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

Background: 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.
Methods: 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.
Findings: Using both unmodified and peptidylarginine deiminase (PAD)-modified phage display libraries consisting of ~250,000 overlapping 90 amino acid peptide tiles spanning the human proteome, PTM PhIP-Seq robustly identified antibodies to citrulline-dependent epitopes.
Interpretation: 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.
Funding: This research is based upon work supported in part by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA). The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of ODNI, IARPA, or the US Government. The US Government is authorized to reproduce and distribute reprints for governmental purposes notwithstanding any copyright annotation therein. This study was made possible by a National Institute of General Medical Sciences (NIGMS) grant R01 GM136724 (HBL). MFK was supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) grant T32AR048522. ED was supported by the Rheumatology Research Foundation.
Competing Interests: Declaration of Competing Interest HBL is a founder of Portal Bioscience, Alchemab and ImmuneID, and is an advisor to TScan Therapeutics. ED is an inventor on a licensed patent (US patent no. 8,975,033) and licensed provisional patent (US patent no. 62/481,158) related to the use of antibodies to PAD3 and PAD2, respectively, in identifying clinically informative disease subsets in RA, has received consulting fees from Celgene and Bristol Myers Squibb, and has received research support from Pfizer, Celgene, and Bristol Myers Squibb outside of this work. MFK has received consulting fees from Celltrion outside of this work. MA is an inventor on a patent (US patent no. 10,415,032) related to detection of antibodies associated with chemical exposure. GDRM, DRM, ED, and HBL are inventors on a provisional patent application related the work described herein.
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