Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

• Published in: Proceedings of the National Academy of Sciences - PNAS 2016-05, Vol.113 (19), p.E2636-E2645
• Main Authors: DeKosky, Brandon J., Lungu, Oana I., Park, Daechan, Johnson, Erik L., Charab, Wissam, Chrysostomou, Constantine, Kuroda, Daisuke, Ellington, Andrew D., Ippolito, Gregory C., Gray, Jeffrey J., Georgiou, George
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Antibodies - chemistry; Antibodies - genetics; Antibodies - immunology; Antigen-Antibody Complex - chemistry; Antigen-Antibody Complex - genetics; Antigen-Antibody Complex - immunology; Antigens; Base Sequence; Biological Sciences; Cells; Comparative analysis; Computer Simulation; Genes; High-Throughput Nucleotide Sequencing - methods; High-Throughput Screening Assays - methods; Humans; Immunology; Models, Chemical; Models, Genetic; Models, Immunological; PNAS Plus; Sequence Alignment - methods; Sequence Homology, Amino Acid; Solvents
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1525510113

Elucidating how antigen exposure and selection shape the human antibody repertoire is fundamental to our understanding of B-cell immunity. We sequenced the paired heavy- and light-chain variable regions (VH and VL, respectively) from large populations of single B cells combined with computational modeling of antibody structures to evaluate sequence and structural features of human antibody repertoires at unprecedented depth. Analysis of a dataset comprising 55,000 antibody clusters from CD19⁺CD20⁺CD27⁻ IgM-naive B cells, >120,000 antibody clusters from CD19⁺CD20⁺CD27⁺ antigen–experienced B cells, and >2,000 RosettaAntibody-predicted structural models across three healthy donors led to a number of key findings: (i) VH and VL gene sequences pair in a combinatorial fashion without detectable pairing restrictions at the population level; (ii) certain VH:VL gene pairs were significantly enriched or depleted in the antigen-experienced repertoire relative to the naive repertoire; (iii) antigen selection increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-chain third complementarity-determining region (CDR-H3) antibodies in the antigen-experienced repertoire showed signs of convergent paired light-chain genetic signatures, including shared light-chain third complementarity-determining region (CDR-L3) amino acid sequences and/or Vκ,λ–Jκ,λ genes. The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease.