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Neira JL, Rizzuti B, Abian O, Velazquez-Campoy A. Isolated auto-citrullinated regions of PADI4 associate to the intact protein without altering their disordered conformation. Biophys Chem 2024; 312:107288. [PMID: 38991454 DOI: 10.1016/j.bpc.2024.107288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/19/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024]
Abstract
PADI4 is one of the human isoforms of a group of enzymes intervening in the conversion of arginine to citrulline. It is involved in the development of several types of tumors, as well as other immunological illnesses, such as psoriasis, multiple sclerosis, or rheumatoid arthritis. PADI4 auto-citrullinates in several regions of its sequence, namely in correspondence of residues Arg205, Arg212, Arg218, and Arg383. We wanted to study whether the citrullinated moiety affects the conformation of nearby regions and its binding to intact PADI4. We designed two series of synthetic peptides comprising either the wild-type or the relative citrullinated versions of such regions - i.e., a first series of peptides comprising the first three arginines, and a second series comprising Arg383. We studied their conformational properties in isolation by using fluorescence, far-ultraviolet (UV) circular dichroism (CD), and 2D1H NMR. Furthermore, we characterized the binding of the wild-type and citrullinated peptides in the two series to the intact PADI4, by using isothermal titration calorimetry (ITC), fluorescence, and biolayer interferometry (BLI), as well as by molecular docking simulations. We observed that citrullination did not alter the local conformational propensities of the isolated peptides. Nevertheless, for all the peptides in the two series, citrullination slowed down the kinetic koff rates of the binding reaction to PADI4, probably due to differences in electrostatic effects compared to the presence of arginine. The affinities of PADI4 for unmodified peptides were slightly larger than those of the corresponding citrullinated ones in the two series, but they were all within the same range, indicating that there were no relevant variations in the thermodynamics of binding due to sequence effects. These results highlight details of the self-citrullination of PADI4 and, more generally, of possible auto-catalytic mechanisms taking place in vivo for other citrullinating enzymes or, alternatively, in proteins undergoing citrullination passively.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
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Araujo-Abad S, Rizzuti B, Soto-Conde L, Vidal M, Abian O, Velazquez-Campoy A, Neira JL, de Juan Romero C. Citrullinating enzyme PADI4 and transcriptional repressor RING1B bind in cancer cells. Int J Biol Macromol 2024; 274:133163. [PMID: 38878927 DOI: 10.1016/j.ijbiomac.2024.133163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/26/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
Polycomb groups (PcGs) are transcriptional repressors, formed by a complex of several proteins, involved in multicellular development and cancer epigenetics. One of these proteins is the E3 ubiquitin-protein ligase RING1 (or RING1B), associated with the regulation of transcriptional repression and responsible for monoubiquitylation of the histone H2A. On the other hand, PADI4 is one of the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline, and it is also involved in the development of glioblastoma, among other types of cancers. In this work, we showed the association of PADI4 and RING1B in the nucleus and cytosol in several cancer cell lines by using immunofluorescence and proximity ligation assays. Furthermore, we demonstrated that binding was hampered in the presence of GSK484, an enzymatic PADI4 inhibitor, suggesting that RING1B could bind to the active site of PADI4, as confirmed by protein-protein docking simulations. In vitro and in silico findings showed that binding to PADI4 occurred for the isolated fragments corresponding to both the N-terminal (residues 1-221) and C-terminal (residues 228-336) regions of RING1B. Binding to PADI4 was also hampered by GSK484, as shown by isothermal titration calorimetry (ITC) experiments for the sole N-terminal region, and by both NMR and ITC for the C-terminal one. The dissociation constants between PADI4 and any of the two isolated RING1B fragments were in the low micromolar range (~2-10 μM), as measured by fluorescence and ITC. The interaction between RING1B and PADI4 might imply citrullination of the former, leading to several biological consequences, as well as being of potential therapeutic relevance for improving cancer treatment with the generation of new antigens.
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Affiliation(s)
- Salome Araujo-Abad
- Cancer Research Group, Faculty of Engineering and Applied Sciences, Universidad de Las Américas, 170124 Quito, Ecuador; IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain.
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | | | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain.
