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Wang B, Fields L, Li L. Recent advances in characterization of citrullination and its implication in human disease research: From method development to network integration. Proteomics 2023; 23:e2200286. [PMID: 36546832 PMCID: PMC10285031 DOI: 10.1002/pmic.202200286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Post-translational modifications (PTM) of proteins increase the functional diversity of the proteome and have been implicated in the pathogenesis of numerous diseases. The most widely understood modifications include phosphorylation, methylation, acetylation, O-linked/N-linked glycosylation, and ubiquitination, all of which have been extensively studied and documented. Citrullination is a historically less explored, yet increasingly studied, protein PTM which has profound effects on protein conformation and protein-protein interactions. Dysregulation of protein citrullination has been associated with disease development and progression. Identification and characterization of citrullinated proteins is highly challenging, complicated by the low cellular abundance of citrullinated proteins, making it difficult to identify and quantify the extent of citrullination in samples, coupled with challenges associated with development of mass spectrometry (MS)-based methods, as the corresponding mass shift is relatively small, +0.984 Da, and identical to the mass shift of deamidation. The focus of this review is to discuss recent advancements of citrullination-specific MS approaches and integration of the potential methodology for improved citrullination identification and characterization. In addition, the association of citrullination in disease networks is also highlighted.
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Affiliation(s)
- Bin Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
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2
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Shi Y, Li Z, Wang B, Shi X, Ye H, Delafield DG, Lv L, Ye Z, Chen Z, Ma F, Li L. Enabling Global Analysis of Protein Citrullination via Biotin Thiol Tag-Assisted Mass Spectrometry. Anal Chem 2022; 94:17895-17903. [PMID: 36512406 DOI: 10.1021/acs.analchem.2c03844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Citrullination is a key post-translational modification (PTM) that affects protein structures and functions. Although it has been linked to various biological processes and disease pathogenesis, the underlying mechanism remains poorly understood due to a lack of effective tools to enrich, detect, and localize this PTM. Herein, we report the design and development of a biotin thiol tag that enables derivatization, enrichment, and confident identification of citrullination via mass spectrometry. We perform global mapping of the citrullination proteome of mouse tissues. In total, we identify 691 citrullination sites from 432 proteins which represents the largest data set to date. We discover novel distribution and functions of this PTM. This study depicts a landscape of protein citrullination and lays the foundation for further deciphering their physiological and pathological roles.
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Affiliation(s)
- Yatao Shi
- School of Pharmacy, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Zihui Li
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Bin Wang
- School of Pharmacy, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Xudong Shi
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin─Madison, Madison, Wisconsin 53792, United States
| | - Hui Ye
- School of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Daniel G Delafield
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Langlang Lv
- School of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengqing Ye
- Medicinal Chemistry Center, School of Pharmacy, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Fengfei Ma
- School of Pharmacy, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin─Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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3
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Villacrés C, Spicer V, Krokhin OV. Confident Identification of Citrullination and Carbamylation Assisted by Peptide Retention Time Prediction. J Proteome Res 2021; 20:1571-1581. [PMID: 33523662 DOI: 10.1021/acs.jproteome.0c00775] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chromatographic behavior of peptides carrying citrulline and homocitrulline residues in proteomic two-dimensional (2D) liquid chromatography-mass spectrometry (LC-MS) experiments has been investigated. The primary goal of this study was to determine the chromatographic conditions that allow differentiating between arginine citrullination and deamidation of asparagine based on retention data, improving the confidence of MS-based identifications. Carbamylation was used as a reference point due to a high degree of similarity between modification products and anticipated changes in chromatographic behavior. We applied 2D LC-MS/MS (a high-pH-low-pH reversed phase (RP), hydrophilic interaction liquid chromatography (HILIC)-low-pH RP, and strong cation exchange (SCX)-low-pH RP) to acquire retention data for modified-nonmodified peptide pairs in the four separation modes. Modifications of a standard protein mixture were induced enzymatically (PAD-2) or chemically (urea) for citrullination and carbamylation, respectively. Deamidation occurs spontaneously. Similar retention shifts were observed for all three modifications in a high-pH RP (decrease) and a low-pH RP (increase), thus limiting the applicability of this 2D LC combination. HILIC on bare silica and strong cation exchange separations have been probed to amplify the effect of charge loss upon citrullination, with SCX demonstrating the most differentiating power: the elimination of basic residues upon citrullination/carbamylation results in an ∼58 mM KCl retention decrease, while retention of deamidated products decreases slightly.
