, Molecular; Molecular Sequence Data; Neutralization Tests; Neutralizing antibodies; Phylogenetics; Phylogeny; Reactivity; Sequence Alignment; Sequencing; Vaccination
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1219320110

Next-generation sequencing of antibody transcripts from HIV-1-infected individuals with broadly neutralizing antibodies could provide an efficient means for identifying somatic variants and characterizing their lineages. Here, we used 454 pyrosequencing and identity/divergence grid sampling to analyze heavy- and lightchain sequences from donor N152, the source of the broadly neutralizing antibody 10E8. We identified variants with up to 28% difference in amino acid sequence. Heavy-and light-chain phylogenetic trees of identified 10E8 variants displayed similar architectures, and 10E8 variants reconstituted from matched and unmatched phylogenetic branches displayed significantly lower autoreactivity when matched. To test the generality of phylogenetic pairing, we analyzed donor International AIDS Vaccine Initiative 84, the source of antibodies PGT141-145. Heavy-and light-chain phylogenetic trees of PGT141-145 somatic variants also displayed remarkably similar architectures; in this case, branch pairings could be anchored by known PGT141-145 antibodies. Altogether, our findings suggest that phylogenetic matching of heavy and light chains can provide a means to approximate natural pairings.