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Guedes S, Perpétuo L, Veloso J, Lima T, Ferreira AF, Pires I, Savaiva F, Lourenço A, Moreira-Costa L, Leite-Moreira A, Barros A, Trindade F, Vitorino R. Comprehensive characterization of protein modifications using mass spectrometry and dry blood spots. Proteomics Clin Appl 2024; 18:e2300102. [PMID: 38169112 DOI: 10.1002/prca.202300102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/19/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
PURPOSE The main objective of this study is to characterize and analyze modified peptides in DBS samples. This includes deciphering their specific PTMs and understanding their potential impact on the population or disease cohort under study. EXPERIMENTAL DESIGN Using mass spectrometry-based proteomic approaches, we performed a comprehensive analysis of DBS samples. Our focus was on the identification and quantification of modified peptides. We also took advantage of recent advances in DBS mass spectrometry to ensure accurate detection and quantification. RESULTS A comprehensive analysis identified 972 modified peptides in DBS samples. Of these, a subset of 211 peptides was consistently present in all samples, highlighting their potential biological importance and relevance. This indicates a diverse spectrum of PTMs in the proteome of DBS samples. CONCLUSIONS AND CLINICAL RELEVANCE Integration of mass spectrometry and proteomics has revealed a broad spectrum of modified peptides in DBS samples and highlighted their importance in biological processes and disease progression. Accurate detection of these PTMs may be critical for risk stratification and disease management. This study improves the understanding of molecular mechanisms underlying biological processes and disease development, providing important insights for clinical applications.
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Affiliation(s)
- Sofia Guedes
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Luís Perpétuo
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Jacinta Veloso
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Tânia Lima
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Ana F Ferreira
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Inês Pires
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Francisca Savaiva
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - André Lourenço
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Liliana Moreira-Costa
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Adelino Leite-Moreira
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Antonio Barros
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Fábio Trindade
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Rui Vitorino
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
- Cardiovascular R&D Centre - UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
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Rebak AS, Hendriks IA, Nielsen ML. Characterizing citrullination by mass spectrometry-based proteomics. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220237. [PMID: 37778389 PMCID: PMC10542455 DOI: 10.1098/rstb.2022.0237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/25/2023] [Indexed: 10/03/2023] Open
Abstract
Citrullination is an important post-translational modification (PTM) of arginine, known to play a role in autoimmune disorders, innate immunity response and maintenance of stem cell potency. However, citrullination remains poorly characterized and not as comprehensively understood compared to other PTMs, such as phosphorylation and ubiquitylation. High-resolution mass spectrometry (MS)-based proteomics offers a valuable approach for studying citrullination in an unbiased manner, allowing confident identification of citrullination modification sites and distinction from deamidation events on asparagine and glutamine. MS efforts have already provided valuable insights into peptidyl arginine deaminase targeting along with site-specific information of citrullination in for example synovial fluids derived from rheumatoid arthritis patients. Still, there is unrealized potential for the wider citrullination field by applying MS-based mass spectrometry approaches for proteome-wide investigations. Here we will outline contemporary methods and current challenges for studying citrullination by MS, and discuss how the development of neoteric citrullination-specific proteomics approaches still may improve our understanding of citrullination networks. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- A. S. Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - I. A. Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - M. L. Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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3
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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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4
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Martín Monreal MT, Hansen BE, Iversen PF, Enevold C, Ødum N, Sellebjerg F, Højrup P, Rode von Essen M, Nielsen CH. Citrullination of myelin basic protein induces a Th17-cell response in healthy individuals and enhances the presentation of MBP85-99 in patients with multiple sclerosis. J Autoimmun 2023; 139:103092. [PMID: 37506490 DOI: 10.1016/j.jaut.2023.103092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The post-translational modification citrullination has been proposed to play a role in the pathogenesis of multiple sclerosis (MS). Myelin basic protein (MBP) is a candidate autoantigen which is citrullinated to a minor extent under physiological conditions and hypercitrullinated in MS. We examined immune cell responses elicited by hypercitrullinated MBP (citMBP) in cultures of mononuclear cells from 18 patients with MS and 42 healthy donors (HDs). The immunodominant peptide of MBP, MBP85-99, containing citrulline in position 99, outcompeted the binding of native MBP85-99 to HLA-DR15, which is strongly linked to MS. Moreover, using the monoclonal antibody MK16 as probe, we observed that B cells and monocytes from HLA-DR15+ patients with MS presented MBP85-99 more efficiently after challenge with citMBP than with native MBP. Both citMBP and native MBP induced proliferation of CD4+ T cells from patients with MS as well as TNF-α production by their B cells and CD4+ T cells, and citrullination of MBP tended to enhance TNF-α secretion by CD4+ T cells from HLA-DR15+ patients. Unlike native MBP, citMBP induced differentiation into Th17 cells in cultures from HDs, while neither form of MBP induced Th17-cell differentiation in cultures from patients with MS. These data suggest a role for citrullination in the breach of tolerance to MBP in healthy individuals and in maintenance of the autoimmune response to MBP in patients with MS.
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Affiliation(s)
- María Teresa Martín Monreal
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Pernille F Iversen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christian Enevold
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Ødum
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Finn Sellebjerg
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Marina Rode von Essen
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Section for Periodontology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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5
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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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6
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Christensen AO, Li G, Young CH, Snow B, Khan SA, DeVore SB, Edwards S, Bouma GJ, Navratil AM, Cherrington BD, Rothfuss HM. Peptidylarginine deiminase enzymes and citrullinated proteins in female reproductive physiology and associated diseases†. Biol Reprod 2022; 107:1395-1410. [PMID: 36087287 PMCID: PMC10248218 DOI: 10.1093/biolre/ioac173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 09/15/2023] Open
Abstract
Citrullination, the post-translational modification of arginine residues, is catalyzed by the four catalytically active peptidylarginine deiminase (PAD or PADI) isozymes and alters charge to affect target protein structure and function. PADs were initially characterized in rodent uteri and, since then, have been described in other female tissues including ovaries, breast, and the lactotrope and gonadotrope cells of the anterior pituitary gland. In these tissues and cells, estrogen robustly stimulates PAD expression resulting in changes in levels over the course of the female reproductive cycle. The best-characterized targets for PADs are arginine residues in histone tails, which, when citrullinated, alter chromatin structure and gene expression. Methodological advances have allowed for the identification of tissue-specific citrullinomes, which reveal that PADs citrullinate a wide range of enzymes and structural proteins to alter cell function. In contrast to their important physiological roles, PADs and citrullinated proteins are also involved in several female-specific diseases including autoimmune disorders and reproductive cancers. Herein, we review current knowledge regarding PAD expression and function and highlight the role of protein citrullination in both normal female reproductive tissues and associated diseases.