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Affiliation(s)
- Carina Villacrés
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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4
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Vitorino R, Guedes S, Vitorino C, Ferreira R, Amado F, Van Eyk JE. Elucidating Citrullination by Mass Spectrometry and Its Role in Disease Pathogenesis. J Proteome Res 2021; 20:38-48. [PMID: 32966086 PMCID: PMC11009872 DOI: 10.1021/acs.jproteome.0c00474] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review focuses on discussing key mechanisms in disease pathogenesis mediated by the protein post-translational modification citrullination. These processes are discussed in depth in the context of complex diseases such as rheumatoid arthritis, cancer, central nervous system disorders, and cardiovascular disease. Additionally, a critical evaluation of challenges in laboratory detection of citrullination sites is also outlined. In this context, the role of mass spectrometry is discussed with a focus on contemporary techniques that offer promising options to detect the exact site of protein citrullination. Novel methods described in the paper have the potential to detect and quantify the occurrence of post-translational modification sites for diagnosis and therapeutic purposes with a high degree of specificity and sensitivity. Furthermore, they offer a much faster performance than traditional techniques making them ideal for large-scale experimentation.
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Affiliation(s)
- Rui Vitorino
- QOPNA & LAQV-REQUIMTE, Departamento de Qúimica, Universidade de Aveiro, Aveiro, Portugal; iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Sofia Guedes
- QOPNA & LAQV-REQUIMTE, Departamento de Qúimica, Universidade de Aveiro, Aveiro, Portugal
| | - Carla Vitorino
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Rita Ferreira
- QOPNA & LAQV-REQUIMTE, Departamento de Qúimica, Universidade de Aveiro, Aveiro, Portugal
| | - Francisco Amado
- QOPNA & LAQV-REQUIMTE, Departamento de Qúimica, Universidade de Aveiro, Aveiro, Portugal
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars-Sinia Medical Center, Los Angeles, California, United States
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Briot J, Simon M, Méchin MC. Deimination, Intermediate Filaments and Associated Proteins. Int J Mol Sci 2020; 21:E8746. [PMID: 33228136 PMCID: PMC7699402 DOI: 10.3390/ijms21228746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Deimination (or citrullination) is a post-translational modification catalyzed by a calcium-dependent enzyme family of five peptidylarginine deiminases (PADs). Deimination is involved in physiological processes (cell differentiation, embryogenesis, innate and adaptive immunity, etc.) and in autoimmune diseases (rheumatoid arthritis, multiple sclerosis and lupus), cancers and neurodegenerative diseases. Intermediate filaments (IF) and associated proteins (IFAP) are major substrates of PADs. Here, we focus on the effects of deimination on the polymerization and solubility properties of IF proteins and on the proteolysis and cross-linking of IFAP, to finally expose some features of interest and some limitations of citrullinomes.
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Affiliation(s)
| | | | - Marie-Claire Méchin
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Toulouse III Paul Sabatier, Université Fédérale de Toulouse Midi-Pyrénées, U1056, 31059 Toulouse, France; (J.B.); (M.S.)
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Steckel A, Uray K, Turiák L, Gömöry Á, Drahos L, Hudecz F, Schlosser G. Mapping the tandem mass spectrometric characteristics of citrulline-containing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:844-850. [PMID: 29575159 DOI: 10.1002/rcm.8105] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/28/2018] [Accepted: 03/04/2018] [Indexed: 05/20/2023]
Abstract
RATIONALE Protein citrullination (deimination) is a post-translational modification of proteins converting arginine(s) into citrulline(s). "Overcitrullination" could be associated with severe pathological conditions. Mass spectrometric analysis of modified proteins is hindered by several problems. A comprehensive study of the fragmentation of deiminated peptides is not yet available. In this paper we have made an attempt to describe the characteristics of these processes, based on the studies of epitope model oligopeptides derived from clinically relevant proteins. METHODS Solutions of purified model peptides containing either one or two citrulline residues as well as their native variants were injected directly into the electrospray source of a high accuracy and resolution quadrupole-time-of-flight instrument and were analysed by tandem mass spectrometry using low-energy collision-induced dissociation. RESULTS Loss of isocyanic acid from citrulline residues is a preferred fragmentation route for deiminated peptides, which yields ornithine residues in the sequence. However, simultaneous detection of both the isocyanic acid loss and sequence fragments is often compromised. A preferential cleavage site was observed between citrulline and any other following amino acids yielding intensive complementary b- and y-type ions. Also, citrulline positioned at the C-termini displays a preferential cleavage N-terminal to this residue yielding characteristic y1 ions. These phenomena are described here for the first time and are referred to as the "citrulline effect". CONCLUSIONS We found that the citrulline effect is very pronounced and could be used as a complementary tool for the confirmation of modification sites in addition to losses of isocyanic acids from the protonated molecules or from fragment ions. Low collision energy applied to peptide ions having partially mobile protons reveals the site of modification by generating specific and intensive fragments of the sequence. On the other hand, fragmenting precursor ions with mobile protons usually allows full sequence coverage, although citrulline-specific fragments may exhibit lower intensities compared to other fragments.
