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Rebak AS, Hendriks IA, Elsborg JD, Buch-Larsen SC, Nielsen CH, Terslev L, Kirsch R, Damgaard D, Doncheva NT, Lennartsson C, Rykær M, Jensen LJ, Christophorou MA, Nielsen ML. A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates. Nat Struct Mol Biol 2024; 31:977-995. [PMID: 38321148 PMCID: PMC11189309 DOI: 10.1038/s41594-024-01214-9] [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: 12/22/2022] [Accepted: 01/04/2024] [Indexed: 02/08/2024]
Abstract
Despite the importance of citrullination in physiology and disease, global identification of citrullinated proteins, and the precise targeted sites, has remained challenging. Here we employed quantitative-mass-spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites within the HL60 leukemia cell line following differentiation into neutrophil-like cells. We identified 14,056 citrullination sites within 4,008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. With this resource, we provide quantitative and site-specific information on thousands of PADI4 substrates, including signature histone marks and transcriptional regulators. Additionally, using peptide microarrays, we demonstrate the potential clinical relevance of certain identified sites, through distinct reactivities of antibodies contained in synovial fluid from anti-CCP-positive and anti-CCP-negative people with rheumatoid arthritis. Collectively, we describe the human citrullinome at a systems-wide level, provide a resource for understanding citrullination at the mechanistic level and link the identified targeted sites to rheumatoid arthritis.
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Affiliation(s)
- Alexandra S Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas D Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara C Buch-Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lene Terslev
- Copenhagen Center for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rebecca Kirsch
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dres Damgaard
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Nadezhda T Doncheva
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Lennartsson
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Rykær
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Bryant L, Sangree A, Clark K, Bhoj E. Histone 3.3-related chromatinopathy: missense variants throughout H3-3A and H3-3B cause a range of functional consequences across species. Hum Genet 2024; 143:497-510. [PMID: 36867246 DOI: 10.1007/s00439-023-02536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/20/2023] [Indexed: 03/04/2023]
Abstract
There has been considerable recent interest in the role that germline variants in histone genes play in Mendelian syndromes. Specifically, missense variants in H3-3A and H3-3B, which both encode Histone 3.3, were discovered to cause a novel neurodevelopmental disorder, Bryant-Li-Bhoj syndrome. Most of the causative variants are private and scattered throughout the protein, but all seem to have either a gain-of-function or dominant negative effect on protein function. This is highly unusual and not well understood. However, there is extensive literature about the effects of Histone 3.3 mutations in model organisms. Here, we collate the previous data to provide insight into the elusive pathogenesis of missense variants in Histone 3.3.
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Affiliation(s)
- Laura Bryant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Annabel Sangree
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelly Clark
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elizabeth Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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3
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Harada K, Carr SM, Shrestha A, La Thangue NB. Citrullination and the protein code: crosstalk between post-translational modifications in cancer. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220243. [PMID: 37778382 PMCID: PMC10542456 DOI: 10.1098/rstb.2022.0243] [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: 03/23/2023] [Accepted: 06/05/2023] [Indexed: 10/03/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins are central to epigenetic regulation and cellular signalling, playing an important role in the pathogenesis and progression of numerous diseases. Growing evidence indicates that protein arginine citrullination, catalysed by peptidylarginine deiminases (PADs), is involved in many aspects of molecular and cell biology and is emerging as a potential druggable target in multiple diseases including cancer. However, we are only just beginning to understand the molecular activities of PADs, and their underlying mechanistic details in vivo under both physiological and pathological conditions. Many questions still remain regarding the dynamic cellular functions of citrullination and its interplay with other types of PTMs. This review, therefore, discusses the known functions of PADs with a focus on cancer biology, highlighting the cross-talk between citrullination and other types of PTMs, and how this interplay regulates downstream biological events. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Koyo Harada
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Simon M. Carr
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Amit Shrestha
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Nicholas B. La Thangue
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
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Barasa L, Thompson PR. Protein citrullination: inhibition, identification and insertion. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220240. [PMID: 37778377 PMCID: PMC10542963 DOI: 10.1098/rstb.2022.0240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/26/2023] [Indexed: 10/03/2023] Open
Abstract
Protein citrullination is a post-translational modification (PTM) that is catalysed by the protein arginine deiminase (PAD) family of enzymes. This PTM involves the transformation of an arginine residue into citrulline. Protein citrullination is associated with several physiological processes, including the epigenetic regulation of gene expression, neutrophil extracellular trap formation and DNA damage-induced apoptosis. Aberrant protein citrullination is relevant to several autoimmune and neurodegenerative diseases and certain forms of cancer. PAD inhibitors have shown remarkable efficacy in a range of diseases including rheumatoid arthritis (RA), lupus, atherosclerosis and ulcerative colitis. In RA, anti-citrullinated protein antibodies can be detected prior to disease onset and are thus a valuable diagnostic tool for RA. Notably, citrullinated proteins may serve more generally as biomarkers of specific disease states; however, the identification of citrullinated protein residues remains challenging owing to the small 1 Da mass change that occurs upon citrullination. Herein, we highlight the progress made so far in the development of pan-PAD and isozyme selective inhibitors as well as the identification of citrullinated proteins and the site-specific incorporation of citrulline into proteins. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Leonard Barasa
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Paul R. Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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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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Jennings CE, Zoss CJ, Morrison EA. Arginine anchor points govern H3 tail dynamics. Front Mol Biosci 2023; 10:1150400. [PMID: 37261328 PMCID: PMC10228543 DOI: 10.3389/fmolb.2023.1150400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/11/2023] [Indexed: 06/02/2023] Open
Abstract
Chromatin is dynamically reorganized spatially and temporally, and the post-translational modification of histones is a key component of this regulation. The basic subunit of chromatin is the nucleosome core particle, consisting of two copies each of the histones H2A, H2B, H3, and H4 around which ∼147 base pairs of DNA wrap. The intrinsically disordered histone termini, or tails, protrude from the core and are heavily post-translationally modified. Previous studies have shown that the histone tails exist in dynamic ensembles of DNA-bound states within the nucleosome. Histone tail interactions with DNA are involved in nucleosome conformation and chromatin organization. Charge-modulating histone post-translational modifications (PTMs) are poised to perturb the dynamic interactions between histone tails and DNA. Arginine side chains form favorable interactions with DNA and are sites of charge-modulating PTMs such as citrullination. Our current focus is on the H3 tail, the longest histone tail. Four arginine residues are relatively evenly spaced along the H3 tail sequence, suggesting multivalent interactions with DNA poised for regulation by PTMs. In this study, we use NMR nuclear spin relaxation experiments to investigate the contribution of arginine residues to H3 tail dynamics within the nucleosome core particle. By neutralizing arginine via mutation to glutamine, we begin to work towards a comprehensive understanding of the contribution of individual residues to H3 tail dynamics. We find that neutralization of arginine residues results in increased regional mobility of the H3 tails, with implications for understanding the direct effects of arginine citrullination. Altogether, these studies support a role for dynamics within the histone language and emphasize the importance of charge-modulating histone PTMs in regulating chromatin dynamics, starting at the level of the basic subunit of chromatin.
