Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires.
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.
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712;
Brandon J
BJ
DeKosky
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712;
Oana I
OI
Lungu
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712;
Daechan
D
Park
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712;
Erik L
EL
Johnson
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712;
Wissam
W
Charab
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712;
Constantine
C
Chrysostomou
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218;
Daisuke
D
Kuroda
Center for Systems and Synthetic Biology University of Texas at Austin, Austin, TX 78712;
Andrew D
AD
Ellington
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712;
Gregory C
GC
Ippolito
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218;
Jeffrey J
JJ
Gray
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.
George
G
Georgiou
D000595:Amino Acid Sequence; D000906:Antibodies / Q000737:chemistry* / Q000235:genetics / Q000276:immunology*; D000936:Antigen-Antibody Complex / Q000737:chemistry* / Q000235:genetics / Q000276:immunology*; D001483:Base Sequence; D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D008956:Models, Chemical; D008957:Models, Genetic; D018448:Models, Immunological; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D000906:Antibodies; D000936:Antigen-Antibody Complex
B cell; antibody; computational modeling; high-throughput sequencing; immunology