Citrullination of a phage displayed human peptidome library reveals the fine specificities of rheumatoid arthritis-associated autoantibodies

Abstract

Post-translational modifications (PTMs) on proteins can be targeted by antibodies associated with autoimmunity. Despite a growing appreciation for their intrinsic role in disease, there is a lack of highly multiplexed serological assays to characterize the fine specificities of PTM-directed autoantibodies. In this study, we used the programmable phage display technology, Phage ImmunoPrecipitation Sequencing (PhIP-Seq), to profile rheumatoid arthritis (RA) associated anti-citrullinated protein antibody (ACPA) reactivities. Using both an unmodified and peptidylarginine deiminases (PAD)-modified phage display library consisting of ~250,000 overlapping 90 amino acid peptide tiles spanning the human proteome, PTM PhIP-Seq robustly identifies antibodies to citrulline-dependent epitopes. PTM PhIP-Seq was used to quantify key differences among RA patients, including PAD isoform specific ACPA profiles, and thus represents a powerful tool for proteome-scale antibody-binding analyses.

Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire

“…Finally, the co-occurrence of, to all appearances, unrelated peptides comprising allergens, ll Resource Immunity 56, 1376-1392, June 13, 2023 1387 pathogens, self-antigens, and commensal microbiota, and the ostensibly shared motifs among them, are findings that require further investigation and validation and might help elucidate the development of allergies 91 and autoimmunity. 92 Limitations of the study PhIP-seq is currently limited to linear epitopes and lacks posttranslational modification information, and thus, new technologies or improvements of the current method (e.g., as previously shown 14 ) are still to be developed. Similarly, the nature of the assay will also miss tridimensional structure information from the antigens that might be recognized by the antibodies.…”

“…Subsequently, all the reactive antibodies present in a sample will bind to their corresponding antigens, with bound phages then extracted by immunoprecipitation and sequenced to obtain an ''immunological fingerprint'' of the individual's antibody repertoire. PhIP-seq has been described previously 11,12 and successfully applied to characterize autoimmune antibody prevalence in patients with multiple sclerosis, type 1 diabetes, and rheumatoid arthritis, 13,14 the human virome, [15][16][17][18][19] and the widespread presence of antibodies against virulence factors 20,21 and the gut microbiome. 21 In addition, previous studies characterized environmental and genetic contributors to immunological traits other than PhIP-seq, such as cytokine responses, 22 blood cell composition, 23 T cell receptor repertoire, 24 and BCRs.…”