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Affiliation(s)
- Christine E. Jennings
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Casey J. Zoss
- Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Emma A. Morrison
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
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7
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Zhu C, Liu C, Chai Z. Role of the PADI family in inflammatory autoimmune diseases and cancers: A systematic review. Front Immunol 2023; 14:1115794. [PMID: 37020554 PMCID: PMC10067674 DOI: 10.3389/fimmu.2023.1115794] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/08/2023] [Indexed: 04/07/2023] Open
Abstract
The peptidyl arginine deiminase (PADI) family is a calcium ion-dependent group of isozymes with sequence similarity that catalyze the citrullination of proteins. Histones can serve as the target substrate of PADI family isozymes, and therefore, the PADI family is involved in NETosis and the secretion of inflammatory cytokines. Thus, the PADI family is associated with the development of inflammatory autoimmune diseases and cancer, reproductive development, and other related diseases. In this review, we systematically discuss the role of the PADI family in the pathogenesis of various diseases based on studies from the past decade to provide a reference for future research.
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Affiliation(s)
- Changhui Zhu
- Department of Plastic Surgery, Shandong Provincial Qianfoshan Hospital, School of Basic Medical Sciences, Weifang Medical University, Weifang, Shandong, China
- Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Chunyan Liu
- Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- *Correspondence: Chunyan Liu, ; Zhengbin Chai,
| | - Zhengbin Chai
- Department of Clinical Laboratory Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
- *Correspondence: Chunyan Liu, ; Zhengbin Chai,
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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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Zhu D, Lu Y, Wang Y, Wang Y. PAD4 and Its Inhibitors in Cancer Progression and Prognosis. Pharmaceutics 2022; 14:2414. [PMID: 36365233 PMCID: PMC9699117 DOI: 10.3390/pharmaceutics14112414] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 07/24/2023] Open
Abstract
The systemic spread of malignancies and the risk of cancer-associated thrombosis are major clinical challenges in cancer therapy worldwide. As an important post-translational modification enzyme, peptidyl arginine deiminase 4 (PAD4) could mediate the citrullination of protein in different components (including nucleus and cytoplasm, etc.) of a variety of cells (tumor cells, neutrophils, macrophages, etc.), thus participating in gene regulation, neutrophil extracellular trap (NET) and macrophage extracellular trap (MET). Thereby, PAD4 plays an important role in enhancing the growth of primary tumors and facilitating the distant metastasis of cancer cells. In addition, it is related to the formation of cancer-associated thrombosis. Therefore, the development of PAD4-specific inhibitors may be a promising strategy for treating cancer, and it may improve patient prognosis. In this review, we describe PAD4 involvement in gene regulation, protein citrullination, and NET formation. We also discuss its potential role in cancer and cancer-associated thrombosis, and we summarize the development and application of PAD4 inhibitors.
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Affiliation(s)
- Di Zhu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
| | - Yu Lu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
| | - Yanming Wang
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yuji Wang
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
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Sarnik J, Makowska J. Citrullination good or bad guy? Immunobiology 2022; 227:152233. [DOI: 10.1016/j.imbio.2022.152233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/11/2022] [Accepted: 05/21/2022] [Indexed: 11/16/2022]
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Li Z, Wang B, Yu Q, Shi Y, Li L. 12-Plex DiLeu Isobaric Labeling Enabled High-Throughput Investigation of Citrullination Alterations in the DNA Damage Response. Anal Chem 2022; 94:3074-3081. [PMID: 35129972 PMCID: PMC9055876 DOI: 10.1021/acs.analchem.1c04073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein citrullination is a key post-translational modification (PTM) that leads to the loss of positive charge on arginine and consequent protein structural and functional changes. Though it has been indicated to play critical roles in various physiological and pathological processes, effective analytical tools are largely limited due to a few challenges such as the small mass shift induced by this PTM and its low-abundance nature. Recently, we developed a biotin thiol tag, which enabled large-scale profiling of protein citrullination from complex biological samples via mass spectrometry. However, a high-throughput quantitative approach is still in great need to further improve the understanding of this PTM. In this study, we report an efficient pipeline using our custom-developed N,N-dimethyl leucine isobaric tags to achieve a multiplexed quantitative analysis of citrullination from up to 12 samples for the first time. We then apply this strategy to investigating citrullination alterations in response to DNA damage stress using human cell lines. We unveil important biological functions regulated by protein citrullination and observe hypercitrullination on RNA-binding proteins and DNA repair proteins, respectively. Our results reveal the involvement of citrullination in DNA damage pathways and may provide new insights into DNA-damage-related disease pathogenesis.