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Affiliation(s)
- Arnold Steckel
- Doctoral School of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Katalin Uray
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágnes Gömöry
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ferenc Hudecz
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Analytical Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
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Lee CY, Wang D, Wilhelm M, Zolg DP, Schmidt T, Schnatbaum K, Reimer U, Pontén F, Uhlén M, Hahne H, Kuster B. Mining the Human Tissue Proteome for Protein Citrullination. Mol Cell Proteomics 2018; 17:1378-1391. [PMID: 29610271 DOI: 10.1074/mcp.ra118.000696] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/28/2018] [Indexed: 11/06/2022] Open
Abstract
Citrullination is a posttranslational modification of arginine catalyzed by five peptidylarginine deiminases (PADs) in humans. The loss of a positive charge may cause structural or functional alterations, and while the modification has been linked to several diseases, including rheumatoid arthritis (RA) and cancer, its physiological or pathophysiological roles remain largely unclear. In part, this is owing to limitations in available methodology to robustly enrich, detect, and localize the modification. As a result, only a few citrullination sites have been identified on human proteins with high confidence. In this study, we mined data from mass-spectrometry-based deep proteomic profiling of 30 human tissues to identify citrullination sites on endogenous proteins. Database searching of ∼70 million tandem mass spectra yielded ∼13,000 candidate spectra, which were further triaged by spectrum quality metrics and the detection of the specific neutral loss of isocyanic acid from citrullinated peptides to reduce false positives. Because citrullination is easily confused with deamidation, we synthetized ∼2,200 citrullinated and 1,300 deamidated peptides to build a library of reference spectra. This led to the validation of 375 citrullination sites on 209 human proteins. Further analysis showed that >80% of the identified modifications sites were new, and for 56% of the proteins, citrullination was detected for the first time. Sequence motif analysis revealed a strong preference for Asp and Gly, residues around the citrullination site. Interestingly, while the modification was detected in 26 human tissues with the highest levels found in the brain and lung, citrullination levels did not correlate well with protein expression of the PAD enzymes. Even though the current work represents the largest survey of protein citrullination to date, the modification was mostly detected on high abundant proteins, arguing that the development of specific enrichment methods would be required in order to study the full extent of cellular protein citrullination.
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Affiliation(s)
- Chien-Yun Lee
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,§Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.,¶Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
| | - Dongxue Wang
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Daniel P Zolg
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tobias Schmidt
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Ulf Reimer
- ‖JPT Peptide Technologies GmbH, Berlin, Germany
| | - Fredrik Pontén
- **Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- ‡‡Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Bernhard Kuster
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; .,¶¶Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
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Lourido L, Blanco FJ, Ruiz-Romero C. Defining the proteomic landscape of rheumatoid arthritis: progress and prospective clinical applications. Expert Rev Proteomics 2017; 14:431-444. [PMID: 28425787 DOI: 10.1080/14789450.2017.1321481] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The heterogeneity of Rheumatoid Arthritis (RA) and the absence of clinical tests accurate enough to identify the early stages of this disease have hampered its management. Therefore, proteomics research is increasingly focused on the discovery of novel biological markers, which would not only be able make an early diagnosis, but also to gain insight into the different pathological mechanisms underlying the heterogeneity of RA and also to stratify patients, which is critical to enabling effective treatments. Areas covered: The proteomic approaches that have been utilised to provide knowledge about RA pathogenesis, and to identify biomarkers for RA diagnosis, prognosis, disease monitoring and prediction of response to therapy, are summarized. Expert commentary: Although each proteomic study is unique in its design, all of them have contributed to the understanding of RA pathogenesis and the discovery of promising biomarkers for patient stratification, which would improve clinical care of RA patients. Still, efforts need to be made to validate these findings and translate them into clinical practice.