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3
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Nakamura A, Sakai S, Taketomi Y, Tsuyama J, Miki Y, Hara Y, Arai N, Sugiura Y, Kawaji H, Murakami M, Shichita T. PLA2G2E-mediated lipid metabolism triggers brain-autonomous neural repair after ischemic stroke. Neuron 2023; 111:2995-3010.e9. [PMID: 37490917 DOI: 10.1016/j.neuron.2023.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 03/08/2023] [Accepted: 06/23/2023] [Indexed: 07/27/2023]
Abstract
The brain is generally resistant to regeneration after damage. The cerebral endogenous mechanisms triggering brain self-recovery have remained unclarified to date. We here discovered that the secreted phospholipase PLA2G2E from peri-infarct neurons generated dihomo-γ-linolenic acid (DGLA) as necessary for triggering brain-autonomous neural repair after ischemic brain injury. Pla2g2e deficiency diminished the expression of peptidyl arginine deiminase 4 (Padi4), a global transcriptional regulator in peri-infarct neurons. Single-cell RNA sequencing (scRNA-seq) and epigenetic analysis demonstrated that neuronal PADI4 had the potential for the transcriptional activation of genes associated with recovery processes after ischemic stroke through histone citrullination. Among various DGLA metabolites, we identified 15-hydroxy-eicosatrienoic acid (15-HETrE) as the cerebral metabolite that induced PADI4 in peri-infarct-surviving neurons. Administration of 15-HETrE enhanced functional recovery after ischemic stroke. Thus, our research clarifies the promising potential of brain-autonomous neural repair triggered by the specialized lipids that initiate self-recovery processes after brain injury.
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Affiliation(s)
- Akari Nakamura
- Stroke Renaissance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Department of Neuroinflammation and Repair, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Core Research for Evolutionary Medical Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan
| | - Seiichiro Sakai
- Stroke Renaissance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Department of Neuroinflammation and Repair, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Core Research for Evolutionary Medical Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan
| | - Yoshitaka Taketomi
- Laboratory of Microenvironmental and Metabolic Health Science Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Jun Tsuyama
- Stroke Renaissance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Department of Neuroinflammation and Repair, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Core Research for Evolutionary Medical Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan
| | - Yoshimi Miki
- Laboratory of Microenvironmental and Metabolic Health Science Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yuichiro Hara
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Nobutaka Arai
- Laboratory for Neuropathology, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Makoto Murakami
- Laboratory of Microenvironmental and Metabolic Health Science Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takashi Shichita
- Stroke Renaissance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Department of Neuroinflammation and Repair, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Core Research for Evolutionary Medical Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan.
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Li X, Xiao S, Filipczak N, Yalamarty SSK, Shang H, Zhang J, Zheng Q. Role and Therapeutic Targeting Strategies of Neutrophil Extracellular Traps in Inflammation. Int J Nanomedicine 2023; 18:5265-5287. [PMID: 37746050 PMCID: PMC10516212 DOI: 10.2147/ijn.s418259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
Neutrophil extracellular traps (NETs) are large DNA reticular structures secreted by neutrophils and decorated with histones and antimicrobial proteins. As a key mechanism for neutrophils to resist microbial invasion, NETs play an important role in the killing of microorganisms (bacteria, fungi, and viruses). Although NETs are mostly known for mediating microbial killing, increasing evidence suggests that excessive NETs induced by stimulation of physical and chemical components, microorganisms, and pathological factors can exacerbate inflammation and organ damage. This review summarizes the induction and role of NETs in inflammation and focuses on the strategies of inhibiting NETosis and the mechanisms involved in pathogen evasion of NETs. Furthermore, herbal medicine inhibitors and nanodelivery strategies improve the efficiency of inhibition of excessive levels of NETs.