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Affiliation(s)
- Amanda O Christensen
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Guangyuan Li
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Coleman H Young
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Bryce Snow
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Stanley B DeVore
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Sydney Edwards
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gerrit J Bouma
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Amy M Navratil
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Brian D Cherrington
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Heather M Rothfuss
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
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7
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Mohammed AS, Uversky VN. Intrinsic Disorder as a Natural Preservative: High Levels of Intrinsic Disorder in Proteins Found in the 2600-Year-Old Human Brain. BIOLOGY 2022; 11:biology11121704. [PMID: 36552214 PMCID: PMC9775155 DOI: 10.3390/biology11121704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022]
Abstract
Proteomic analysis revealed the preservation of many proteins in the Heslington brain (which is at least 2600-year-old brain tissue uncovered within the skull excavated in 2008 from a pit in Heslington, Yorkshire, England). Five of these proteins-"main proteins": heavy, medium, and light neurofilament proteins (NFH, NFM, and NFL), glial fibrillary acidic protein (GFAP), and myelin basic (MBP) protein-are engaged in the formation of non-amyloid protein aggregates, such as intermediate filaments and myelin sheath. We used a wide spectrum of bioinformatics tools to evaluate the prevalence of functional disorder in several related sets of proteins, such as the main proteins and their 44 interactors, all other proteins identified in the Heslington brain, as well as the entire human proteome (20,317 manually curated proteins), and 10,611 brain proteins. These analyses revealed that all five main proteins, half of their interactors and almost one third of the Heslington brain proteins are expected to be mostly disordered. Furthermore, most of the remaining Heslington brain proteins are expected to contain sizable levels of disorder. This is contrary to the expected substantial (if not complete) elimination of the disordered proteins from the Heslington brain. Therefore, it seems that the intrinsic disorder of NFH, NFM, NFL, GFAP, and MBP, their interactors, and many other proteins might play a crucial role in preserving the Heslington brain by forming tightly folded brain protein aggregates, in which different parts are glued together via the disorder-to-order transitions.
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Affiliation(s)
- Aaron S. Mohammed
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
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Steckel A, Révész Á, Papp D, Uray K, Drahos L, Schlosser G. Stepwise Collision Energy-Resolved Tandem Mass Spectrometric Experiments for the Improved Identification of Citrullinated Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1176-1186. [PMID: 35621259 DOI: 10.1021/jasms.2c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The use of tandem mass spectrometry (MS/MS) is a fundamental prerequisite of reliable protein identification and quantification in mass-spectrometry-based proteomics. In bottom-up and middle-down proteomics, proteins are identified by the characteristic fragments of their constituting peptides. Post-translational modifications (PTMs) often further complicate proteome analyses. Citrullination is an increasingly studied PTM converting arginines to citrullines (Cit, X) and is implicated in several autoimmune and neurological diseases as well as different types of cancer. Confirmation of citrullination is known to be very challenging since it results in the same molecular mass change as Asn/Gln deamidation. In this study, we explore which MS/MS characteristics can be used for the reliable identification of citrullination. We synthesized several peptides incorporating Cit residues that model enzymatic cleavages of different proteins with verified or putative citrullination. Collision-induced dissociation was used to investigate the energy dependence of Byonic and Mascot scores and confirmed sequence coverage (CSC) along with the neutral loss of HNCO characteristic to citrulline side chains. We found that although the recommended values (19-45 V) for ramped collision energy settings cover the optimal Mascot, Byonic, or %CSC scores effectively, the diagnostic HNCO loss from precursors and fragments may reach their maximum intensities at lower and higher collision energies, respectively. Therefore, we suggest broadening the ramp range to ∼5-60 V to obtain more favorable identification rates for citrullinated peptides. We also found that Byonic was more successful in correctly identifying citrullinated peptides with deamidated residues than Mascot.
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Affiliation(s)
- Arnold Steckel
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, ELTE Eötvös Loránd University, Institute of Chemistry, Department of Analytical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Ágnes Révész
- Research Centre for Natural Sciences, MS Proteomics Research Group, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Dávid Papp
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, ELTE Eötvös Loránd University, Institute of Chemistry, Department of Analytical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Katalin Uray
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - László Drahos
- Research Centre for Natural Sciences, MS Proteomics Research Group, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, ELTE Eötvös Loránd University, Institute of Chemistry, Department of Analytical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
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Ganne A, Balasubramaniam M, Griffin WST, Shmookler Reis RJ, Ayyadevara S. Glial Fibrillary Acidic Protein: A Biomarker and Drug Target for Alzheimer’s Disease. Pharmaceutics 2022; 14:pharmaceutics14071354. [PMID: 35890250 PMCID: PMC9322874 DOI: 10.3390/pharmaceutics14071354] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament structural protein involved in cytoskeleton assembly and integrity, expressed in high abundance in activated glial cells. GFAP is neuroprotective, as knockout mice are hypersensitive to traumatic brain injury. GFAP in cerebrospinal fluid is a biomarker of Alzheimer’s disease (AD), dementia with Lewy bodies, and frontotemporal dementia (FTD). Here, we present novel evidence that GFAP is markedly overexpressed and differentially phosphorylated in AD hippocampus, especially in AD with the apolipoprotein E [ε4, ε4] genotype, relative to age-matched controls (AMCs). Kinases that phosphorylate GFAP are upregulated in AD relative to AMC. A knockdown of these kinases in SH-SY5Y-APPSw human neuroblastoma cells reduced amyloid accrual and lowered protein aggregation and associated behavioral traits in C. elegans models of polyglutamine aggregation (as observed in Huntington’s disease) and of Alzheimer’s-like amyloid formation. In silico screening of the ChemBridge structural library identified a small molecule, MSR1, with stable and specific binding to GFAP. Both MSR1 exposure and GF AP-specific RNAi knockdown reduce aggregation with remarkably high concordance of aggregate proteins depleted. These data imply that GFAP and its phosphorylation play key roles in neuropathic aggregate accrual and provide valuable new biomarkers, as well as novel therapeutic targets to alleviate, delay, or prevent AD.