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Affiliation(s)
- 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
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yatao Shi
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States,School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States,Corresponding Author: . Phone: +1-608-265-8491. Fax: +1-608-262-5345
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Choudhury RH, Symonds P, Paston SJ, Daniels I, Cook KW, Gijon M, Metheringham RL, Brentville VA, Durrant LG. PAD-2-mediated citrullination of nucleophosmin provides an effective target for tumor immunotherapy. J Immunother Cancer 2022; 10:jitc-2021-003526. [PMID: 35140112 PMCID: PMC8830261 DOI: 10.1136/jitc-2021-003526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The enzymatic conversion of arginine to citrulline is involved in gene and protein regulation and in alerting the immune system to stressed cells, including tumor cells. Nucleophosmin (NPM) is a nuclear protein that plays key roles in cellular metabolism including ribosome biogenesis, mRNA processing and chromatin remodeling and is regulated by citrullination. In this study, we explored if the same citrullinated arginines within NPM are involved in gene regulation and immune activation. METHODS HLA-DP4 and HLA-DR4 transgenic mice were immunized with 22 citrullinated NPM overlapping peptides and immune responses to the peptides were assessed by ex vivo ELISpot assays. Antitumor immunity of NPM targeted vaccination was assessed by challenging transgenic mice with B16F1 HHDII/iDP4, B16F1 HHDII/PAD2KOcDP4, B16F1 HHDII and Lewis lung carcinoma cells/cDP4 cells subcutaneously. Peripheral blood mononuclear cells isolated from healthy donors were stimulated with NPM266-285cit peptides with/without CD45RO+memory cell depletion to assess if the responses in human were naïve or memory. RESULTS In contrast to NPM regulation, which is mediated by peptidylarginine deiminase (PAD4) citrullination of arginine at position 197, only citrullinated NPM266-285 peptide induced a citrulline-specific CD4 T cell response in transgenic mice models expressing human HLA-DP4 or HLA-DR4. Vaccinations with the NPM266-285cit peptide stimulated antitumor responses that resulted in dramatic tumor therapy, greatly improved survival, and protected against rechallenge without further vaccination. The antitumor response was lost if MHCII expression on the tumor cells was knocked out demonstrating direct presentation of the NPM266-285cit epitope in tumors. This antitumor response was lost in B16 tumors lacking PAD2 enzyme indicating NPM266cit is citrullinated by PAD2 in this model. Assessment of the T cell repertoire in healthy individuals and patients with lung cancer also showed CD4 T cells that respond to NPM266-285cit. The proliferative CD4 responses displayed a Th1 profile as they were accompanied with increased IFNγ and granzyme B expression. Depletion of CD45RO+ memory cells prior to stimulation suggested that responses originated from a naïve population in healthy donors. CONCLUSION This study indicates PAD2 can citrullinate the nuclear antigen NPM at position 277 which can be targeted by CD4 T cells for antitumor therapy. This is distinct from PAD4 citrullination of arginine 197 within NPM which results in its transport from the nucleoli to the nucleoplasm.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lindy G Durrant
- Scancell Ltd, Nottingham, UK .,University of Nottingham Biodiscovery Institute, Scancell Ltd, Nottingham, UK
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13
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Pan B, Li Y, Liu Y, Wang W, Huang G, Ouyang Y. Circulating CitH3 Is a Reliable Diagnostic and Prognostic Biomarker of Septic Patients in Acute Pancreatitis. Front Immunol 2021; 12:766391. [PMID: 34868018 PMCID: PMC8637845 DOI: 10.3389/fimmu.2021.766391] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/25/2021] [Indexed: 01/02/2023] Open
Abstract
Purpose Acute pancreatitis (AP) is an inflammatory disease. AP starts with sterile inflammation and is often complicated with critical local or systemic infection or sepsis in severe cases. Septic AP activates peptidyl arginine deiminase (PAD) and citrullinates histone H3 (CitH3), leading to neutrophil extracellular trap (NET) formation. Investigating the role of NETs and underlying mechanisms in septic AP may facilitate developing diagnostic and therapeutic approaches. In this study, we sought to identify the expression of CitH3 in septic AP patients and to analyze the correlation of CitH3 concentration with NET components as well as clinical outcomes. Methods Seventy AP patients with or without sepsis (40 septic cases, 30 nonseptic cases) and 30 healthy volunteers were recruited in this study. Concentration of NET components (CitH3 and double-strain DNA) and key enzymes (PAD2/4) were measured. Clinical and laboratory characteristics of patients were recorded and analyzed. Results Levels of CitH3 were elevated significantly in septic AP patients compared with those in nonseptic AP and healthy volunteers. The area under the curve (AUC, 95% confidence interval) for diagnosing septic AP was 0.93 (0.86–1.003), and the cutoff was 43.05 pg/ml. Among septic AP cases (n = 40), the concentration of CitH3 was significantly increased in those who did not survive or were admitted to the intensive care unit, when compared with that in those who survived or did not require intensive care unit. Association analysis revealed that CitH3 concentration was positively correlated with PAD2, PAD4, dsDNA concentration, and Sequential Organ Failure Assessment scores. Conclusion CitH3 concentration increased in septic AP patients and was closely correlated with disease severity and clinical outcomes. CitH3 may potentially be a diagnostic and prognostic biomarker of septic AP.