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Affiliation(s)
- Lucía Lourido
- a Rheumatology Division, ProteoRed/ISCIII Proteomics Group , INIBIC - Hospital Universitario de A Coruña , A Coruña , Spain.,b RIER-RED de Inflamación y Enfermedades Reumáticas , INIBIC-CHUAC , A Coruña , Spain
| | - Francisco J Blanco
- a Rheumatology Division, ProteoRed/ISCIII Proteomics Group , INIBIC - Hospital Universitario de A Coruña , A Coruña , Spain.,b RIER-RED de Inflamación y Enfermedades Reumáticas , INIBIC-CHUAC , A Coruña , Spain
| | - Cristina Ruiz-Romero
- a Rheumatology Division, ProteoRed/ISCIII Proteomics Group , INIBIC - Hospital Universitario de A Coruña , A Coruña , Spain.,c CIBER-BBN Instituto de Salud Carlos III , INIBIC-CHUAC , A Coruña , Spain
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Badillo-Soto MA, Rodríguez-Rodríguez M, Pérez-Pérez ME, Daza-Benitez L, Bollain-Y-Goytia JJ, Carrillo-Jiménez MA, Avalos-Díaz E, Herrera-Esparza R. Potential protein targets of the peptidylarginine deiminase 2 and peptidylarginine deiminase 4 enzymes in rheumatoid synovial tissue and its possible meaning. Eur J Rheumatol 2016; 3:44-49. [PMID: 27708970 DOI: 10.5152/eurjrheum.2015.0055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/05/2015] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE The molecular mechanism of citrullination involves the calcium-dependent peptidylarginine deiminase (PAD) family of enzymes. These enzymes induce a stereochemical modification of normal proteins and transform them into autoantigens, which in rheumatoid arthritis trigger a complex cascade of joint inflammatory events followed by chronic synovitis, pannus formation, and finally, cartilage destruction. By hypothesizing that PAD2 and PAD4 enzymes produce autoantigens, we investigated five possible synovial protein targets of PAD enzymes. MATERIAL AND METHODS We measured PAD2, PAD4, and citrullinated proteins in 10 rheumatoid and 10 osteoarthritis synovial biopsies and then assessed the post-translational modifications of fibrinogen, cytokeratin, tubulin, IgG, and vimentin proteins using a double-fluorescence assay with specific antibodies and an affinity-purified anti-citrullinated peptide (CCP) antibody. The degree of co-localization was analyzed, and statistical significance was determined by ANOVA, Fisher's exact test, and regression analysis. RESULTS The principal results of this study demonstrated that citrullinated proteins, such as fibrinogen, IgG, and other probed proteins, were targets of PAD2 and PAD4 activity in rheumatoid synovial biopsies, whereas osteoarthritis biopsies were negative for this enzyme (p<0.0001). An analysis of citrullination sites using the UniProtKB/Swiss-Prot data bank predicts that the secondary structure of the analyzed proteins displays most of the sites for citrullination; a discussion regarding its possible meaning in terms of pathogenesis is made. CONCLUSION Our results support the conclusion that the synovial citrullination of proteins is PAD2 and PAD4 dependent. Furthermore, there is a collection of candidate proteins that can be citrullinated.
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Affiliation(s)
- Martha Adriana Badillo-Soto
- Department of Immunology, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Mayra Rodríguez-Rodríguez
- Department of Immunology, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - María Elena Pérez-Pérez
- Department of Immunology, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Leonel Daza-Benitez
- Unidad Médica de Alta Especialidad (UMAE) T1, Instituto Mexicano del Seguro Social (IMSS), León, Guanajuato, México
| | - Juan José Bollain-Y-Goytia
- Department of Immunology, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, México
| | | | - Esperanza Avalos-Díaz
- Department of Immunology, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Rafael Herrera-Esparza
- Department of Immunology, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, México
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Fert-Bober J, Giles JT, Holewinski RJ, Kirk JA, Uhrigshardt H, Crowgey EL, Andrade F, Bingham CO, Park JK, Halushka MK, Kass DA, Bathon JM, Van Eyk JE. Citrullination of myofilament proteins in heart failure. Cardiovasc Res 2015; 108:232-42. [PMID: 26113265 PMCID: PMC4614685 DOI: 10.1093/cvr/cvv185] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 06/12/2015] [Accepted: 06/17/2015] [Indexed: 11/12/2022] Open
Abstract
AIMS Citrullination, the post-translational conversion of arginine to citrulline by the enzyme family of peptidylarginine deiminases (PADs), is associated with several diseases, and specific citrullinated proteins have been shown to alter function while others act as auto-antigens. In this study, we identified citrullinated proteins in human myocardial samples, from healthy and heart failure patients, and determined several potential functional consequences. Further we investigated PAD isoform cell-specific expression in the heart. METHODS AND RESULTS A citrullination-targeted proteomic strategy using data-independent (SWATH) acquisition method was used to identify the modified cardiac proteins. Citrullinated-induced sarcomeric proteins were validated using two-dimensional gel electrophoresis and investigated using biochemical and functional assays. Myocardial PAD isoforms were confirmed by RT-PCR with PAD2 being the major isoform in myocytes. In total, 304 citrullinated sites were identified that map to 145 proteins among the three study groups: normal, ischaemia, and dilated cardiomyopathy. Citrullination of myosin (using HMM fragment) decreased its intrinsic ATPase activity and inhibited the acto-HMM-ATPase activity. Citrullinated TM resulted in stronger F-actin binding and inhibited the acto-HMM-ATPase activity. Citrullinated TnI did not alter the binding to F-actin or acto-HMM-ATPase activity. Overall, citrullination of sarcomeric proteins caused a decrease in Ca(2+) sensitivity in skinned cardiomyocytes, with no change in maximal calcium-activated force or hill coefficient. CONCLUSION Citrullination unique to the cardiac proteome was identified. Our data indicate important structural and functional alterations to the cardiac sarcomere and the contribution of protein citrullination to this process.
