Prevalence, persistence, and genetics of antibody responses to protein toxins and virulence factors

Angkeow, Julia W.; Monaco, Daniel R.; Chen, Athena; Venkataraman, Thiagarajan; Jayaraman, Sahana; Valencia, Cristian; Sie, Brandon M.; Liechti, Thomas; Farhadi, Payam Noroozi; Funez-dePagnier, Gabriela; Sherman-Baust, Cheryl A.; Wong, May Q.; Sears, Cynthia L.; Simner, Patricia J.; Round, June L.; Duggal, Priya; Laserson, Uri; Steiner, Theodore S.; Sen, Ranjan; Lloyd, Thomas E.; Roederer, Mario; Mammen, Andrew L.; Longman, Randy S.; Rider, Lisa G.; Larman, H. Benjamin

Microbial exposures are crucial environmental factors that impact healthspan by sculpting the immune system and microbiota. Antibody profiling via programmable Phage ImmunoPrecipitation Sequencing (PhIP-Seq) provides a high-throughput, costeffective approach for multiplexed detection of exposure and response to thousands of microbial protein products. Here we designed and constructed a library of 95,601 56 amino acid peptide tiles spanning a subset of environmental proteins more likely to be associated with immune responses: those with “toxin” or “virulence factor” keyword annotations. PhIP-Seq was used to profile the circulating antibodies of ~1,000 individuals against this “ToxScan” library of 14,430 toxins and virulence factors from 1,312 genera of organisms. In addition to a detailed analysis of six commonly encountered human commensals and pathogens, we study the age-dependent stability of the ToxScan profile and use a genome-wide association study (GWAS) to find that the MHC-II locus modulates the selection of bacterial epitopes. We detect previously described anti-flagellin antibody responses in a Crohn’s disease cohort and identify a novel association between anti-flagellin antibodies and juvenile dermatomyositis (JDM). PhIP-Seq with the ToxScan library provides a new window into exposure and immune responses to environmental protein toxins and virulence factors, which can be used to study human health and disease at cohort scale.