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bioRxiv · 10.1101/641787

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

Paull, M.·Johnston, T.·Ibsen, K. N.·Bozekowski, J. D.·Daugherty, P. S.
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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 identify 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 identify 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 identify antibody-binding epitopes. As a positive control, we used this approach, termed K-mer Tiling of Protein Epitopes (K-TOPE), to identify 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, identifying three epitopes recognized by antibodies present in 83% of sera (n = 250). An analysis of 2,908 proteins from 400 viral taxa that infect humans revealed seven enterovirus epitopes and five Epstein-Barr virus epitopes recognized by >30% of specimens. Analysis of Staphylococcus and Streptococcus proteomes similarly revealed six epitopes recognized by >40% of specimens. These common viral and bacterial epitopes exhibited excellent agreement with previously mapped epitopes. Additionally, we identified 30 HSV2-specific epitopes that were 100% specific against HSV1 in novel and previously reported antigens. The K-TOPE approach thus provides a powerful new tool to elucidate the organisms, antigens, and epitopes targeted by human antibody repertoires.

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Paull, M., Johnston, T., Ibsen, K. N., Bozekowski, J. D., Daugherty, P. S.. 2019-05-17. A general approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes. https://doi.org/10.1101/641787

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