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Affiliation(s)
- Justyna Fert-Bober
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Advanced Clinical BioSystems Research Institute, Advanced Health Science Building, 9229, Los Angeles, CA, USA Bayview Proteomics Center, Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - John T Giles
- Division of Rheumatology, Department of Medicine, Columbia University, New York, NY, USA
| | - Ronald J Holewinski
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Advanced Clinical BioSystems Research Institute, Advanced Health Science Building, 9229, Los Angeles, CA, USA
| | - Jonathan A Kirk
- Division of Cardiology, Department of Medicine, The Johns Hopkins University Medical Institutions, Baltimore, MD, USA
| | - Helge Uhrigshardt
- Bayview Proteomics Center, Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Erin L Crowgey
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Advanced Clinical BioSystems Research Institute, Advanced Health Science Building, 9229, Los Angeles, CA, USA
| | - Felipe Andrade
- Division of Cardiology, Department of Medicine, The Johns Hopkins University Medical Institutions, Baltimore, MD, USA
| | - Clifton O Bingham
- Division of Rheumatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA Division of Rheumatology, Department of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jin Kyun Park
- Division of Rheumatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA Division of Rheumatology, Department of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David A Kass
- Division of Cardiology, Department of Medicine, The Johns Hopkins University Medical Institutions, Baltimore, MD, USA
| | - Joan M Bathon
- Division of Rheumatology, Department of Medicine, Columbia University, New York, NY, USA
| | - Jennifer E Van Eyk
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Advanced Clinical BioSystems Research Institute, Advanced Health Science Building, 9229, Los Angeles, CA, USA Bayview Proteomics Center, Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
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11
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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12
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Biomarkers of early stage osteoarthritis, rheumatoid arthritis and musculoskeletal health. Sci Rep 2015; 5:9259. [PMID: 25788417 PMCID: PMC4365413 DOI: 10.1038/srep09259] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/27/2015] [Indexed: 12/17/2022] Open
Abstract
There is currently no biochemical test for detection of early-stage osteoarthritis (eOA). Tests for early-stage rheumatoid arthritis (eRA) such as rheumatoid factor (RF) and anti–cyclic citrullinated peptide (CCP) antibodies require refinement to improve clinical utility. We developed robust mass spectrometric methods to quantify citrullinated protein (CP) and free hydroxyproline in body fluids. We detected CP in the plasma of healthy subjects and surprisingly found that CP was increased in both patients with eOA and eRA whereas anti–CCP antibodies were predominantly present in eRA. A 4-class diagnostic algorithm combining plasma/serum CP, anti-CCP antibody and hydroxyproline applied to a cohort gave specific and sensitive detection and discrimination of eOA, eRA, other non-RA inflammatory joint diseases and good skeletal health. This provides a first-in-class plasma/serum-based biochemical assay for diagnosis and type discrimination of early-stage arthritis to facilitate improved treatment and patient outcomes, exploiting citrullinated protein and related differential autoimmunity.
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13
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Gudmann NS, Hansen NUB, Jensen ACB, Karsdal MA, Siebuhr AS. Biological relevance of citrullinations: diagnostic, prognostic and therapeutic options. Autoimmunity 2014; 48:73-9. [PMID: 25520183 DOI: 10.3109/08916934.2014.962024] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Citrullination has become a hot topic within recent years due to its involvement in diseases such as rheumatoid arthritis (RA), multiple sclerosis and fibrosis. Citrullinations are the conversion of arginine to citrulline by peptidylarginine deiminase (PAD) enzymes, which affect protein properties. The aim of this review is to summarize the advances in citrullination research and further explore the potential of citrullination as a diagnostic tool as well as inhibition of PAD enzymes as a target for treatment. METHOD We reviewed current literature with emphasis on the role of citrullination in health and disease, the nature of enzymes responsible for citrullination, and the potential of applying citrullinations in diagnostics and pharmaceuticals. CONCLUSION Current literature suggests that increased levels of citrullinated proteins are found in several if not all inflammatory diseases. In RA measurement of anti-citrullinated protein antibodies (ACPA) against citrullinated protein fragments are widely used as a prognostic biomarker. More recently, it has been indicated that levels of selected citrullinated proteins carries additional potential as biomarkers. This includes citrullinated vimentin which provide prognostic information in diseases as fibrosis and ankylosing spondylitis. In addition, recent studies suggest that inhibition of PAD is a target for treatment of diseases such as RA and cancer where proteins that are citrullinated are believed to influence the disease activity.
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14
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Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat Commun 2014; 5:4405. [PMID: 25059763 PMCID: PMC4279252 DOI: 10.1038/ncomms5405] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 06/16/2014] [Indexed: 12/27/2022] Open
Abstract
Detailed characterization of post-translational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further, Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.