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Affiliation(s)
- Baihong Pan
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yaozhen Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yu Liu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Gengwen Huang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yang Ouyang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
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14
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Sun B, Tomita B, Salinger A, Tilvawala RR, Li L, Hakami H, Liu T, Tsoyi K, Rosas IO, Reinhardt DP, Thompson PR, Ho IC. PAD2-mediated citrullination of Fibulin-5 promotes elastogenesis. Matrix Biol 2021; 102:70-84. [PMID: 34274450 DOI: 10.1016/j.matbio.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/14/2022]
Abstract
The formation of elastic fibers is active only in the perinatal period. How elastogenesis is developmentally regulated is not fully understood. Citrullination is a unique form of post-translational modification catalyzed by peptidylarginine deiminases (PADs), including PAD1-4. Its physiological role is largely unknown. By using an unbiased proteomic approach of lung tissues, we discovered that FBLN5 and LTBP4, two key elastogenic proteins, were temporally modified in mouse and human lungs. We further demonstrated that PAD2 citrullinated FBLN5 preferentially in young lungs compared to adult lungs. Genetic ablation of PAD2 resulted in attenuated elastogenesis in vitro and age-dependent emphysema in vivo. Mechanistically, citrullination protected FBLN5 from proteolysis and subsequent inactivation of its elastogenic activity. Furthermore, citrullinated but not native FBLN5 partially rescued in vitro elastogenesis in the absence of PAD activity. Our data uncover a novel function of citrullination, namely promoting elastogenesis, and provide additional insights to how elastogenesis is regulated.
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Affiliation(s)
- Bo Sun
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Beverly Tomita
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Ari Salinger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ronak R Tilvawala
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ling Li
- Department of Anatomy and Cell Biology and Faculty of Dentistry, McGill University, Montreal, QC H3A 0C7, Canada
| | - Hana Hakami
- Department of Anatomy and Cell Biology and Faculty of Dentistry, McGill University, Montreal, QC H3A 0C7, Canada
| | - Tao Liu
- Harvard Medical School, Boston, MA 02115, USA; Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Konstantin Tsoyi
- Pulmonary, Critical Care and Sleep Medicine Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan O Rosas
- Pulmonary, Critical Care and Sleep Medicine Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dieter P Reinhardt
- Department of Anatomy and Cell Biology and Faculty of Dentistry, McGill University, Montreal, QC H3A 0C7, Canada
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - I-Cheng Ho
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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15
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Zhu D, Zhang Y, Wang S. Histone citrullination: a new target for tumors. Mol Cancer 2021; 20:90. [PMID: 34116679 PMCID: PMC8192683 DOI: 10.1186/s12943-021-01373-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/13/2021] [Indexed: 01/08/2023] Open
Abstract
As the main protein components of chromatin, histones play central roles in gene regulation as spools of winding DNA. Histones are subject to various modifications, including phosphorylation, acetylation, glycosylation, methylation, ubiquitination and citrullination, which affect gene transcription. Histone citrullination, a posttranscriptional modification catalyzed by peptidyl arginine deiminase (PAD) enzymes, is involved in human carcinogenesis. In this study, we highlighted the functions of histone citrullination in physiological regulation and tumors. Additionally, because histone citrullination involves forming neutrophil extracellular traps (NETs), the relationship between NETs and tumors was illustrated. Finally, the clinical application of histone citrullination and PAD inhibitors was discussed.
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Affiliation(s)
- Dongwei Zhu
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yue Zhang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China.
| | - Shengjun Wang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China. .,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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16
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Site-specific incorporation of citrulline into proteins in mammalian cells. Nat Commun 2021; 12:45. [PMID: 33398026 PMCID: PMC7782748 DOI: 10.1038/s41467-020-20279-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/20/2020] [Indexed: 12/02/2022] Open
Abstract
Citrullination is a post-translational modification (PTM) of arginine that is crucial for several physiological processes, including gene regulation and neutrophil extracellular trap formation. Despite recent advances, studies of protein citrullination remain challenging due to the difficulty of accessing proteins homogeneously citrullinated at a specific site. Herein, we report a technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits an engineered E. coli-derived leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently, SM60 is readily converted to Cit with light in vitro and in living cells. To demonstrate the utility of the method, we biochemically characterize the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and show that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme. This technology possesses the potential to decipher the biology of citrullination. Citrullination of arginine is crucial for several physiological processes. Here the authors report the site-specific incorporation of citrulline into proteins in mammalian cells using an engineered tRNA synthetase/tRNA pair and a photocaged-citrulline.
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17
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Garciafigueroa Y, Phillips BE, Engman C, Trucco M, Giannoukakis N. Neutrophil-Associated Inflammatory Changes in the Pre-Diabetic Pancreas of Early-Age NOD Mice. Front Endocrinol (Lausanne) 2021; 12:565981. [PMID: 33776903 PMCID: PMC7988208 DOI: 10.3389/fendo.2021.565981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 02/01/2021] [Indexed: 12/23/2022] Open
Abstract
A growing body of evidence indicates that neutrophils are the first major leukocyte population accumulating inside the pancreas even before the onset of a lymphocytic-driven impairment of functional beta cells in type 1 diabetes mellitus (T1D). In humans, pancreata from T1D deceased donors exhibit significant neutrophil accumulation. We present a time course of previously unknown inflammatory changes that accompany neutrophil and neutrophil elastase accumulation in the pancreas of the non-obese diabetic (NOD) mouse strain as early as 2 weeks of age. We confirm earlier findings in NOD mice that neutrophils accumulate as early as 2 weeks of age. We also observe a concurrent increase in the expression of neutrophil elastase in this time period. We also detect components of neutrophil extracellular traps (NET) mainly in the exocrine tissue of the pancreas during this time as well as markers of vascular pathology as early as 2 weeks of age. Age- and sex-matched C57BL/6 mice do not exhibit these features inside the pancreas. When we treated NOD mice with inhibitors of myeloperoxidase and neutrophil elastase, two key effectors of activated neutrophil activity, alone or in combination, we were unable to prevent the progression to hyperglycemia in any manner different from untreated control mice. Our data confirm and add to the body of evidence demonstrating neutrophil accumulation inside the pancreas of mice genetically susceptible to T1D and also offer novel insights into additional pathologic mechanisms involving the pancreatic vasculature that have, until now, not been discovered inside the pancreata of these mice. However, inhibition of key neutrophil enzymes expressed in activated neutrophils could not prevent diabetes. These findings add to the body of data supporting a role for neutrophils in the establishment of early pathology inside the pancreas, independently of, and earlier from the time at onset of lymphocytic infiltration. However, they also suggest that inhibition of neutrophils alone, acting via myeloperoxidase and neutrophil elastase only, in the absence of other other effector cells, is insufficient to alter the natural course of autoimmune diabetes, at least in the NOD model of the disease.