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Affiliation(s)
- Xiang Li
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, People’s Republic of China
| | - Shanghua Xiao
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, People’s Republic of China
| | - Nina Filipczak
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA, USA
| | | | - Hongming Shang
- Department of Biochemistry & Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - Jing Zhang
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, People’s Republic of China
| | - Qin Zheng
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, People’s Republic of China
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Araujo-Abad S, Fuentes-Baile M, Rizzuti B, Bazán JF, Villamarin-Ortiz A, Saceda M, Fernández E, Vidal M, Abian O, Velazquez-Campoy A, de Juan Romero C, Neira JL. The intrinsically disordered, epigenetic factor RYBP binds to the citrullinating enzyme PADI4 in cancer cells. Int J Biol Macromol 2023; 246:125632. [PMID: 37399862 DOI: 10.1016/j.ijbiomac.2023.125632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
RYBP (Ring1 and YY 1 binding protein) is a multifunctional, intrinsically disordered protein (IDP), best described as a transcriptional regulator. It exhibits a ubiquitin-binding functionality, binds to other transcription factors, and has a key role during embryonic development. RYBP, which folds upon binding to DNA, has a Zn-finger domain at its N-terminal region. By contrast, PADI4 is a well-folded protein and it is one the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline. As both proteins intervene in signaling pathways related to cancer development and are found in the same localizations within the cell, we hypothesized they may interact. We observed their association in the nucleus and cytosol in several cancer cell lines, by using immunofluorescence (IF) and proximity ligation assays (PLAs). Binding also occurred in vitro, as measured by isothermal titration calorimetry (ITC) and fluorescence, with a low micromolar affinity (~1 μM). AlphaFold2-multimer (AF2) results indicate that PADI4's catalytic domain interacts with the Arg53 of RYBP docking into its active site. As RYBP sensitizes cells to PARP (Poly (ADP-ribose) polymerase) inhibitors, we applied them in combination with an enzymatic inhibitor of PADI4 observing a change in cell proliferation, and the hampering of the interaction of both proteins. This study unveils for the first time the possible citrullination of an IDP, and suggests that this new interaction, whether it involves or not citrullination of RYBP, might have implications in cancer development and progression.
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Affiliation(s)
- Salomé Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, 110111 Loja, Ecuador
| | - María Fuentes-Baile
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - J Fernando Bazán
- ħ Bioconsulting, LLC, Stillwater, MN, USA; Unit for Structural Biology, Vlaams Instituut voor Biotechnologie-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | | | - Miguel Saceda
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain
| | - Eduardo Fernández
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Centro de Investigación Biomédica en Red CIBER-BBN, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrián Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain.
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
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Indeglia A, Leung JC, Miller SA, Leu JIJ, Dougherty JF, Clarke NL, Kirven NA, Shao C, Ke L, Lovell S, Barnoud T, Lu DY, Lin C, Kannan T, Battaile KP, Yang THL, Batista Oliva I, Claiborne DT, Vogel P, Liu L, Liu Q, Nefedova Y, Cassel J, Auslander N, Kossenkov AV, Karanicolas J, Murphy ME. An African-Specific Variant of TP53 Reveals PADI4 as a Regulator of p53-Mediated Tumor Suppression. Cancer Discov 2023; 13:1696-1719. [PMID: 37140445 PMCID: PMC10326602 DOI: 10.1158/2159-8290.cd-22-1315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 05/05/2023]
Abstract
TP53 is the most frequently mutated gene in cancer, yet key target genes for p53-mediated tumor suppression remain unidentified. Here, we characterize a rare, African-specific germline variant of TP53 in the DNA-binding domain Tyr107His (Y107H). Nuclear magnetic resonance and crystal structures reveal that Y107H is structurally similar to wild-type p53. Consistent with this, we find that Y107H can suppress tumor colony formation and is impaired for the transactivation of only a small subset of p53 target genes; this includes the epigenetic modifier PADI4, which deiminates arginine to the nonnatural amino acid citrulline. Surprisingly, we show that Y107H mice develop spontaneous cancers and metastases and that Y107H shows impaired tumor suppression in two other models. We show that PADI4 is itself tumor suppressive and that it requires an intact immune system for tumor suppression. We identify a p53-PADI4 gene signature that is predictive of survival and the efficacy of immune-checkpoint inhibitors. SIGNIFICANCE We analyze the African-centric Y107H hypomorphic variant and show that it confers increased cancer risk; we use Y107H in order to identify PADI4 as a key tumor-suppressive p53 target gene that contributes to an immune modulation signature and that is predictive of cancer survival and the success of immunotherapy. See related commentary by Bhatta and Cooks, p. 1518. This article is highlighted in the In This Issue feature, p. 1501.