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Affiliation(s)
- Akshatha Ganne
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - W. Sue T. Griffin
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
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10
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Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M. Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer’s Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions. Front Aging Neurosci 2022; 14:749991. [PMID: 35572130 PMCID: PMC9093608 DOI: 10.3389/fnagi.2022.749991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s Disease (AD) is a complex neurodegenerative disease that gravely affects patients and imposes an immense burden on caregivers. Apolipoprotein E4 (APOE4) has been identified as the most common genetic risk factor for AD, yet the molecular mechanisms connecting APOE4 to AD are not well understood. Past transcriptomic analyses in AD have revealed APOE genotype-specific transcriptomic differences; however, these differences have not been explored at a single-cell level. To elucidate more complex APOE genotype-specific disease-relevant changes masked by the bulk analysis, we leverage the first two single-nucleus RNA sequencing AD datasets from human brain samples, including nearly 55,000 cells from the prefrontal and entorhinal cortices. In each brain region, we performed a case versus control APOE genotype-stratified differential gene expression analysis and pathway network enrichment in astrocytes, microglia, neurons, oligodendrocytes, and oligodendrocyte progenitor cells. We observed more global transcriptomic changes in APOE4 positive AD cells and identified differences across APOE genotypes primarily in glial cell types. Our findings highlight the differential transcriptomic perturbations of APOE isoforms at a single-cell level in AD pathogenesis and have implications for precision medicine development in the diagnosis and treatment of AD.
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Affiliation(s)
- Stella A. Belonwu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Yaqiao Li
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Daniel G. Bunis
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
| | - Arjun Arkal Rao
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Caroline Warly Solsberg
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Alice L. Taubes
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Brian Grone
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Kelly A. Zalocusky
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Gabriela K. Fragiadakis
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Yadong Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Marina Sirota,
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11
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Chen Y, Weng L, Liu W, Deng C, Xuan J, Ma Y, Li C, Jiang J, Chen J, Ge S. Characterization of Monoclonal Antibodies Recognizing Citrulline-Modified Residues. Front Immunol 2022; 13:849779. [PMID: 35359951 PMCID: PMC8961739 DOI: 10.3389/fimmu.2022.849779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundCitrullination is a post-translational protein modification linked to the occurrence and development of a variety of diseases. The detection of citrullinated proteins is predominately based on antibody detection although currently available reagents demonstrate detection bias according to the environmental context of the citrullinated residues. This study aimed to develop improved antibody reagents capable of detecting citrullinated residues in proteins in an unbiased manner.MethodsBALB/c mice were sequentially immunized using citrulline conjugates with different carrier proteins, and specific monoclonal antibodies (mAbs) identified by primary screening using citrulline-conjugated proteins unrelated to the immunogen. Secondary screening was performed to identify mAbs whose reactivity could be specifically blocked by free citrulline, followed by identification and performance assessment.ResultsTwo mAbs, 22F1 and 30G2, specifically recognizing a single citrulline residue were screened from 22 mAbs reacting with citrulline conjugates. Compared with commercially available anti-citrulline antibodies (AB6464, AB100932 and MABN328), 22F1 and 30G2 demonstrated significantly higher reactivity as well as a broader detection spectrum against different citrullinated proteins. 22F1 and 30G2 also had higher specificity than commercial antibodies and overall better applicability to a range of different immunoassays.ConclusionTwo mAbs specifically recognizing a single citrulline residue were successfully produced, each possessing good specificity against different citrullinated proteins. The improved utility of these reagents is expected to make a strong contribution to protein citrullination-related research.
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Affiliation(s)
- Yaqiong Chen
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Lin Weng
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Wei Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
| | - Chenxi Deng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
| | - Jinxiu Xuan
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yuan Ma
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Cao Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
| | - Jinlu Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
| | - Juan Chen
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- *Correspondence: Juan Chen, ; Shengxiang Ge,
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen, China
- *Correspondence: Juan Chen, ; Shengxiang Ge,
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12
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van Asperen JV, Robe PA, Hol EM. GFAP Alternative Splicing and the Relevance for Disease – A Focus on Diffuse Gliomas. ASN Neuro 2022; 14:17590914221102065. [PMID: 35673702 PMCID: PMC9185002 DOI: 10.1177/17590914221102065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament protein that is
characteristic for astrocytes and neural stem cells, and their malignant analogues in
glioma. Since the discovery of the protein 50 years ago, multiple alternative splice
variants of the GFAP gene have been discovered, leading to different GFAP isoforms. In
this review, we will describe GFAP isoform expression from gene to protein to network,
taking the canonical isoforms GFAPα and the main alternative variant GFAPδ as the starting
point. We will discuss the relevance of studying GFAP and its isoforms in disease, with a
specific focus on diffuse gliomas.
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Affiliation(s)
- Jessy V. van Asperen
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Pierre A.J.T. Robe
- Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, University Utrecht, Utrecht, The Netherlands
| | - Elly M. Hol
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
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13
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Chatterjee O, Gopalakrishnan L, Mol P, Advani J, Nair B, Shankar SK, Mahadevan A, Prasad TSK. The Normal Human Adult Hypothalamus Proteomic Landscape: Rise of Neuroproteomics in Biological Psychiatry and Systems Biology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:693-710. [PMID: 34714154 DOI: 10.1089/omi.2021.0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The human hypothalamus is central to the regulation of neuroendocrine and neurovegetative systems, as well as modulation of chronobiology and behavioral aspects in human health and disease. Surprisingly, a deep proteomic analysis of the normal human hypothalamic proteome has been missing for such an important organ so far. In this study, we delineated the human hypothalamus proteome using a high-resolution mass spectrometry approach which resulted in the identification of 5349 proteins, while a multiple post-translational modification (PTM) search identified 191 additional proteins, which were missed in the first search. A proteogenomic analysis resulted in the discovery of multiple novel protein-coding regions as we identified proteins from noncoding regions (pseudogenes) and proteins translated from short open reading frames that can be missed using the traditional pipeline of prediction of protein-coding genes as a part of genome annotation. We also identified several PTMs of hypothalamic proteins that may be required for normal hypothalamic functions. Moreover, we observed an enrichment of proteins pertaining to autophagy and adult neurogenesis in the proteome data. We believe that the hypothalamic proteome reported herein would help to decipher the molecular basis for the diverse range of physiological functions attributed to it, as well as its role in neurological and psychiatric diseases. Extensive proteomic profiling of the hypothalamic nuclei would further elaborate on the role and functional characterization of several hypothalamus-specific proteins and pathways to inform future research and clinical discoveries in biological psychiatry, neurology, and system biology.