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Affiliation(s)
- Yesica Garciafigueroa
- Institute of Cellular Therapeutics, Allegheny Health Network, Pittsburgh, PA, United States
| | - Brett E. Phillips
- Institute of Cellular Therapeutics, Allegheny Health Network, Pittsburgh, PA, United States
| | - Carl Engman
- Institute of Cellular Therapeutics, Allegheny Health Network, Pittsburgh, PA, United States
| | - Massimo Trucco
- Institute of Cellular Therapeutics, Allegheny Health Network, Pittsburgh, PA, United States
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Nick Giannoukakis
- Institute of Cellular Therapeutics, Allegheny Health Network, Pittsburgh, PA, United States
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
- *Correspondence: Nick Giannoukakis,
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18
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Tian Y, Qu S, Alam HB, Williams AM, Wu Z, Deng Q, Pan B, Zhou J, Liu B, Duan X, Ma J, Mondal S, Thompson PR, Stringer KA, Standiford TJ, Li Y. Peptidylarginine deiminase 2 has potential as both a biomarker and therapeutic target of sepsis. JCI Insight 2020; 5:138873. [PMID: 33055424 PMCID: PMC7605547 DOI: 10.1172/jci.insight.138873] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
Peptidylarginine deiminases (PADs) are a family of calcium-dependent enzymes that are involved in a variety of human disorders, including cancer and autoimmune diseases. Although targeting PAD4 has shown no benefit in sepsis, the role of PAD2 remains unknown. Here, we report that PAD2 is engaged in sepsis and sepsis-induced acute lung injury in both human patients and mice. Pad2–/– or selective inhibition of PAD2 by a small molecule inhibitor increased survival and improved overall outcomes in mouse models of sepsis. Pad2 deficiency decreased neutrophil extracellular trap (NET) formation. Importantly, Pad2 deficiency inhibited Caspase-11–dependent pyroptosis in vivo and in vitro. Suppression of PAD2 expression reduced inflammation and increased macrophage bactericidal activity. In contrast to Pad2–/–, Pad4 deficiency enhanced activation of Caspase-11–dependent pyroptosis in BM-derived macrophages and displayed no survival improvement in a mouse sepsis model. Collectively, our findings highlight the potential of PAD2 as an indicative marker and therapeutic target for sepsis. Peptidylarginine deiminases 2 (PAD2) regulates neutrophil extracellular trap (NET) formation in sepsis and sepsis-induced acute lung injury.
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Affiliation(s)
- Yuzi Tian
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Shibin Qu
- Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA.,Department of Hepatobiliary Surgery, Xijing Hospital, Xian, Shanxi, China
| | - Hasan B Alam
- Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Aaron M Williams
- Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Zhenyu Wu
- Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA.,Department of Infectious Disease, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiufang Deng
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Baihong Pan
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Jing Zhou
- Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA.,Trauma Center, Department of Orthopedic and Traumatology, Peking University People's Hospital, Beijing, China
| | - Baoling Liu
- Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Xiuzhen Duan
- Department of Pathology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Jianjie Ma
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Santanu Mondal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kathleen A Stringer
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Theodore J Standiford
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Yongqing Li
- Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
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19
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Tian Y, Russo RM, Li Y, Karmakar M, Liu B, Puskarich MA, Jones AE, Stringer KA, Standiford TJ, Alam HB. Serum citrullinated histone H3 concentrations differentiate patients with septic verses non-septic shock and correlate with disease severity. Infection 2020; 49:83-93. [PMID: 33000445 PMCID: PMC7527151 DOI: 10.1007/s15010-020-01528-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022]
Abstract
Purpose Microbial infection stimulates neutrophil/macrophage/monocyte extracellular trap formation, which leads to the release of citrullinated histone H3 (CitH3) catalyzed by peptidylarginine deiminase (PAD) 2 and 4. Understanding these molecular mechanisms in the pathogenesis of septic shock will be an important next step for developing novel diagnostic and treatment modalities. We sought to determine the expression of CitH3 in patients with septic shock, and to correlate CitH3 levels with PAD2/PAD4 and clinically relevant outcomes. Methods Levels of CitH3 were measured in serum samples of 160 critically ill patients with septic and non-septic shock, and healthy volunteers. Analyses of clinical and laboratory characteristics of patients were conducted. Results Levels of circulating CitH3 at enrollment were significantly increased in septic shock patients (n = 102) compared to patients hospitalized with non-infectious shock (NIC) (n = 32, p < 0.0001). The area under the curve (95% CI) for distinguishing septic shock from NIC using CitH3 was 0.76 (0.65–0.86). CitH3 was positively correlated with PAD2 and PAD4 concentrations and Sequential Organ Failure Assessment Scores [total score (r = 0.36, p < 0.0001)]. The serum levels of CitH3 at 24 h (p < 0.01) and 48 h (p < 0.05) were significantly higher in the septic patients that did not survive. Conclusion CitH3 is increased in patients with septic shock. Its serum concentrations correlate with disease severity and prognosis, which may yield vital insights into the pathophysiology of sepsis. Electronic supplementary material The online version of this article (10.1007/s15010-020-01528-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuzi Tian
- Department of Surgery, University of Michigan Health System, University of Michigan Medical School, 1500 E Medical Center Dr. SPC 5331, Ann Arbor, MI, 48109-5331, USA.,Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rachel M Russo
- Department of Surgery, University of Michigan Health System, University of Michigan Medical School, 1500 E Medical Center Dr. SPC 5331, Ann Arbor, MI, 48109-5331, USA
| | - Yongqing Li
- Department of Surgery, University of Michigan Health System, University of Michigan Medical School, 1500 E Medical Center Dr. SPC 5331, Ann Arbor, MI, 48109-5331, USA.
