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Proc Natl Acad Sci U S A. 2016 May 10;113(19):E2636-45. doi: 10.1073/pnas.1525510113. Epub 2016 Apr 25.

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

Author information

1
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712;
2
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712;
3
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218;
4
Center for Systems and Synthetic Biology University of Texas at Austin, Austin, TX 78712;
5
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712;
6
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712; Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712 gg@che.utexas.edu.

Abstract

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.

KEYWORDS:

B cell; antibody; computational modeling; high-throughput sequencing; immunology

PMID:
27114511
PMCID:
PMC4868480
DOI:
10.1073/pnas.1525510113
[Indexed for MEDLINE]
Free PMC Article

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