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Affiliation(s)
- Oishi Chatterjee
- Institute of Bioinformatics, Bangalore India.,Amrita School of Biotechnology, Amrita University, Kollam, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Lathika Gopalakrishnan
- Institute of Bioinformatics, Bangalore India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Praseeda Mol
- Institute of Bioinformatics, Bangalore India.,Amrita School of Biotechnology, Amrita University, Kollam, India
| | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita University, Kollam, India
| | - Susarla Krishna Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore, India
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14
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Maurais AJ, Salinger AJ, Tobin M, Shaffer SA, Weerapana E, Thompson PR. A Streamlined Data Analysis Pipeline for the Identification of Sites of Citrullination. Biochemistry 2021; 60:2902-2914. [PMID: 34491035 DOI: 10.1021/acs.biochem.1c00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Citrullination is an enzyme-catalyzed post-translational modification (PTM) that is essential for a host of biological processes, including gene regulation, programmed cell death, and organ development. While this PTM is required for normal cellular functions, aberrant citrullination is a hallmark of autoimmune disorders as well as cancer. Although aberrant citrullination is linked to human pathology, the exact role of citrullination in disease remains poorly characterized, in part because of the challenges associated with identifying the specific arginine residues that are citrullinated. Tandem mass spectrometry is the most precise method for uncovering sites of citrullination; however, due to the small mass shift (+0.984 Da) that results from citrullination, current database search algorithms commonly misannotate spectra, leading to a high number of false-positive assignments. To address this challenge, we developed an automated workflow to rigorously and rapidly mine proteomic data to unambiguously identify the sites of citrullination from complex peptide mixtures. The crux of this streamlined workflow is the ionFinder software program, which classifies citrullination sites with high confidence on the basis of the presence of diagnostic fragment ions. These diagnostic ions include the neutral loss of isocyanic acid, which is a dissociative event that is unique to citrulline residues. Using the ionFinder program, we have mapped the sites of autocitrullination on purified protein arginine deiminases (PAD1-4) and mapped the global citrullinome in a PAD2-overexpressing cell line. The ionFinder algorithm is a highly versatile, user-friendly, and open-source program that is agnostic to the type of instrument and mode of fragmentation that are used.
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Affiliation(s)
- Aaron J Maurais
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Ari J Salinger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States.,Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Micaela Tobin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 826, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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15
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Abstract
Fifty years have passed since the discovery of glial fibrillary acidic protein (GFAP) by Lawrence Eng and colleagues. Now recognized as a member of the intermediate filament family of proteins, it has become a subject for study in fields as diverse as structural biology, cell biology, gene expression, basic neuroscience, clinical genetics and gene therapy. This review covers each of these areas, presenting an overview of current understanding and controversies regarding GFAP with the goal of stimulating continued study of this fascinating protein.
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Affiliation(s)
- Albee Messing
- Waisman Center, University of Wisconsin-Madison.,Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Michael Brenner
- Department of Neurobiology, University of Alabama-Birmingham
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16
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Deolankar SC, Patil AH, Rex DAB, Subba P, Mahadevan A, Prasad TSK. Mapping Post-Translational Modifications in Brain Regions in Alzheimer's Disease Using Proteomics Data Mining. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:525-536. [PMID: 34255573 DOI: 10.1089/omi.2021.0054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is a leading cause of dementia and a neurodegenerative disease. Proteomics and post-translational modification (PTM) analyses offer new opportunities for a comprehensive understanding of pathophysiology of brain in AD. We report here multiple PTMs in patients with AD, harnessing publicly available proteomics data from nine brain regions and at three different Braak stages of disease progression. Specifically, we identified 7190 peptides with PTMs, corresponding to 2545 proteins from brain regions with intermediate tangles, and 6864 peptides with PTMs corresponding to 2465 proteins from brain regions with severe tangles. A total of 103 proteins with PTMs were expressed uniquely to intermediate tangles and severe tangles compared to no tangles. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis suggested the association of these proteins in AD progression through platelet activation. These modified proteins were also found to be enriched for the tricarboxylic acid (TCA) cycle, respiratory electron cycle, and detoxification of reactive oxygen species. The multi-PTM data reported here contribute to our understanding of the neurobiology of AD and highlight the prospects of omics systems science research in neurodegenerative diseases. The present study provides a region-wise classification for the proteins with PTMs along with their differential expression patterns, providing insights into the localization of these proteins upon modification. The catalog of multi-PTMs identified in the context of AD from different brain regions provides a unique platform for generating newer hypotheses in understanding the putative role of specific PTMs in AD pathogenesis.
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Affiliation(s)
- Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Arun H Patil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore, India
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17
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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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18
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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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19
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Fert-Bober J, Darrah E, Andrade F. Insights into the study and origin of the citrullinome in rheumatoid arthritis. Immunol Rev 2019; 294:133-147. [PMID: 31876028 DOI: 10.1111/imr.12834] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/08/2019] [Indexed: 12/11/2022]
Abstract
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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Affiliation(s)
- Justyna Fert-Bober
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Erika Darrah
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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20
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An Overview of the Intrinsic Role of Citrullination in Autoimmune Disorders. J Immunol Res 2019; 2019:7592851. [PMID: 31886309 PMCID: PMC6899306 DOI: 10.1155/2019/7592851] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/03/2019] [Accepted: 09/28/2019] [Indexed: 02/07/2023] Open
Abstract
A protein undergoes many types of posttranslation modification. Citrullination is one of these modifications, where an arginine amino acid is converted to a citrulline amino acid. This process depends on catalytic enzymes such as peptidylarginine deiminase enzymes (PADs). This modification leads to a charge shift, which affects the protein structure, protein-protein interactions, and hydrogen bond formation, and it may cause protein denaturation. The irreversible citrullination reaction is not limited to a specific protein, cell, or tissue. It can target a wide range of proteins in the cell membrane, cytoplasm, nucleus, and mitochondria. Citrullination is a normal reaction during cell death. Apoptosis is normally accompanied with a clearance process via scavenger cells. A defect in the clearance system either in terms of efficiency or capacity may occur due to massive cell death, which may result in the accumulation and leakage of PAD enzymes and the citrullinated peptide from the necrotized cell which could be recognized by the immune system, where the immunological tolerance will be avoided and the autoimmune disorders will be subsequently triggered. The induction of autoimmune responses, autoantibody production, and cytokines involved in the major autoimmune diseases will be discussed.
