Mining the Human Tissue Proteome for Protein Citrullination

Lee, Chien-Yun; Wang, Dongxue; Wilhelm, Mathias; Zolg, Daniel Paul; Schmidt, Tobias; Schnatbaum, Karsten; Reimer, Ulf; Pontén, Fredrik; Uhlén, Mathias; Hahne, Hannes; Küster, Bernhard

doi:10.1074/mcp.ra118.000696

Cited by 92 publications

(174 citation statements)

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“…This series of analytical steps was shown to improve the specificity for identifying citrullinated residues and has been incorporated under one algorithm, Cit Finder, that is a robust tool for the correct assignment of protein citrullination in large data sets . Consistent with the report by Lee et al, the largest number of citrullinated proteins in this study was found in the brain and lung . In addition, unique cellular diversity of the citrullinated proteins suggests a broad biological role for protein citrullination.…”

Section: Mass Spectrometry Applied To the Study Of Citrullination Inmentioning

confidence: 97%

“…Recently, Lee et al used a straightforward method to look at the MS‐based data of 30 human tissues to identify citrullination sites on endogenous proteins. This data mining process allows for the discovery of patterns in large data sets.…”

Section: Mass Spectrometry Applied To the Study Of Citrullination Inmentioning

confidence: 99%

“…In order to resolve the aforementioned ambiguity, Lee's group synthetized ∼2200 citrullinated and 1300 deamidated peptides to build a library of reference spectra. Conceptually, the premise of this approach is that the MS/MS fragmentation pattern of a peptide under some fixed conditions is a reproducible fingerprint of that peptide, such that spectral matching can identify unknown spectra acquired under the same conditions.…”

Section: Mass Spectrometry Applied To the Study Of Citrullination Inmentioning

confidence: 99%

“…The validation confirmed that loss of isocyanic acid was not entirely specific for citrulline and loss from fragment ions should always be included in the analysis if relying only on MS spectra interpretation. Nevertheless, this is the largest review of protein citrullination in human tissues, including 375 citrullination sites on 209 human proteins …”

Section: Mass Spectrometry Applied To the Study Of Citrullination Inmentioning

confidence: 99%

“…In colon mucosa, patterns of citrullination in RA and healthy controls are almost identical among 223 citrullinated peptides from 121 proteins, with the exception of 3 citrullinated peptides that were specific for some patients with RA . Indeed, the majority of citrullinated autoantigen candidates targeted in RA are found across normal tissues, demonstrating that citrullination of these antigens is not an exclusive feature of RA. Nevertheless, although the targets and magnitude of citrullination may not differ among controls and RA patients in some tissues, it is interesting that the rheumatoid joint is enriched in citrullination …”

Section: The Normal and Ra Citrullinomesmentioning

confidence: 99%

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Insights into the study and origin of the citrullinome in rheumatoid arthritis

Fert-Bober

Darrah

Andrade

2019

Immunological Reviews

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The presence of autoantibodies and autoreactive T cells to citrullinated proteins and citrullinating enzymes in patients with rheumatoid arthritis (RA), together with the accumulation of citrullinated proteins in rheumatoid joints, provides substantial evidence that dysregulated citrullination is a hallmark feature of RA. However, understanding mechanisms that dysregulate citrullination in RA has important challenges. Citrullination is a normal process in immune and non‐immune cells, which is likely activated by different conditions (eg, inflammation) with no pathogenic consequences. In a complex inflammatory environment such as the RA joint, unique strategies are therefore required to dissect specific mechanisms involved in the abnormal production of citrullinated proteins. Here, we will review current models of citrullination in RA and discuss critical components that, in our view, are relevant to understanding the accumulation of citrullinated proteins in the RA joint, collectively referred to as the RA citrullinome. In particular, we will focus on potential caveats in the study of citrullination in RA and will highlight methods to precisely detect citrullinated proteins in complex biological samples, which is a confirmatory approach to mechanistically link the RA citrullinome with unique pathogenic pathways in RA.