| | - Monita Karmakar
- Department of Surgery, University of Michigan Health System, University of Michigan Medical School, 1500 E Medical Center Dr. SPC 5331, Ann Arbor, MI, 48109-5331, USA
| | - Baoling Liu
- Department of Surgery, University of Michigan Health System, University of Michigan Medical School, 1500 E Medical Center Dr. SPC 5331, Ann Arbor, MI, 48109-5331, USA
| | - Michael A Puskarich
- Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, MN, USA.,Department of Emergency Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Alan E Jones
- Department of Emergency Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kathleen A Stringer
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Theodore J Standiford
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Hasan B Alam
- Department of Surgery, University of Michigan Health System, University of Michigan Medical School, 1500 E Medical Center Dr. SPC 5331, Ann Arbor, MI, 48109-5331, USA.
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20
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Wang Y, Chen R, Gan Y, Ying S. The roles of PAD2- and PAD4-mediated protein citrullination catalysis in cancers. Int J Cancer 2020; 148:267-276. [PMID: 33459350 DOI: 10.1002/ijc.33205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023]
Abstract
Peptidylarginine deiminases (PADs) catalyze the conversion of arginine residues to citrulline residues on target proteins in the presence of calcium ions. This elaborate type of posttranslational modification is termed citrullination. PADs may regulate gene transcriptional activity via histone citrullination. There has been an increasing appreciation for the roles of PADs in a wide variety of biological processes. In this review article, we summarize recent evidence indicating that PADs and citrullinated proteins are involved in several physiological and pathological processes related to cancer. Of particular interest is that PAD2 and PAD4 exhibit characteristic expression levels, activities and specific biological effects in diverse types of cancer. We also list several PAD inhibitors, propose the possible mechanisms underlying the biological actions of PAD-mediated protein citrullination in experimental models and discuss the potential therapeutic value of PADs and their inhibitors for disease diagnosis and treatment.
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Affiliation(s)
- Yanbin Wang
- Hangzhou Medical College, Hangzhou, Zhejiang, China.,Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Riping Chen
- Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yihan Gan
- Hangzhou Medical College, Hangzhou, Zhejiang, China.,Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Shibo Ying
- Hangzhou Medical College, Hangzhou, Zhejiang, China
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21
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Hayashi-Takanaka Y, Kina Y, Nakamura F, Becking LE, Nakao Y, Nagase T, Nozaki N, Kimura H. Histone modification dynamics as revealed by multicolor immunofluorescence-based single-cell analysis. J Cell Sci 2020; 133:jcs243444. [PMID: 32576661 PMCID: PMC7390643 DOI: 10.1242/jcs.243444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/08/2020] [Indexed: 01/02/2023] Open
Abstract
Post-translational modifications on histones can be stable epigenetic marks or transient signals that can occur in response to internal and external stimuli. Levels of histone modifications fluctuate during the cell cycle and vary among different cell types. Here, we describe a simple system to monitor the levels of multiple histone modifications in single cells by multicolor immunofluorescence using directly labeled modification-specific antibodies. We analyzed histone H3 and H4 modifications during the cell cycle. Levels of active marks, such as acetylation and H3K4 methylation, were increased during the S phase, in association with chromatin duplication. By contrast, levels of some repressive modifications gradually increased during G2 and the next G1 phases. We applied this method to validate the target modifications of various histone demethylases in cells using a transient overexpression system. In extracts of marine organisms, we also screened chemical compounds that affect histone modifications and identified psammaplin A, which was previously reported to inhibit histone deacetylases. Thus, the method presented here is a powerful and convenient tool for analyzing the changes in histone modifications.
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Affiliation(s)
- Yoko Hayashi-Takanaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3, Yamadaoka, Suita 565-0871, Japan
| | - Yuto Kina
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Fumiaki Nakamura
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Leontine E Becking
- Marine Animal Ecology Group, Wageningen University & Research, PO Box 338, Bode 36, 6700 AH Wageningen, The Netherlands
| | - Yoichi Nakao
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | | | | | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
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22
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Jefferson WN, Kinyamu HK, Wang T, Miranda AX, Padilla-Banks E, Suen AA, Williams CJ. Widespread enhancer activation via ERα mediates estrogen response in vivo during uterine development. Nucleic Acids Res 2019; 46:5487-5503. [PMID: 29648668 PMCID: PMC6009594 DOI: 10.1093/nar/gky260] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 01/07/2023] Open
Abstract
Little is known regarding how steroid hormone exposures impact the epigenetic landscape in a living organism. Here, we took a global approach to understanding how exposure to the estrogenic chemical, diethylstilbestrol (DES), affects the neonatal mouse uterine epigenome. Integration of RNA- and ChIP-sequencing data demonstrated that ∼80% of DES-altered genes had higher H3K4me1/H3K27ac signal in close proximity. Active enhancers, of which ∼3% were super-enhancers, had a high density of estrogen receptor alpha (ERα) binding sites and were correlated with alterations in nearby gene expression. Conditional uterine deletion of ERα, but not the pioneer transcription factors FOXA2 or FOXO1, prevented the majority of DES-mediated changes in gene expression and H3K27ac signal at target enhancers. An ERα dependent super-enhancer was located at the Padi gene locus and a topological connection to the Padi1 TSS was documented using 3C-PCR. Chromosome looping at this site was independent of ERα and DES exposure, indicating that the interaction is established prior to ligand signaling. However, enrichment of H3K27ac and transcriptional activation at this locus was both DES and ERα-dependent. These data suggest that DES alters uterine development and consequently adult reproductive function by modifying the enhancer landscape at ERα binding sites near estrogen-regulated genes.