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21
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Fert-Bober J, Murray CI, Parker SJ, Van Eyk JE. Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. Circ Res 2019; 122:1221-1237. [PMID: 29700069 DOI: 10.1161/circresaha.118.310966] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is an exponential increase in biological complexity as initial gene transcripts are spliced, translated into amino acid sequence, and post-translationally modified. Each protein can exist as multiple chemical or sequence-specific proteoforms, and each has the potential to be a critical mediator of a physiological or pathophysiological signaling cascade. Here, we provide an overview of how different proteoforms come about in biological systems and how they are most commonly measured using mass spectrometry-based proteomics and bioinformatics. Our goal is to present this information at a level accessible to every scientist interested in mass spectrometry and its application to proteome profiling. We will specifically discuss recent data linking various protein post-translational modifications to cardiovascular disease and conclude with a discussion for enablement and democratization of proteomics across the cardiovascular and scientific community. The aim is to inform and inspire the readership to explore a larger breadth of proteoform, particularity post-translational modifications, related to their particular areas of expertise in cardiovascular physiology.
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Affiliation(s)
- Justyna Fert-Bober
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Christopher I Murray
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Sarah J Parker
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA.
| | - Jennifer E Van Eyk
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
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22
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Gallart-Palau X, Tan LM, Serra A, Gao Y, Ho HH, Richards AM, Kandiah N, Chen CP, Kalaria RN, Sze SK. Degenerative protein modifications in the aging vasculature and central nervous system: A problem shared is not always halved. Ageing Res Rev 2019; 53:100909. [PMID: 31116994 DOI: 10.1016/j.arr.2019.100909] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/16/2019] [Accepted: 05/16/2019] [Indexed: 02/08/2023]
Abstract
Aging influences the pathogenesis and progression of several major diseases affecting both the cardiovascular system (CVS) and central nervous system (CNS). Defining the common molecular features that underpin these disorders in these crucial body systems will likely lead to increased quality of life and improved 'health-span' in the global aging population. Degenerative protein modifications (DPMs) have been strongly implicated in the molecular pathogenesis of several age-related diseases affecting the CVS and CNS, including atherosclerosis, heart disease, dementia syndromes, and stroke. However, these isolated findings have yet to be integrated into a wider framework, which considers the possibility that, despite their distinct features, CVS and CNS disorders may in fact be closely related phenomena. In this work, we review the current literature describing molecular roles of the major age-associated DPMs thought to significantly impact on human health, including carbamylation, citrullination and deamidation. In particular, we focus on data indicating that specific DPMs are shared between multiple age-related diseases in both CVS and CNS settings. By contextualizing these data, we aim to assist future studies in defining the universal mechanisms that underpin both vascular and neurological manifestations of age-related protein degeneration.
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23
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Fert-Bober J, Venkatraman V, Hunter CL, Liu R, Crowgey EL, Pandey R, Holewinski RJ, Stotland A, Berman BP, Van Eyk JE. Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library. J Proteome Res 2019; 18:2270-2278. [PMID: 30990720 PMCID: PMC10363406 DOI: 10.1021/acs.jproteome.9b00118] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein citrullination (or deimination), an irreversible post-translational modification, has been implicated in several physiological and pathological processes, including gene expression regulation, apoptosis, rheumatoid arthritis, and Alzheimer's disease. Several research studies have been carried out on citrullination under many conditions. However, until now, challenges in sample preparation and data analysis have made it difficult to confidently identify a citrullinated protein and assign the citrullinated site. To overcome these limitations, we generated a mouse hyper-citrullinated spectral library and set up coordinates to confidently identify and validate citrullinated sites. Using this workflow, we detect a four-fold increase in citrullinated proteome coverage across six mouse organs compared with the current state-of-the art techniques. Our data reveal that the subcellular distribution of citrullinated proteins is tissue-type-dependent and that citrullinated targets are involved in fundamental physiological processes, including the metabolic process. These data represent the first report of a hyper-citrullinated library for the mouse and serve as a central resource for exploring the role of citrullination in this organism.
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Affiliation(s)
- Justyna Fert-Bober
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Vidya Venkatraman
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | | | - Ruining Liu
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Erin L. Crowgey
- Nemours Biomedical Research, Nemours - Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803, United States
| | - Rakhi Pandey
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Ronald J. Holewinski
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandr Stotland
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Benjamin P. Berman
- Bioinformatics and Computational Biology Research Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E. Van Eyk
- The Smidt Heart Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
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Tilvawala R, Thompson PR. Peptidyl arginine deiminases: detection and functional analysis of protein citrullination. Curr Opin Struct Biol 2019; 59:205-215. [PMID: 30833201 DOI: 10.1016/j.sbi.2019.01.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 11/29/2022]
Abstract
Citrullination is a post-translational modification of arginine that is catalyzed by the protein arginine deiminases (PADs). Abnormal citrullination is observed in many autoimmune diseases and cancers. Anti-citrullinated protein antibodies (ACPA) are hallmarks of RA and used as diagnostic markers for disease diagnosis. Even though citrullination is associated with many different pathologies, its role remains unclear due to the challenges associated with the detection of citrullinated proteins since the mass change is only 0.984 Da. Moreover, the functional effects of protein citrullination remain mostly unknown. Herein, we discuss a brief overview of PAD structure and function, recent advances in the detection of citrullinated proteins in complex biological systems and the functional consequences of protein citrullination.
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Affiliation(s)
- Ronak Tilvawala
- Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States
| | - Paul R Thompson
- Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States.
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25
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An Z, Zhai L, Ying W, Qian X, Gong F, Tan M, Fu Y. PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome. Mol Cell Proteomics 2019; 18:391-405. [PMID: 30420486 PMCID: PMC6356076 DOI: 10.1074/mcp.ra118.000812] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 11/02/2018] [Indexed: 12/27/2022] Open
Abstract
The open (mass tolerant) search of tandem mass spectra of peptides shows great potential in the comprehensive detection of post-translational modifications (PTMs) in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) detected in an open search. After mass-shift-grouped false discovery rate (FDR) control of peptide-spectrum matches (PSMs), PTMiner uses an empirical Bayesian method to localize modifications through iterative learning of the prior probabilities of each type of modification occurring on different amino acids. The performance of PTMiner was evaluated on three data sets, including simulated data, chemically synthesized peptide library data and modified-peptide spiked-in proteome data. The results showed that PTMiner can effectively control the PSM FDR and accurately localize the modification sites. At 1% real false localization rate (FLR), PTMiner localized 93%, 84 and 83% of the modification sites in the three data sets, respectively, far higher than two open search engines we used and an extended version of the Ascore localization algorithm. We then used PTMiner to analyze a draft map of human proteome containing 25 million spectra from 30 tissues, and confidently identified over 1.7 million modified PSMs at 1% FDR and 1% FLR, which provided a system-wide view of both known and unknown PTMs in the human proteome.
