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

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

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.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Antibodies / chemistry*
  • Antibodies / genetics
  • Antibodies / immunology*
  • Antigen-Antibody Complex / chemistry*
  • Antigen-Antibody Complex / genetics
  • Antigen-Antibody Complex / immunology*
  • Base Sequence
  • Computer Simulation
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Screening Assays / methods
  • Humans
  • Models, Chemical
  • Models, Genetic
  • Models, Immunological
  • Sequence Alignment / methods*
  • Sequence Homology, Amino Acid

Substances

  • Antibodies
  • Antigen-Antibody Complex