A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes

PLoS One. 2019 Sep 6;14(9):e0217668. doi: 10.1371/journal.pone.0217668. eCollection 2019.

Abstract

Antibodies are essential to functional immunity, yet the epitopes targeted by antibody repertoires remain largely uncharacterized. To aid in characterization, we developed a generalizable strategy to predict antibody-binding epitopes within individual proteins and entire proteomes. Specifically, we selected antibody-binding peptides for 273 distinct sera out of a random library and identified the peptides using next-generation sequencing. To predict antibody-binding epitopes and the antigens from which these epitopes were derived, we tiled the sequences of candidate antigens into short overlapping subsequences of length k (k-mers). We used the enrichment over background of these k-mers in the antibody-binding peptide dataset to predict antibody-binding epitopes. As a positive control, we used this approach, termed K-mer Tiling of Protein Epitopes (K-TOPE), to predict epitopes targeted by monoclonal and polyclonal antibodies of well-characterized specificity, accurately recovering their known epitopes. K-TOPE characterized a commonly targeted antigen from Rhinovirus A, predicting four epitopes recognized by antibodies present in 87% of sera (n = 250). An analysis of 2,908 proteins from 400 viral taxa that infect humans predicted seven enterovirus epitopes and five Epstein-Barr virus epitopes recognized by >30% of specimens. Analysis of Staphylococcus and Streptococcus proteomes similarly predicted 22 epitopes recognized by >30% of specimens. Twelve of these common viral and bacterial epitopes agreed with previously mapped epitopes with p-values < 0.05. Additionally, we predicted 30 HSV2-specific epitopes that were 100% specific against HSV1 in novel and previously reported antigens. Experimentally validating these candidate epitopes could help identify diagnostic biomarkers, vaccine components, and therapeutic targets. The K-TOPE approach thus provides a powerful new tool to elucidate the organisms, antigens, and epitopes targeted by human antibody repertoires.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Algorithms
  • Antibodies / chemistry
  • Antibodies / immunology
  • Antigens, Bacterial / chemistry
  • Antigens, Bacterial / immunology
  • Antigens, Viral / chemistry
  • Antigens, Viral / immunology
  • Child
  • Enterovirus / immunology
  • Epitopes / chemistry
  • Epitopes / immunology*
  • Humans
  • Middle Aged
  • Proteome / chemistry
  • Proteome / immunology*
  • Proteomics / methods*
  • Sequence Analysis, Protein / methods*
  • Staphylococcus / immunology
  • Streptococcus / immunology

Substances

  • Antibodies
  • Antigens, Bacterial
  • Antigens, Viral
  • Epitopes
  • Proteome

Associated data

  • Dryad/10.5061/dryad.v7d0350

Grant support

This work was funded in part by grant M2016219 from the Brightfocus Foundation (https://www.brightfocus.org/) to PSD. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.