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Affiliation(s)
- Alexandra Indeglia
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jessica C. Leung
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Sven A. Miller
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Julia I-Ju Leu
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - James F. Dougherty
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Nicole L. Clarke
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Nicole A. Kirven
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Chunlei Shao
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Lei Ke
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Scott Lovell
- Del Shankel Structural Biology Center, The University of Kansas, Lawrence, Kansas
| | - Thibaut Barnoud
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - David Y. Lu
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Cindy Lin
- Program in Immunology, Microenvironment and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Toshitha Kannan
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania
| | | | - Tyler Hong Loong Yang
- Program in Immunology, Microenvironment and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Isabela Batista Oliva
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Daniel T. Claiborne
- Program in Immunology, Microenvironment and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Peter Vogel
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lijun Liu
- Del Shankel Structural Biology Center, The University of Kansas, Lawrence, Kansas
| | - Qin Liu
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Yulia Nefedova
- Program in Immunology, Microenvironment and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Joel Cassel
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Noam Auslander
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Andrew V. Kossenkov
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Maureen E. Murphy
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
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7
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Araujo-Abad S, Neira JL, Rizzuti B, García-Morales P, de Juan Romero C, Santofimia-Castaño P, Iovanna J. Intrinsically Disordered Chromatin Protein NUPR1 Binds to the Enzyme PADI4. J Mol Biol 2023; 435:168033. [PMID: 36858171 DOI: 10.1016/j.jmb.2023.168033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
The nuclear protein 1 (NUPR1) is an intrinsically disordered protein involved in stress-mediated cellular conditions. Its paralogue nuclear protein 1-like (NUPR1L) is p53-regulated, and its expression down-regulates that of the NUPR1 gene. Peptidyl-arginine deiminase 4 (PADI4) is an isoform of a family of enzymes catalyzing arginine to citrulline conversion; it is also involved in stress-mediated cellular conditions. We characterized the interaction between NUPR1 and PADI4 in vitro, in silico, and in cellulo. The interaction of NUPR1 and PADI4 occurred with a dissociation constant of 18 ± 6 μM. The binding region of NUPR1, mapped by NMR, was a hydrophobic polypeptide patch surrounding the key residue Ala33, as pinpointed by: (i) computational results; and, (ii) site-directed mutagenesis of residues of NUPR1. The association between PADI4 and wild-type NUPR1 was also assessed in cellulo by using proximity ligation assays (PLAs) and immunofluorescence (IF), and it occurred mainly in the nucleus. Moreover, binding between NUPR1L and PADI4 also occurred in vitro with an affinity similar to that of NUPR1. Molecular modelling provided information on the binding hot spot for PADI4. This is an example of a disordered partner of PADI4, whereas its other known interacting proteins are well-folded. Altogether, our results suggest that the NUPR1/PADI4 complex could have crucial functions in modulating DNA-repair, favoring metastasis, or facilitating citrullination of other proteins.
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Affiliation(s)
- Salomé Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, Loja, 110111 Loja, Ecuador
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | | | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain
| | - Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France.
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
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8
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Neira JL, Rizzuti B, Araujo-Abad S, Abian O, Fárez-Vidal ME, Velazquez-Campoy A, de Juan Romero C. The armadillo-repeat domain of Plakophilin 1 binds to human enzyme PADI4. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140868. [PMID: 36372391 DOI: 10.1016/j.bbapap.2022.140868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
Plakophilin 1 (PKP1), a member of the armadillo repeat family of proteins, is a key structural component of cell-cell adhesion scaffolds, although it can also be found in other cell locations, including the cytoplasm and the nucleus. PADI4 (peptidyl-arginine deiminase 4) is one of the human isoforms of a family of enzymes engaged in the conversion of arginine to citrulline, and is present in monocytes, macrophages, granulocytes, and in several types of cancer cells. It is the only family member observed both within the nucleus and the cytoplasm under ordinary conditions. We studied the binding of the armadillo domain of PKP1 (ARM-PKP1) with PADI4, by using several biophysical methods, namely fluorescence, far-ultraviolet (far-UV) circular dichroism (CD), isothermal titration calorimetry (ITC), and molecular simulations; furthermore, binding was also tested by Western-blot (WB) analyses. Our results show that there was binding between the two proteins, with a dissociation constant in the low micromolar range (∼ 1 μM). Molecular modelling provided additional information on the possible structure of the binding complex, and especially on the binding hot-spot predicted for PADI4. This is the first time that the interaction between these two proteins has been described and studied. Our findings could be of importance to understand the development of tumors, where PKP1 and PADI4 are involved. Moreover, our findings pave the way to describe the formation of neutrophil extracellular traps (NETs), whose construction is modulated by PADI4, and which mediate the proteolysis of cell-cell junctions where PKP1 intervenes.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Salome Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, Loja, 110111 Loja, Ecuador
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain; Instituto de Investigación Biomédica IBS, Granada, Spain; Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain.
