Phage display of environmental protein toxins and virulence factors reveals the prevalence, persistence, and genetics of antibody responses

Microbial exposures are crucial environmental factors that impact healthspan by sculpting the immune system and microbiota. Antibody profiling via Phage ImmunoPrecipitation Sequencing (PhIP-Seq) provides a high-throughput, cost-effective approach for detecting exposure and response to microbial protein products. We designed and constructed a library of 95,601 56-amino acid peptide tiles spanning 14,430 proteins with “toxin” or “virulence factor” keyword annotations. We used PhIP-Seq to profile the antibodies of ∼1,000 individuals against this “ToxScan” library. In addition to enumerating immunodominant antibody epitopes, we studied the age-dependent stability of the ToxScan profile and used a genome-wide association study to find that the MHC-II locus modulates bacterial epitope selection. We detected previously described anti-flagellin antibody responses in a Crohn’s disease cohort and identified an association between anti-flagellin antibodies and juvenile dermatomyositis. PhIP-Seq with the ToxScan library is thus an effective tool for studying the environmental determinants of health and disease at cohort scale. [Display omitted] •ToxScan phage library covers >14k toxins and virulence factors for antibody profiling•Serum antibody binding to ToxScan peptides is unique and stable in adulthood•MHC-II locus influences toxin and/or virulence factor antibody epitope selection•Crohn’s-disease-associated flagellin antibodies are also found in juvenile dermatomyositis Lifelong exposures to microbes and their protein products profoundly impact human health. Angkeow et al. employed pan-toxin, pan-virulence factor PhIP-Seq to profile the antibodies of healthy volunteers and patients with autoinflammatory diseases. They report that peptide binding repertoires are unique and stable in adulthood and are modulated by the MHC-II locus. Crohn’s-disease-associated flagellin antibodies are found in juvenile dermatomyositis patients.