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15
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Tutturen AEV, Fleckenstein B, de Souza GA. Assessing the citrullinome in rheumatoid arthritis synovial fluid with and without enrichment of citrullinated peptides. J Proteome Res 2014; 13:2867-73. [PMID: 24724574 DOI: 10.1021/pr500030x] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein citrullination is a posttranslational modification that has attracted increased attention, especially for its involvement in rheumatoid arthritis (RA). Here, we assess the citrullinome in RA synovial fluid by direct LC-MS/MS analysis and by the use of an enrichment strategy based on citrulline specific biotinylation. RA synovial fluid was depleted for abundant proteins, and total and depleted fractions were analyzed. Frequency of citrullinated peptides and their degree of citrullination could be determined for four known RA autoantigens, as well as a novel in vivo autocitrullination site of peptidylarginine deiminase 4. From the analysis of total and depleted synovial fluid after enrichment we could estimate the numbers of citrullinated peptides to be approximately 3600 and 2100, respectively. However, identification of these biotinylated peptides by MS/MS turned out to be very difficult due to fragmentation of the biotin moiety. By direct MS analysis of the total and depleted synovial fluid without enrichment, 119 and 157 citrullinated peptides were identified, respectively. This indicates that direct analysis allows identification of only a fraction of the citrullinated proteins present in synovial fluid and that specific enrichment is still needed for a comprehensive in-depth elucidation of the citrullinome.
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Affiliation(s)
- Astrid E V Tutturen
- Centre for Immune Regulation, Department of Immunology, University of Oslo, Oslo University Hospital-Rikshospitalet , Oslo 0372, Norway
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16
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Bennike T, Birkelund S, Stensballe A, Andersen V. Biomarkers in inflammatory bowel diseases: Current status and proteomics identification strategies. World J Gastroenterol 2014; 20:3231-3244. [PMID: 24696607 PMCID: PMC3964395 DOI: 10.3748/wjg.v20.i12.3231] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/13/2014] [Accepted: 02/20/2014] [Indexed: 02/06/2023] Open
Abstract
Unambiguous diagnosis of the two main forms of inflammatory bowel diseases (IBD): Ulcerative colitis (UC) and Crohn’s disease (CD), represents a challenge in the early stages of the diseases. The diagnosis may be established several years after the debut of symptoms. Hence, protein biomarkers for early and accurate diagnostic could help clinicians improve treatment of the individual patients. Moreover, the biomarkers could aid physicians to predict disease courses and in this way, identify patients in need of intensive treatment. Patients with low risk of disease flares may avoid treatment with medications with the concomitant risk of adverse events. In addition, identification of disease and course specific biomarker profiles can be used to identify biological pathways involved in the disease development and treatment. Knowledge of disease mechanisms in general can lead to improved future development of preventive and treatment strategies. Thus, the clinical use of a panel of biomarkers represents a diagnostic and prognostic tool of potentially great value. The technological development in recent years within proteomic research (determination and quantification of the complete protein content) has made the discovery of novel biomarkers feasible. Several IBD-associated protein biomarkers are known, but none have been successfully implemented in daily use to distinguish CD and UC patients. The intestinal tissue remains an obvious place to search for novel biomarkers, which blood, urine or stool later can be screened for. When considering the protein complexity encountered in intestinal biopsy-samples and the recent development within the field of mass spectrometry driven quantitative proteomics, a more thorough and accurate biomarker discovery endeavor could today be performed than ever before. In this review, we report the current status of the proteomics IBD biomarkers and discuss various emerging proteomic strategies for identifying and characterizing novel biomarkers, as well as suggesting future targets for analysis.
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17
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Specific biotinylation and sensitive enrichment of citrullinated peptides. Anal Bioanal Chem 2013; 405:9321-31. [DOI: 10.1007/s00216-013-7376-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/11/2013] [Accepted: 09/13/2013] [Indexed: 12/18/2022]
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18
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Semba RD, Enghild JJ, Venkatraman V, Dyrlund TF, Van Eyk JE. The Human Eye Proteome Project: perspectives on an emerging proteome. Proteomics 2013; 13:2500-11. [PMID: 23749747 PMCID: PMC3978387 DOI: 10.1002/pmic.201300075] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/26/2013] [Accepted: 05/15/2013] [Indexed: 12/22/2022]
Abstract
There are an estimated 285 million people with visual impairment worldwide, of whom 39 million are blind. The pathogenesis of many eye diseases remains poorly understood. The human eye is currently an emerging proteome that may provide key insight into the biological pathways of disease. We review proteomic investigations of the human eye and present a catalogue of 4842 nonredundant proteins identified in human eye tissues and biofluids to date. We highlight the need to identify new biomarkers for eye diseases using proteomics. Recent advances in proteomics do now allow the identification of hundreds to thousands of proteins in tissues and fluids, characterization of various PTMs and simultaneous quantification of multiple proteins. To facilitate proteomic studies of the eye, the Human Eye Proteome Project (HEPP) was organized in September 2012. The HEPP is one of the most recent components of the Biology/Disease-driven Human Proteome Project (B/D-HPP) whose overarching goal is to support the broad application of state-of-the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. The large repertoire of investigative proteomic tools has great potential to transform vision science and enhance understanding of physiology and disease processes that affect sight.