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9
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Akboua H, Eghbalzadeh K, Keser U, Wahlers T, Paunel-Görgülü A. Impaired non-canonical transforming growth factor-β signalling prevents profibrotic phenotypes in cultured peptidylarginine deiminase 4-deficient murine cardiac fibroblasts. J Cell Mol Med 2021; 25:9674-9684. [PMID: 34523218 PMCID: PMC8505821 DOI: 10.1111/jcmm.16915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Transforming growth factor‐β (TGF‐β) becomes rapidly activated in the infarcted heart. Hence, TGF‐β‐mediated persistent activation of cardiac fibroblasts (CFs) and exaggerated fibrotic responses may result in adverse cardiac remodelling and heart failure. Additionally, peptidylarginine deiminase 4 (PAD4) was described to be implicated in organ fibrosis. Here, we investigated the impact of PAD4 on CF function and myofibroblast transdifferentiation in vitro. The expression of fibrosis‐related genes was largely similar in cultured WT and PAD4‐/‐ CFs of passage 3, although collagen III was reduced in PAD4‐/‐ CFs. Exposure to TGF‐β inhibited proliferation and increased contractile activity and migration of WT CFs, but not of PAD4‐/‐ CFs. However, under baseline conditions, PAD4−/− CFs showed comparable functional characteristics as TGF‐β‐stimulated WT CFs. Although the SMAD‐dependent TGF‐β pathway was not disturbed in PAD4‐/‐ CFs, TGF‐β failed to activate protein kinase B (Akt) and signal transducer and activator of transcription 3 (STAT3) in these cells. Similar results were obtained in WT CFs treated with the PAD4 inhibitor Cl‐amidine. Abrogated Akt activation was associated with diminished levels of phosphorylated, inactive glycogen synthase kinase‐3β (GSK‐3β). Consequently, PAD4‐/‐ CFs did not upregulate collagen I and α‐smooth muscle actin (α‐SMA) expression after TGF‐β treatment. Thus, PAD4 is substantially involved in the regulation of non‐canonical TGF‐β signalling and may represent a therapeutic target for the treatment of adverse cardiac remodelling.
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Affiliation(s)
- Hanane Akboua
- Department of Cardiothoracic Surgery, Heart Center of the University of Cologne, Cologne, Germany
| | - Kaveh Eghbalzadeh
- Department of Cardiothoracic Surgery, Heart Center of the University of Cologne, Cologne, Germany
| | - Ugur Keser
- Department of Cardiothoracic Surgery, Heart Center of the University of Cologne, Cologne, Germany
| | - Thorsten Wahlers
- Department of Cardiothoracic Surgery, Heart Center of the University of Cologne, Cologne, Germany
| | - Adnana Paunel-Görgülü
- Department of Cardiothoracic Surgery, Heart Center of the University of Cologne, Cologne, Germany
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10
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Peptidylarginine deiminases 4 as a promising target in drug discovery. Eur J Med Chem 2021; 226:113840. [PMID: 34520958 DOI: 10.1016/j.ejmech.2021.113840] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/21/2021] [Accepted: 09/07/2021] [Indexed: 12/23/2022]
Abstract
Peptidylarginine deaminase 4 (PAD4) is a crucial post-translational modifying enzyme catalyzing the conversion of arginine into citrulline residues, and mediating the formation of neutrophil extracellular traps (NETs). PAD4 plays a vital role in the occurrence and development of cardiovascular diseases, autoimmune diseases, and various tumors. Therefore, PAD4 is considered as a promising drug target for disease diagnosis and treatment. More and more efforts are devoted to developing highly efficient and selective PAD4 inhibitors via high-throughput screening, structure-based drug design and structure-activity relationship study. This article outlined the physiological and pathological functions of PAD4, and corresponding representative small molecule inhibitors reported in recent years.
