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

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.

Systematic profiling of SARS-CoV-2 specific IgG epitopes at single amino acid resolution

“…However, these platforms could not provide epitope information at amino acid level, and pathogen specific protein or peptide library need to be constructed individually, which is costly and time-consuming. Alternatively, random peptide libraries were attempted for dissecting pathogen specific IgG responses from sera ( 34, 35 ). For SARS-CoV-2, following the protocol of testing serum directly that we established ( 34 ), and the K-TOPE algorithm ( 35 ), we tried to profile the virus specific IgG responses at proteome level.…”

“…Alternatively, random peptide libraries were attempted for dissecting pathogen specific IgG responses from sera ( 34, 35 ). For SARS-CoV-2, following the protocol of testing serum directly that we established ( 34 ), and the K-TOPE algorithm ( 35 ), we tried to profile the virus specific IgG responses at proteome level. However, most of the identified epitopes that match the sequence of SARS-CoV-2 proteins are of low frequency.…”

Antibody epitope repertoire analysis enables rapid antigen discovery and multiplex serology

“…Sequencing data from each sample was processed to generate a non-redundant peptide list of antibody binding epitopes using publicly available software as described 30 . FASTQ DNA sequencing files were deposited into the NCBI Sequence Read Archive (SRA) for public access.…”

Comparison of motif-based and whole-unique-sequence-based analyses of phage display library datasets generated by biopanning of anti-Borrelia burgdorferi immune sera

“…burgdorderi immune response. Given that most of the binding energy is typically derived from 4-6 amino acids [17], the specificity of antigen-antibody interaction is defined by only a few anchor residues within an epitope [29, [96][97][98]. Previoulsy, we [27] and others [34] demonstrated that the four-amino-acid consensus is a minimum motif length, which is sufficient to define an antibody specificity.…”