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

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          Abstract

          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.

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          Most cited references51

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          MEME Suite: tools for motif discovery and searching

          Timothy L. Bailey, Mikael Bodén, Fabian Buske … (2009)
          The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms—MAST, FIMO and GLAM2SCAN—allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm Tomtom. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and Tomtom), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.
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            ACR/EULAR 2010 rheumatoid arthritis classification criteria.

            Jonathan Kay, Katherine Upchurch (2012)
            Advances in our understanding of the pathogenesis of RA over the past two decades, particularly the identification of cytokines that promote synovial inflammation (e.g. TNF-α, IL-1 and IL-6), have led to treatment courses that affect the disease process itself, beyond alleviation of symptoms. In turn, emphasis has shifted to intervention early enough in the disease course to prevent the joint destruction that follows inflammation. Accordingly, in 2010 the ACR and the European League Against Rheumatism (EULAR) put forward revised classification criteria emphasizing RA characteristics that emerge early in the disease course, including ACPAs, a biomarker that predicts aggressive disease. These were in contrast with the 1987 ARA criteria, which distinguished established RA patients from those with other forms of arthritis, and identified patients with later disease. The categories of the 2010 ACR/EULAR criteria are grouped into four classifications, with point scores for each: joint symptoms; serology (including RF and/or ACPA); symptom duration, whether 6 weeks; and acute-phase reactants (CRP and/or ESR). The criteria were developed in a three-phase process, beginning with an analysis of patient cohorts to determine what disease characteristics had persuaded clinicians to initiate MTX therapy, followed by consensus-based decisions and the creation of a scoring system that would predict which patients would go on to develop persistent and/or erosive disease.
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              Peptidyl arginine deiminase type 2 (PAD-2) and PAD-4 but not PAD-1, PAD-3, and PAD-6 are expressed in rheumatoid arthritis synovium in close association with tissue inflammation.

              Christian Vincent, Cyril Clavel, Céline Foulquier … (2007)
              Autoantibodies to citrullinated proteins (ACPAs) are specific for rheumatoid arthritis (RA) and probably are involved in its pathophysiology. Citrullyl residues, posttranslationally generated by peptidyl arginine deiminase (PAD), are indispensable components of ACPA-targeted epitopes. The aim of this study was to identify which PAD isotypes are expressed in the synovial tissue (ST) of patients with RA and are involved in the citrullination of fibrin, the major synovial target of ACPAs. Expression of all PAD isotypes, including the recently described PAD type 6 (PAD-6), was explored by reverse transcription-polymerase chain reaction and immunoblotting, first in blood-derived mononuclear leukocytes from healthy donors, then in ST samples from 16 patients with RA and 11 control patients (4 with other arthritides and 7 with osteoarthritis [OA]). In ST samples from patients with RA, PADs were localized by immunohistochemistry. In lymphocytic and monocytic cells and, similarly, in ST samples from patients with RA, the PAD-2, PAD-4, and PAD-6 genes were found to be transcribed, but only PAD-2 and PAD-4 enzymes were detected. PAD-2 was also expressed in ST from control patients, including those with OA, while PAD-4 was preferentially expressed in ST from patients with other arthritides. In RA, the expression levels of PAD-2 and PAD-4 were correlated with the intensity of inflammation (cell infiltration, hypervascularization, and synovial lining hyperplasia), and both enzymes were demonstrable within or in the vicinity of citrullinated fibrin deposits. PAD-2 and PAD-4 are the only PAD isotypes expressed in the ST of patients with RA and those with other arthritides. Inflammatory cells are a major source, but PAD-4 also comes from hyperplastic synoviocytes. Both isotypes are probably involved in the citrullination of fibrin.
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                Author and article information

                Contributors
                Erika Darrah
                H. Benjamin Larman
                Journal
                Journal ID (nlm-ta): EBioMedicine
                Journal ID (iso-abbrev): EBioMedicine
                Title: EBioMedicine
                Publisher: Elsevier
                ISSN (Electronic): 2352-3964
                Publication date PMC-release: 01 September 2021
                Publication date Collection: September 2021
                Publication date (Electronic): 01 September 2021
                Volume: 71
                Electronic Location Identifier: 103506
                Affiliations
                [a ]Immunology Division, Department of Pathology, Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD, USA
                [b ]Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
                [c ]Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
                Author notes
                [1]

                These authors contributed equally to this work.

                Article
                Publisher Item ID: S2352-3964(21)00299-1 Publisher ID: 103506
                DOI: 10.1016/j.ebiom.2021.103506
                PMC ID: 8414044
                PubMed ID: 34481243
                SO-VID: 919444e6-62c9-4fec-858d-60f44ef80b73
                Copyright © © 2021 The Authors
                License:

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                Date received : 29 April 2021
                Date revision received : 9 July 2021
                Date accepted : 13 July 2021
                Categories
                Subject: Research Paper

                Keywords: phage immunoprecipitation sequencing,citrullination,peptidylarginine deiminase,rheumatoid arthritis
                Data availability:
                Keywords: phage immunoprecipitation sequencing, citrullination, peptidylarginine deiminase, rheumatoid arthritis

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