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Affiliation(s)
- Zhiwu An
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wantao Ying
- State key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing 102206, China, Beijing Institute of Lifeomics, Beijing 100850, China
| | - Xiaohong Qian
- State key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing 102206, China, Beijing Institute of Lifeomics, Beijing 100850, China
| | - Fuzhou Gong
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;.
| | - Yan Fu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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26
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A liquid chromatography tandem mass spectroscopy approach for quantification of protein methylation stoichiometry. Anal Biochem 2018; 545:72-77. [PMID: 29407179 DOI: 10.1016/j.ab.2018.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/19/2018] [Accepted: 01/20/2018] [Indexed: 01/01/2023]
Abstract
Post-translational modifications are biologically important and wide-spread modulators of protein function. Although methods for detecting the presence of specific modifications are becoming established, approaches for quantifying their mol modification/mol protein stoichiometry are less well developed. Here we introduce a ratiometric, label-free, targeted liquid chromatography tandem mass spectroscopy-based method for estimating Lys and Arg methylation stoichiometry on post-translationally modified proteins. Methylated Lys and Arg were detected with limits of quantification at low fmol and with linearity extending from 20 to 5000 fmol. This level of sensitivity allowed estimation of methylation stoichiometry from microgram quantities of various proteins, including those derived from either recombinant or tissue sources. The method also disaggregated total methylation stoichiometry into its elementary mono-, di-, and tri-methylated residue components. In addition to being compatible with kinetic experiments of protein methylation, the approach will be especially useful for characterizing methylation states of proteins isolated from cells and tissues.
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27
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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: 82] [Impact Index Per Article: 13.7] [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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Tanikawa C, Ueda K, Suzuki A, Iida A, Nakamura R, Atsuta N, Tohnai G, Sobue G, Saichi N, Momozawa Y, Kamatani Y, Kubo M, Yamamoto K, Nakamura Y, Matsuda K. Citrullination of RGG Motifs in FET Proteins by PAD4 Regulates Protein Aggregation and ALS Susceptibility. Cell Rep 2018; 22:1473-1483. [DOI: 10.1016/j.celrep.2018.01.031] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/18/2017] [Accepted: 01/10/2018] [Indexed: 02/08/2023] Open
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Sarg B, Faserl K, Lindner HH. Identification of Novel Site-Specific Alterations in the Modification Level of Myelin Basic Protein Isolated from Mouse Brain at Different Ages Using Capillary Electrophoresis-Mass Spectrometry. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/07/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Bettina Sarg
- Division of Clinical Biochemistry, Biocenter; Medical University of Innsbruck; Innsbruck Austria
| | - Klaus Faserl
- Division of Clinical Biochemistry, Biocenter; Medical University of Innsbruck; Innsbruck Austria
| | - Herbert H. Lindner
- Division of Clinical Biochemistry, Biocenter; Medical University of Innsbruck; Innsbruck Austria
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30
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Brain ureido degenerative protein modifications are associated with neuroinflammation and proteinopathy in Alzheimer's disease with cerebrovascular disease. J Neuroinflammation 2017; 14:175. [PMID: 28865468 PMCID: PMC5581431 DOI: 10.1186/s12974-017-0946-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/23/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Brain degenerative protein modifications (DPMs) are associated with the apparition and progression of dementia, and at the same time, Alzheimer's disease with cerebrovascular disease (AD + CVD) is the most prevalent form of dementia in the elder population. Thus, understanding the role(s) of brain DPMs in this dementia subtype may provide novel insight on the disease pathogenesis and may aid on the development of novel diagnostic and therapeutic tools. Two essential DPMs known to promote inflammation in several human diseases are the ureido DPMs (uDPMs) arginine citrullination and lysine carbamylation, although they have distinct enzymatic and non-enzymatic origins, respectively. Nevertheless, the implication of uDPMs in the neuropathology of dementia remains poorly understood. METHODS In this study, we use the state-of-the-art, ultracentrifugation-electrostatic repulsion hydrophilic interaction chromatography (UC-ERLIC)-coupled mass spectrometry technology to undertake a comparative characterization of uDPMs in the soluble and particulate postmortem brain fractions of subjects diagnosed with AD + CVD and age-matched controls. RESULTS An increase in the formation of uDPMs was observed in all the profiled AD + CVD brains. Citrulline-containing proteins were found more abundant in the soluble fraction of AD + CVD whereas homocitrulline-containing proteins were preferentially abundant in the particulate fraction of AD + CVD brains. Several dementia-specific citrulline residues were also identified in soluble proteins previously categorized as pro-immunogenic, which include the receptor P2X7, alpha-internexin, GFAP, CNP, MBP, and histones. Similarly, diverse dementia-specific homocitrulline residues were also observed in the particulate fractions of AD + CVD in proteins that have been vastly implicated in neuropathology. Intriguingly, we also found that the amino acids immediately flanking arginine residues may specifically influence the increase in protein citrullination. CONCLUSIONS Taken together, these results indicate that uDPMs widely contribute to the pathophysiology of AD + CVD by promoting neuroinflammation and proteinopathy. Furthermore, the obtained results could help to identify disease-associated proteins that can act as potential targets for therapeutic intervention or as novel biomarkers of specific neuropathology.
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31
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The Effects of Blast Exposure on Protein Deimination in the Brain. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017. [PMID: 28626499 PMCID: PMC5463117 DOI: 10.1155/2017/8398072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Oxidative stress and calcium excitotoxicity are hallmarks of traumatic brain injury (TBI). While these early disruptions may be corrected over a relatively short period of time, long-lasting consequences of TBI including impaired cognition and mood imbalances can persist for years, even in the absence of any evidence of overt injury based on neuroimaging. This investigation examined the possibility that disordered protein deimination occurs as a result of TBI and may thus contribute to the long-term pathologies of TBI. Protein deimination is a calcium-activated, posttranslational modification implicated in the autoimmune diseases rheumatoid arthritis and multiple sclerosis, where aberrant deimination creates antigenic epitopes that elicit an autoimmune attack. The present study utilized proteomic analyses to show that blast TBI alters the deimination status of proteins in the porcine cerebral cortex. The affected proteins represent a small subset of the entire brain proteome and include glial fibrillary acidic protein and vimentin, proteins reported to be involved in autoimmune-based pathologies. The data also indicate that blast injury is associated with an increase in immunoglobulins in the brain, possibly representing autoantibodies directed against novel protein epitopes. These findings indicate that aberrant protein deimination is a biomarker for blast TBI and may therefore underlie chronic neuropathologies of head injury.