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Affiliation(s)
- Wendy N Jefferson
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - H Karimi Kinyamu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Adam X Miranda
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Elizabeth Padilla-Banks
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Alisa A Suen
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Carmen J Williams
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
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23
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Zheng L, Nagar M, Maurais AJ, Slade DJ, Parelkar SS, Coonrod SA, Weerapana E, Thompson PR. Calcium Regulates the Nuclear Localization of Protein Arginine Deiminase 2. Biochemistry 2019; 58:3042-3056. [PMID: 31243954 DOI: 10.1021/acs.biochem.9b00225] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein arginine deiminases (PADs) are calcium-dependent enzymes that mediate the post-translational conversion of arginine into citrulline. Dysregulated PAD activity is associated with numerous autoimmune disorders and cancers. In breast cancer, PAD2 citrullinates histone H3R26 and activates the transcription of estrogen receptor target genes. However, PAD2 lacks a canonical nuclear localization sequence, and it is unclear how this enzyme is transported into the nucleus. Here, we show for the first time that PAD2 translocates into the nucleus in response to calcium signaling. Using BioID2, a proximity-dependent biotinylation method for identifying interacting proteins, we found that PAD2 preferentially associates with ANXA5 in the cytoplasm. Binding of calcium to PAD2 weakens this cytoplasmic interaction, which generates a pool of calcium-bound PAD2 that can interact with Ran. We hypothesize that this latter interaction promotes the translocation of PAD2 into the nucleus. These findings highlight a critical role for ANXA5 in regulating PAD2 and identify an unusual mechanism whereby proteins translocate between the cytosol and nucleus.
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Affiliation(s)
- Li Zheng
- Department of Biochemistry and Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.,Program in Chemical Biology , University of Massachusetts Medical School , 364 Plantation Street , Worcester , Massachusetts 01605 , United States
| | - Mitesh Nagar
- Department of Biochemistry and Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.,Program in Chemical Biology , University of Massachusetts Medical School , 364 Plantation Street , Worcester , Massachusetts 01605 , United States
| | - Aaron J Maurais
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Daniel J Slade
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Sangram S Parelkar
- Department of Biochemistry and Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Scott A Coonrod
- James A. Baker Institute for Animal Health, College of Veterinary Medicine , Cornell University , Ithaca , New York 14853 , United States
| | - Eranthie Weerapana
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Paul R Thompson
- Department of Biochemistry and Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.,Program in Chemical Biology , University of Massachusetts Medical School , 364 Plantation Street , Worcester , Massachusetts 01605 , United States
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24
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Collemare J, Seidl MF. Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? FEMS Microbiol Rev 2019; 43:591-607. [PMID: 31301226 PMCID: PMC8038932 DOI: 10.1093/femsre/fuz018] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/07/2023] Open
Abstract
Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.
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Affiliation(s)
| | - Michael F Seidl
- Corresponding author: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands. E-mail: ; Present address: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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25
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Song S, Xiang Z, Li J, Ji J, Yan R, Zhu Z, Yu Y. A Novel Citrullinated Modification of Histone 3 and Its Regulatory Mechanisms Related to IPO-38 Antibody-Labeled Protein. Front Oncol 2019; 9:304. [PMID: 31058095 PMCID: PMC6482251 DOI: 10.3389/fonc.2019.00304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022] Open
Abstract
IPO-38 is a potential biomarker for early diagnosis of gastric cancer that we recently identified. Although we characterized its chemical nature as a nucleosome histone, we suspected the existence of histone modification for the IPO-38 antibody-labeled protein. Here, we used a commercially available modified histone peptide array to identify the type and site of histone modification labeled by the IPO-38 monoclonal antibody. In protein array analysis, the citrulline modification of histone 3 on arginine 26 (H3R26Cit) yielded the strongest signal. Although peptidyl arginine deiminase-2 and -4 (PADI2 and PADI4, respectively) can catalyze the conversion of arginine to citrulline, we observed that only PADI4 expression correlated with the citrulline histone modification of H3R26Cit. Overexpression of PADI4, via transfection of a eukaryotic expression vector, and knockdown of PADI4 gene expression, by a PADI4 CRISPR/Cas9 vector, confirmed the crucial function of PADI4 on the increased level of H3R26Cit in gastric cancer cell lines. By immunoprecipitation and immunoblotting, we found an interaction between H3R26Cit and H3K27me3. Our study established the first link between the IPO-38 antigen and citrullinated histone 3, and clarified the upstream regulatory enzyme PADI4. The new findings suggest an important role for the citrullination modification of histone in gastric cancer biology, and should help us optimize the development of a sensitive and specific diagnostic reagent.