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Affiliation(s)
- Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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19
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Fu Z, Wang M, Everett A, Lakatta E, Van Eyk J. Can proteomics yield insight into aging aorta? Proteomics Clin Appl 2013; 7:477-89. [PMID: 23788441 DOI: 10.1002/prca.201200138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 12/16/2022]
Abstract
The aging aorta exhibits structural and physiological changes that are reflected in the proteome of its component cells types. The advance in proteomic technologies has made it possible to analyze the quantity of proteins associated with the natural history of aortic aging. These alterations reflect the molecular and cellular mechanisms of aging and could provide an opportunity to predict vascular health. This paper focuses on whether discoveries stemming from the application of proteomic approaches of the intact aging aorta or vascular smooth muscle cells can provide useful insights. Although there have been limited studies to date, a number of interesting proteins have been identified that are closely associated with aging in the rat aorta. Such proteins, including milk fat globule-EGF factor 8, matrix metalloproteinase type-2, and vitronectin, could be used as indicators of vascular health, or even explored as therapeutic targets for aging-related vascular diseases.
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Affiliation(s)
- Zongming Fu
- Department of Pediatrics, The Johns Hopkins University, Baltimore, MD 21224, USA
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20
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Menni C, Kastenmüller G, Petersen AK, Bell JT, Psatha M, Tsai PC, Gieger C, Schulz H, Erte I, John S, Brosnan MJ, Wilson SG, Tsaprouni L, Lim EM, Stuckey B, Deloukas P, Mohney R, Suhre K, Spector TD, Valdes AM. Metabolomic markers reveal novel pathways of ageing and early development in human populations. Int J Epidemiol 2013; 42:1111-9. [PMID: 23838602 PMCID: PMC3781000 DOI: 10.1093/ije/dyt094] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Human ageing is a complex, multifactorial process and early developmental factors affect health outcomes in old age. METHODS Metabolomic profiling on fasting blood was carried out in 6055 individuals from the UK. Stepwise regression was performed to identify a panel of independent metabolites which could be used as a surrogate for age. We also investigated the association with birthweight overall and within identical discordant twins and with genome-wide methylation levels. RESULTS We identified a panel of 22 metabolites which combined are strongly correlated with age (R(2) = 59%) and with age-related clinical traits independently of age. One particular metabolite, C-glycosyl tryptophan (C-glyTrp), correlated strongly with age (beta = 0.03, SE = 0.001, P = 7.0 × 10(-157)) and lung function (FEV1 beta = -0.04, SE = 0.008, P = 1.8 × 10(-8) adjusted for age and confounders) and was replicated in an independent population (n = 887). C-glyTrp was also associated with bone mineral density (beta = -0.01, SE = 0.002, P = 1.9 × 10(-6)) and birthweight (beta = -0.06, SE = 0.01, P = 2.5 × 10(-9)). The difference in C-glyTrp levels explained 9.4% of the variance in the difference in birthweight between monozygotic twins. An epigenome-wide association study in 172 individuals identified three CpG-sites, associated with levels of C-glyTrp (P < 2 × 10(-6)). We replicated one CpG site in the promoter of the WDR85 gene in an independent sample of 350 individuals (beta = -0.20, SE = 0.04, P = 2.9 × 10(-8)). WDR85 is a regulator of translation elongation factor 2, essential for protein synthesis in eukaryotes. CONCLUSIONS Our data illustrate how metabolomic profiling linked with epigenetic studies can identify some key molecular mechanisms potentially determined in early development that produce long-term physiological changes influencing human health and ageing.
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Affiliation(s)
- Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK, Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany, Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany, Institute of Epidemiology I, Helmholtz Zentrum München, Neuherberg, Germany, Pfizer Research Laboratories, Groton, CT, USA, Worldwide R&D, Pfizer Inc., Cambridge, MA, USA, School of Medicine and Pharmacology, University of Western Australia, Crawley, WA, Australia, Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK, Metabolon Inc., 617 Davis Drive, Durham, NC 27713, USA; Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, State of Qatar and Academic Rheumatology, University of Nottingham, Nottingham City Hospital, Nottingham, UK
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21
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Ling S, Cline EN, Haug TS, Fox DA, Holoshitz J. Citrullinated calreticulin potentiates rheumatoid arthritis shared epitope signaling. ACTA ACUST UNITED AC 2013; 65:618-26. [PMID: 23233327 DOI: 10.1002/art.37814] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 11/27/2012] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Citrullinated proteins are immunogenic in rheumatoid arthritis (RA), particularly in patients who carry shared epitope (SE)-coding HLA-DRB1 alleles. The mechanism underlying this association is unknown. We have previously identified the SE as a ligand that interacts with cell surface calreticulin (CRT) and activates immune dysregulation. This study was undertaken to determine the effect of CRT citrullination on SE signaling. METHODS CRT-SE binding affinity was measured by surface plasmon resonance. The role of individual CRT arginine residues was determined by site-directed mutagenesis, and nitric oxide levels were measured using a fluorochrome-based assay. CRT citrullination in synovial tissue samples and cell cultures was determined by 2-dimensional gel electrophoresis, immunoblotting, and mass spectrometry techniques. RESULTS Synovial tissue and fibroblast-like synoviocytes from RA patients were found to express a higher abundance of citrullinated CRT than samples from osteoarthritis patients. Citrullinated CRT showed more robust interaction with the SE ligand, and transduced SE signaling at a 10,000-fold higher potency, compared to noncitrullinated CRT. Site-directed mutation analysis identified Arg(205), which is spatially adjacent to the SE binding site in the CRT P-domain, as a dominant inhibitor of SE-CRT interaction and signaling, while a more remote arginine residue, Arg(261), was found to enhance these SE functions. CONCLUSION Our findings indicate that citrullinated CRT is overabundant in the RA synovium and potentiates SE-activated signaling in vitro. These findings could introduce a new mechanistic model of gene-environment interaction in RA.