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32
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Partial Immunoblotting of 2D-Gels: A Novel Method to Identify Post-Translationally Modified Proteins Exemplified for the Myelin Acetylome. Proteomes 2017; 5:proteomes5010003. [PMID: 28248254 PMCID: PMC5372224 DOI: 10.3390/proteomes5010003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/23/2016] [Accepted: 01/04/2017] [Indexed: 11/17/2022] Open
Abstract
Post-translational modifications (PTMs) play a key role in regulating protein function, yet their identification is technically demanding. Here, we present a straightforward workflow to systematically identify post-translationally modified proteins based on two-dimensional gel electrophoresis. Upon colloidal Coomassie staining the proteins are partially transferred, and the investigated PTMs are immunodetected. This strategy allows tracking back the immunopositive antigens to the corresponding spots on the original gel, from which they are excised and mass spectrometrically identified. Candidate proteins are validated on the same membrane by immunodetection using a second fluorescence channel. We exemplify the power of partial immunoblotting with the identification of lysine-acetylated proteins in myelin, the oligodendroglial membrane that insulates neuronal axons. The excellent consistency of the detected fluorescence signals at all levels allows the differential comparison of PTMs across multiple conditions. Beyond PTM screening, our multi-level workflow can be readily adapted to clinical applications such as identifying auto-immune antigens or host-pathogen interactions.
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33
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Multiple and Selective Reaction Monitoring Using Triple Quadrupole Mass Spectrometer: Preclinical Large Cohort Analysis. Methods Mol Biol 2016; 1410:249-64. [PMID: 26867749 DOI: 10.1007/978-1-4939-3524-6_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Multiple reaction monitoring (MRM), sometimes referred to as selective reaction monitoring (SRM), is a mass spectrometry method that can target selective peptides for the detection and quantitation of a protein. Compared to traditional ELISA, MRM assays have a number of advantages including ease in multiplexing several proteins in the same assay and independence from the necessity for high-quality, expensive, and at times unreliable antibodies. Furthermore, MRM assays can be developed to quantify multiple proteoforms of a single protein allowing the quantification of allelic expression of a particular sequence polymorphism, protein isoform, as well as determining site occupancy of posttranslational modification(s). In this chapter, we describe our workflow for target peptide selection, assay optimization, and acquisition multiplexing. Our workflow is presented using the example of constrained MRM assays developed for the serum protein ApoL1 in its various proteoforms to highlight the specific technical considerations necessary for the difficult task of quantifying peptide targets based on highly specific amino acid sequences by MRM.
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34
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Microbiomic and Posttranslational Modifications as Preludes to Autoimmune Diseases. Trends Mol Med 2016; 22:746-757. [DOI: 10.1016/j.molmed.2016.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/08/2023]
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36
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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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37
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Detection and identification of protein citrullination in complex biological systems. Curr Opin Chem Biol 2015; 30:1-6. [PMID: 26517730 DOI: 10.1016/j.cbpa.2015.10.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/11/2015] [Indexed: 11/21/2022]
Abstract
Protein citrullination is a post-translational modification of arginine that is catalyzed by the Protein Arginine Deiminase (PAD) family of enzymes. Aberrantly increased citrullination is associated with a host of inflammatory diseases and cancer and PAD inhibitors have shown remarkable efficacy in a range of diseases including rheumatoid arthritis, lupus, atherosclerosis, and ulcerative colitis. In rheumatoid arthritis, citrullinated proteins serve as key antigens for rheumatoid arthritis-associated autoantibodies. These data suggest that citrullinated proteins may serve more generally as biomarkers of specific disease states, however, the identification of citrullinated residues remains challenging due to the small 1Da mass change that occurs upon citrullination. Herein, we highlight the available techniques to identify citrullinated proteins/residues focusing on advanced MS techniques as well as chemical derivatization strategies that are currently being employed to identify citrullinated proteins as well as the specific residues modified within those proteins.
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38
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C-terminal neurogranin is increased in cerebrospinal fluid but unchanged in plasma in Alzheimer's disease. Alzheimers Dement 2015; 11:1461-1469. [PMID: 26092348 DOI: 10.1016/j.jalz.2015.05.012] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/27/2015] [Accepted: 05/09/2015] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Biomarkers monitoring synaptic degeneration/loss would be valuable for Alzheimer's disease (AD) diagnosis. Postsynaptic protein neurogranin may be a promising cerebrospinal fluid (CSF) biomarker but has not yet been evaluated as a plasma biomarker. METHODS Using an in-house designed prototype enzyme-linked immunosorbent assay (ELISA) targeting neurogranin C-terminally, we studied neurogranin in paired CSF/plasma samples of controls (n = 29) versus patients experiencing MCI, or dementia, due to AD (in total n = 59). RESULTS CSF neurogranin was increased in AD and positively correlated with CSF tau, whereas there was a negative relationship between CSF neurogranin (and tau) and CSF Aβ1-42/Aβ1-40. No differences were detected in plasma neurogranin between controls and AD. Also, there was no correlation between CSF and plasma neurogranin, excluding confounding effects of the latter. DISCUSSION This study strengthens the potential of neurogranin as an AD CSF biomarker, which now needs validation in larger studies. As tools, straightforward immunoassays can be used, as demonstrated by the described ELISA.
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39
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Yang Z, Wang KKW. Glial fibrillary acidic protein: from intermediate filament assembly and gliosis to neurobiomarker. Trends Neurosci 2015; 38:364-74. [PMID: 25975510 PMCID: PMC4559283 DOI: 10.1016/j.tins.2015.04.003] [Citation(s) in RCA: 515] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/03/2015] [Accepted: 04/07/2015] [Indexed: 12/20/2022]
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament (IF) III protein uniquely found in astrocytes in the central nervous system (CNS), non-myelinating Schwann cells in the peripheral nervous system (PNS), and enteric glial cells. GFAP mRNA expression is regulated by several nuclear-receptor hormones, growth factors, and lipopolysaccharides (LPSs). GFAP is also subject to numerous post-translational modifications (PTMs), while GFAP mutations result in protein deposits known as Rosenthal fibers in Alexander disease. GFAP gene activation and protein induction appear to play a critical role in astroglial cell activation (astrogliosis) following CNS injuries and neurodegeneration. Emerging evidence also suggests that, following traumatic brain and spinal cord injuries and stroke, GFAP and its breakdown products are rapidly released into biofluids, making them strong candidate biomarkers for such neurological disorders.