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Affiliation(s)
- Shuzheng Song
- Department of Surgery, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
| | - Zhen Xiang
- Department of Surgery, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
| | - Jun Li
- Department of Surgery, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
| | - Jun Ji
- Department of Surgery, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
| | - Ranlin Yan
- Department of Surgery, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
| | - Zhenggang Zhu
- Department of Surgery, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
| | - Yingyan Yu
- Department of Surgery, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai, China
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26
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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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27
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Nagar M, Tilvawala R, Thompson PR. Thioredoxin Modulates Protein Arginine Deiminase 4 (PAD4)-Catalyzed Citrullination. Front Immunol 2019; 10:244. [PMID: 30853960 PMCID: PMC6396667 DOI: 10.3389/fimmu.2019.00244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/28/2019] [Indexed: 01/01/2023] Open
Abstract
Protein citrullination is a post-translational modification catalyzed by the protein arginine deiminases (PADs). This modification plays a crucial role in the pathophysiology of numerous autoimmune disorders including RA. Recently, there has been a growing interest in investigating physiological regulators of PAD activity to understand the primary cause of the associated disorders. Apart from calcium, it is well-documented that a reducing environment activates the PADs. Although the concentration of thioredoxin (hTRX), an oxidoreductase that maintains the cellular reducing environment, is elevated in RA patients, its contribution toward RA progression or PAD activity has not been explored. Herein, we demonstrate that hTRX activates PAD4. Kinetic characterization of PAD4 using hTRX as the reducing agent yielded parameters that are comparable to those obtained with a routinely used non-physiological reducing agent, e.g., DTT, suggesting the importance of hTRX in PAD regulation under physiological conditions. Furthermore, we show that various hTRX mutants, including redox inactive hTRX variants, are capable of activating PAD4. This indicates a mechanism that does not require oxidoreductase activity. Indeed, we observed non-covalent interactions between PAD4 and hTRX variants, and propose that these redox-independent interactions are sufficient for hTRX-mediated PAD4 activation.
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Affiliation(s)
- Mitesh Nagar
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States.,Program in Chemical Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Ronak Tilvawala
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States.,Program in Chemical Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States.,Program in Chemical Biology, University of Massachusetts Medical School, Worcester, MA, United States
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28
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Peptidylarginine Deiminases Post-Translationally Deiminate Prohibitin and Modulate Extracellular Vesicle Release and MicroRNAs in Glioblastoma Multiforme. Int J Mol Sci 2018; 20:ijms20010103. [PMID: 30597867 PMCID: PMC6337164 DOI: 10.3390/ijms20010103] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive form of adult primary malignant brain tumour with poor prognosis. Extracellular vesicles (EVs) are a key-mediator through which GBM cells promote a pro-oncogenic microenvironment. Peptidylarginine deiminases (PADs), which catalyze the post-translational protein deimination of target proteins, are implicated in cancer, including via EV modulation. Pan-PAD inhibitor Cl-amidine affected EV release from GBM cells, and EV related microRNA cargo, with reduced pro-oncogenic microRNA21 and increased anti-oncogenic microRNA126, also in combinatory treatment with the chemotherapeutic agent temozolomide (TMZ). The GBM cell lines under study, LN18 and LN229, differed in PAD2, PAD3 and PAD4 isozyme expression. Various cytoskeletal, nuclear and mitochondrial proteins were identified to be deiminated in GBM, including prohibitin (PHB), a key protein in mitochondrial integrity and also involved in chemo-resistance. Post-translational deimination of PHB, and PHB protein levels, were reduced after 1 h treatment with pan-PAD inhibitor Cl-amidine in GBM cells. Histone H3 deimination was also reduced following Cl-amidine treatment. Multifaceted roles for PADs on EV-mediated pathways, as well as deimination of mitochondrial, nuclear and invadopodia related proteins, highlight PADs as novel targets for modulating GBM tumour communication.
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29
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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30
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Mondal S, Parelkar SS, Nagar M, Thompson PR. Photochemical Control of Protein Arginine Deiminase (PAD) Activity. ACS Chem Biol 2018. [PMID: 29517899 DOI: 10.1021/acschembio.8b00053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein arginine deiminases (PADs) play an important role in the pathogenesis of various diseases, including rheumatoid arthritis, multiple sclerosis, lupus, ulcerative colitis, and breast cancer. Therefore, the development of PAD inhibitors has drawn significant research interest in recent years. Herein, we describe the development of the first photoswitchable PAD inhibitors. These compounds possess an azobenzene photoswitch to optically control PAD activity. Screening of a series of inhibitors structurally similar to BB-Cl-amidine afforded compounds 1 and 2 as the most promising candidates for the light-controlled inhibition of PAD2; the cis isomer of 1 is 10-fold more potent than its trans isomer, whereas the trans isomer of 2 is 45-fold more potent than the corresponding cis isomer. The altered inhibitory potency upon photoisomerization has been confirmed in a competitive activity-based protein profiling (ABPP) assay. Further investigations indicate that the trans isomer of 2 is an irreversible inhibitor, whereas the cis isomer acts as a competitive inhibitor. In cells, the trans isomer of compound 1 is completely inactive, whereas the cis isomer inhibits histone H3-citrullination in a dose-dependent manner. Taken together, 1 serves as the foundation for developing photopharmaceuticals that can be activated at the desired tissue, using light, to treat diseases where PAD activity is dysregulated.
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Affiliation(s)
- Santanu Mondal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Sangram S. Parelkar
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Mitesh Nagar
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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31
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Development of Activity-Based Proteomic Probes for Protein Citrullination. Curr Top Microbiol Immunol 2018; 420:233-251. [PMID: 30203394 DOI: 10.1007/82_2018_132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein arginine deiminases (PADs) catalyze the post-translational deimination of peptidyl arginine to form peptidyl citrulline. This modification is increased in multiple inflammatory diseases and in certain cancers. PADs regulate a variety of signaling pathways including apoptosis, terminal differentiation, and transcriptional regulation. Activity-based protein profiling (ABPP) probes have been developed to understand the role of the PADs in vivo and to investigate the effect of protein citrullination in various pathological conditions. Furthermore, these ABPPs have been utilized as a platform for high-throughput inhibitor discovery. This review will showcase the development of ABPPs targeting the PADs. In addition, it provides a brief overview of PAD structure and function along with recent advances in PAD inhibitor development.
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