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Section: Mass Spectrometry Applied To the Study Of Citrullination Inmentioning

confidence: 97%

Section: Mass Spectrometry Applied To the Study Of Citrullination Inmentioning

confidence: 99%

Section: Mass Spectrometry Applied To the Study Of Citrullination Inmentioning

confidence: 99%

Section: Mass Spectrometry Applied To the Study Of Citrullination Inmentioning

confidence: 99%

Section: The Normal and Ra Citrullinomesmentioning

confidence: 99%

See 3 more Smart Citations

Insights into the study and origin of the citrullinome in rheumatoid arthritis

Fert-Bober

Darrah

Andrade

2019

Immunological Reviews

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Disordered Antigens and Epitope Overlap Between Anti–Citrullinated Protein Antibodies and Rheumatoid Factor in Rheumatoid Arthritis

Zheng

Mergaert

Fahmy

et al. 2019

Arthritis & Rheumatology

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Objective. Anti-citrullinated protein antibodies (ACPAs) and rheumatoid factor (RF) are commonly present in rheumatoid arthritis (RA) without a clear rationale for their coexistence. Moreover, autoantibodies develop against proteins with different posttranslational modifications and native proteins without obvious unifying characteristics of the antigens. We undertook this study to broadly evaluate autoantibody binding in seronegative and seropositive RA to identify novel features of reactivity.Methods. An array was created using a total of 172,828 native peptides, citrulline-containing peptides, and homocitrulline-containing peptides derived primarily from proteins citrullinated in the rheumatoid joint. IgG and IgM binding to peptides were compared between cyclic citrullinated peptide (CCP)-positive RF+, CCP+RF−, CCP−RF+, and CCP−RF− serum from RA patients (n = 48) and controls (n = 12). IgG-bound and endogenously citrullinated peptides were analyzed for amino acid patterns and predictors of intrinsic disorder, i.e., unstable 3-dimensional structure. Binding to IgG-derived peptides was specifically evaluated. Enzyme-linked immunosorbent assay confirmed key results.Results. Broadly, CCP+RF+ patients had high citrulline-specific IgG binding to array peptides and CCP+RF− and CCP−RF+ patients had modest citrulline-specific IgG binding (median Z scores 3.02, 1.42, and 0.75, respectively; P < 0.0001). All RA groups had low homocitrulline-specific binding. CCP+RF+ patients had moderate IgG binding to native peptides (median Z score 2.38; P < 0.0001). The highest IgG binding was to citrulline-containing peptides, irrespective of protein identity, especially if citrulline was adjacent to glycine or serine, motifs also seen in endogenous citrullination in the rheumatoid joint. Highly bound peptides had multiple features predictive of disorder. IgG from CCP+RF+ patients targeted citrulline-containing IgG-derived peptides.Conclusion. Disordered antigens, which are frequently citrullinated, and common epitopes for ACPAs and RF are potentially unifying features for RA autoantibodies.

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Generation of Distinct Patterns of Rheumatoid Arthritis Autoantigens by Peptidylarginine Deiminase Types 2 and 4 During Perforin‐Induced Cell Damage

Romero

Darrah

Andrade

2020

Arthritis & Rheumatology

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Objective To address the independent roles of peptidylarginine deiminase type 2 (PAD2) and PAD4 in generating rheumatoid arthritis (RA) autoantigens by using a system that mimics intracellular citrullination in the RA joint. Methods PAD2‐ or PAD4‐expressing 293T cells and mock‐transfected cells were used as targets in cytotoxic assays using lymphokine‐activated killer cells, cytotoxic YT cell granule contents, or purified human perforin. Protein citrullination and autoantigen production were determined by immunoblotting using the anti–modified citrulline–Senshu method and RA sera (n = 30), respectively. Results RA sera recognized at least 3 categories of autoantigens in PAD‐expressing target cells killed by the cytotoxic lymphocyte granule–induced death pathway. These included: 1) autoantigens targeted in their native form, 2) citrullinated antigens, and 3) antigens cleaved by cytotoxic proteases (e.g., granzymes). Interestingly, although target cells expressing PAD2 or PAD4 showed prominent hypercitrullination of a broad range of proteins during cytotoxic granule–induced cell damage, autoantibodies in RA sera targeted only a very limited number of antigens in hypercitrullinated cells. Furthermore, RA sera showed distinct reactivities to autoantigens generated by PAD2 or PAD4. Conclusion The cytotoxic granule–induced death pathway has the capacity to modify antigens by inducing hypercitrullination and antigen cleavage in target cells. Interestingly, among a large number of citrullinated proteins generated by PAD2 and PAD4 in cells, only a few are likely involved in the production of autoantibodies in RA.

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Mining the Human Tissue Proteome for Protein Citrullination

Cited by 92 publications

References 54 publications

Insights into the study and origin of the citrullinome in rheumatoid arthritis

Insights into the study and origin of the citrullinome in rheumatoid arthritis

Disordered Antigens and Epitope Overlap Between Anti–Citrullinated Protein Antibodies and Rheumatoid Factor in Rheumatoid Arthritis

Generation of Distinct Patterns of Rheumatoid Arthritis Autoantigens by Peptidylarginine Deiminase Types 2 and 4 During Perforin‐Induced Cell Damage

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