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Affiliation(s)
- Zhihui Yang
- Program for Neurotrauma, Neuroproteomics, and Biomarkers Research, Departments of Psychiatry and Neuroscience, McKnight Brain Institute, L4-100, University of Florida, 1149 South Newell Drive, Gainesville, FL 32611, USA
| | - Kevin K W Wang
- Program for Neurotrauma, Neuroproteomics, and Biomarkers Research, Departments of Psychiatry and Neuroscience, McKnight Brain Institute, L4-100, University of Florida, 1149 South Newell Drive, Gainesville, FL 32611, USA.
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40
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Yang J, Korley FK, Dai M, Everett AD. Serum neurogranin measurement as a biomarker of acute traumatic brain injury. Clin Biochem 2015; 48:843-8. [PMID: 26025774 DOI: 10.1016/j.clinbiochem.2015.05.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/15/2015] [Accepted: 05/16/2015] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Neurogranin (NRGN) is a small neuronal protein that plays an important role in synaptic signaling by regulating calmodulin (CaM) availability. In this study, we developed an ELISA to measure NRGN quantitatively in serum samples from a cohort of acute traumatic brain injury (TBI) patients and a non-TBI control cohort, and explored the potential value of NRGN as a circulating biomarker for TBI. DESIGN AND METHODS Recombinant His-NRGN protein was used to develop mouse monoclonal capture and rabbit polyclonal detection antibodies, and they were used to develop a sandwich ELISA. After validation, we used this ELISA to measure serum samples from a cohort of typical adult acute TBI patients (N=76 TBI cases) and non-TBI control patients (N=150 controls). RESULTS The NRGN ELISA lower limit of detection was 0.055ng/mL, lower limit of quantification was 0.2ng/mL, and interassay CVs were ≤10.7%. The average recovery was 99.9% (range from 97.2-102%). Serum NRGN concentrations in TBI cases were significantly higher than in controls (median values were 0.18ng/mL vs. 0.02ng/mL, p<0.0001), but did not discriminate TBI cases with intracranial hemorrhage (p=0.09). CONCLUSIONS We have developed a highly sensitive and reproducible ELISA for measuring circulating NRGN in blood samples. Serum NRGN concentrations in acute TBI patients were significantly higher than in controls, indicating that NRGN could have utility as a circulating biomarker for acute TBI. This report provides evidence to support larger and controlled TBI clinical studies for NRGN validation and prediction of outcomes.
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Affiliation(s)
- Jun Yang
- Department of Pediatrics, Division of Pediatric Cardiology, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Frederick K Korley
- Department of Emergency Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Min Dai
- Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Allen D Everett
- Department of Pediatrics, Division of Pediatric Cardiology, Johns Hopkins University, School of Medicine, Baltimore, MD, United States.
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Petzold A. Glial fibrillary acidic protein is a body fluid biomarker for glial pathology in human disease. Brain Res 2015; 1600:17-31. [DOI: 10.1016/j.brainres.2014.12.027] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 12/01/2014] [Indexed: 12/20/2022]
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Fert-Bober J, Sokolove J. Proteomics of citrullination in cardiovascular disease. Proteomics Clin Appl 2014; 8:522-33. [DOI: 10.1002/prca.201400013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/04/2014] [Accepted: 06/11/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Justyna Fert-Bober
- Johns Hopkins University; Baltimore MD USA
- Cedars Sinai Medical Center; Los Angeles CA USA
| | - Jeremy Sokolove
- VA Palo Alto Healthcare System and Stanford University; Palo Alto CA USA
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Localisation of citrullinated proteins in normal appearing white matter and lesions in the central nervous system in multiple sclerosis. J Neuroimmunol 2014; 273:85-95. [DOI: 10.1016/j.jneuroim.2014.05.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/29/2014] [Accepted: 05/15/2014] [Indexed: 01/07/2023]
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44
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The human peptidylarginine deiminases type 2 and type 4 have distinct substrate specificities. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:829-36. [DOI: 10.1016/j.bbapap.2014.02.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 12/21/2022]
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45
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Hensen SMM, Pruijn GJM. Methods for the detection of peptidylarginine deiminase (PAD) activity and protein citrullination. Mol Cell Proteomics 2014; 13:388-96. [PMID: 24298040 PMCID: PMC3916641 DOI: 10.1074/mcp.r113.033746] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/19/2013] [Indexed: 02/02/2023] Open
Abstract
The post-translational conversion of peptidylarginine to peptidylcitrulline, a process also known as citrullination, is catalyzed by the enzyme family of peptidylarginine deiminases (PADs) and has been demonstrated to be involved in many physiological processes, including the regulation of gene expression. In addition, citrullination has been shown to be associated with several diseases, such as cancer, multiple sclerosis, rheumatoid arthritis, and Alzheimer's disease. To get more insight into the role of PAD enzymes and citrullination in both health and disease, experimental strategies to study PAD activity and to characterize citrullinated proteins in complex biological samples are crucial. Here, we describe the chemical, proteomic and antibody-based procedures that are currently available and discuss their applicability for the analysis of complex samples. The methods that have been developed can be used to provide more insight in the substrate specificity of PAD enzymes. Because the evidence that PADs play a pathophysiological role in the diseases mentioned above is increasing, they become attractive targets for therapeutic interventions. More knowledge of PAD specificity and the availability of reliable, high-throughput assays for PAD activity will facilitate the development of highly specific PAD inhibitors.
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Affiliation(s)
- Sanne M. M. Hensen
- From the ‡Department of Biomolecular Chemistry, Institute for Molecules and Materials, Nijmegen Centre for Molecular Life Sciences and Netherlands Proteomics Centre, Radboud University Nijmegen, P.O. Box 9101, NL-6500 HB Nijmegen, The Netherlands
| | - Ger J. M. Pruijn
- From the ‡Department of Biomolecular Chemistry, Institute for Molecules and Materials, Nijmegen Centre for Molecular Life Sciences and Netherlands Proteomics Centre, Radboud University Nijmegen, P.O. Box 9101, NL-6500 HB Nijmegen, The Netherlands
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