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Affiliation(s)
- Song Ling
- University of Michigan School of Medicine, Ann Arbor, MI 48109-5680, USA
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22
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Liddy KA, White MY, Cordwell SJ. Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics. Genome Med 2013; 5:20. [PMID: 23445784 PMCID: PMC3706772 DOI: 10.1186/gm424] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The more than 300 currently identified post-translational modifications (PTMs) provides great scope for subtle or dramatic alteration of protein structure and function. Furthermore, the rapid and transient nature of many PTMs allows efficient signal transmission in response to internal and environmental stimuli. PTMs are predominantly added by enzymes, and the enzymes responsible (such as kinases) are thus attractive targets for therapeutic interventions. Modifications can be grouped according to their stability or transience (reversible versus irreversible): irreversible types (such as irreversible redox modifications or protein deamidation) are often associated with aging or tissue injury, whereas transient modifications are associated with signal propagation and regulation. This is particularly important in the setting of heart disease, which comprises a diverse range of acute (such as ischemia/reperfusion), chronic (such as heart failure, dilated cardiomyopathy) and genetic (such as hypertrophic cardiomyopathy) disease states, all of which have been associated with protein PTM. Recently the interplay between diverse PTMs has been suggested to also influence cellular function, with cooperation or competition for sites of modification possible. Here we discuss the utility of proteomics for examining PTMs in the context of the molecular mechanisms of heart disease.
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Affiliation(s)
- Kiersten A Liddy
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia
| | - Melanie Y White
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia ; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006 Sydney, Australia
| | - Stuart J Cordwell
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia ; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006 Sydney, Australia
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De Ceuleneer M, Van Steendam K, Dhaenens M, Elewaut D, Deforce D. Quantification of Citrullination by Means of Skewed Isotope Distribution Pattern. J Proteome Res 2012; 11:5245-51. [DOI: 10.1021/pr3004453] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | | | - Maarten, Dhaenens
- Laboratory for Pharmaceutical
Biotechnology, Ghent University, Ghent,
Belgium
| | - Dirk Elewaut
- Department of Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical
Biotechnology, Ghent University, Ghent,
Belgium
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Abstract
Anti-citrullinated protein antibodies (ACPAs) of the IgG subtype have become a critical hallmark of HLA-associated rheumatoid arthritis (RA) and point to important contributions from the adaptive immune system. To dissect the contributing autoimmune reactions, investigators must not only identify the protein targets of ACPA but also define the precise peptides recognized by the immune system. Several possible approaches could be used to achieve this goal, and sensitive mass spectrometry of relevant tissue is a promising way forward in advancing our detailed understanding of autoimmune immune reactions involved in RA pathogenesis.
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Potential role of peptidylarginine deiminase enzymes and protein citrullination in cancer pathogenesis. Biochem Res Int 2012; 2012:895343. [PMID: 23019525 PMCID: PMC3457611 DOI: 10.1155/2012/895343] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/31/2012] [Accepted: 08/09/2012] [Indexed: 11/18/2022] Open
Abstract
The peptidylarginine deiminases (PADs) are a family of posttranslational modification enzymes that catalyze the conversion of positively charged protein-bound arginine and methylarginine residues to the uncharged, nonstandard amino acid citrulline. This enzymatic activity is referred to as citrullination or, alternatively, deimination. Citrullination can significantly affect biochemical pathways by altering the structure and function of target proteins. Five mammalian PAD family members (PADs 1–4 and 6) have been described and show tissue-specific distribution. Recent reviews on PADs have focused on their role in autoimmune diseases. Here, we will discuss the potential role of PADs in tumor progression and tumor-associated inflammation. In the context of cancer, increasing clinical evidence suggests that PAD4 (and possibly PAD2) has important roles in tumor progression. The link between PADs and cancer is strengthened by recent findings showing that treatment of cell lines and mice with PAD inhibitors significantly suppresses tumor growth and, interestingly, inflammatory symptoms. At the molecular level, transcription factors, coregulators, and histones are functional targets for citrullination by PADs, and citrullination of these targets can affect gene expression in multiple tumor cell lines. Next generation isozyme-specific PAD inhibitors may have therapeutic potential to regulate both the inflammatory tumor microenvironment and tumor cell growth.
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