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11
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Chaerkady R, Zhou Y, Delmar JA, Weng SHS, Wang J, Awasthi S, Sims D, Bowen MA, Yu W, Cazares LH, Sims GP, Hess S. Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning. J Proteome Res 2021; 20:3150-3164. [PMID: 34008986 DOI: 10.1021/acs.jproteome.1c00028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Citrullination is an important post-translational modification implicated in many diseases including rheumatoid arthritis (RA), Alzheimer's disease, and cancer. Neutrophil and mast cells have different expression profiles for protein-arginine deiminases (PADs), and ionomycin-induced activation makes them an ideal cellular model to study proteins susceptible to citrullination. We performed high-resolution mass spectrometry and stringent data filtration to identify citrullination sites in neutrophil and mast cells treated with and without ionomycin. We identified a total of 833 validated citrullination sites on 395 proteins. Several of these citrullinated proteins are important components of pathways involved in innate immune responses. Using this benchmark primary sequence data set, we developed machine learning models to predict citrullination in neutrophil and mast cell proteins. We show that our models predict citrullination likelihood with 0.735 and 0.766 AUCs (area under the receiver operating characteristic curves), respectively, on independent validation sets. In summary, this study provides the largest number of validated citrullination sites in neutrophil and mast cell proteins. The use of our novel motif analysis approach to predict citrullination sites will facilitate the discovery of novel protein substrates of protein-arginine deiminases (PADs), which may be key to understanding immunopathologies of various diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Michael A Bowen
- Antibody Discovery and Protein Engineering (ADPE), R&D AstraZeneca, Gaithersburg, Maryland 20878, United States
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12
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Abstract
The COVID-19 pandemic is one of the most significant public health threats in recent history and has impacted the lives of almost everyone worldwide. Epigenetic mechanisms contribute to many aspects of the SARS-CoV-2 replication cycle, including expression levels of viral receptor ACE2, expression of cytokine genes as part of the host immune response, and the implication of various histone modifications in several aspects of COVID-19. SARS-CoV-2 proteins physically associate with many different host proteins over the course of infection, and notably there are several interactions between viral proteins and epigenetic enzymes such as HDACs and bromodomain-containing proteins as shown by correlation-based studies. The many contributions of epigenetic mechanisms to the viral life cycle and the host immune response to infection have resulted in epigenetic factors being identified as emerging biomarkers for COVID-19, and project epigenetic modifiers as promising therapeutic targets to combat COVID-19. This review article highlights the major epigenetic pathways at play during COVID-19 disease and discusses ongoing clinical trials that will hopefully contribute to slowing the spread of SARS-CoV-2.
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Affiliation(s)
- Rwik Sen
- Active Motif, Incorporated, 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA 92008, USA
| | - Michael Garbati
- Active Motif, Incorporated, 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA 92008, USA
| | - Kevin Bryant
- Active Motif, Incorporated, 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA 92008, USA
| | - Yanan Lu
- Active Motif, Incorporated, 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA 92008, USA
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13
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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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14
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Criscitiello MF, Kraev I, Petersen LH, Lange S. Deimination Protein Profiles in Alligator mississippiensis Reveal Plasma and Extracellular Vesicle-Specific Signatures Relating to Immunity, Metabolic Function, and Gene Regulation. Front Immunol 2020; 11:651. [PMID: 32411128 PMCID: PMC7198796 DOI: 10.3389/fimmu.2020.00651] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/23/2020] [Indexed: 12/13/2022] Open
Abstract
Alligators are crocodilians and among few species that endured the Cretaceous-Paleogene extinction event. With long life spans, low metabolic rates, unusual immunological characteristics, including strong antibacterial and antiviral ability, and cancer resistance, crocodilians may hold information for molecular pathways underlying such physiological traits. Peptidylarginine deiminases (PADs) are a group of calcium-activated enzymes that cause posttranslational protein deimination/citrullination in a range of target proteins contributing to protein moonlighting functions in health and disease. PADs are phylogenetically conserved and are also a key regulator of extracellular vesicle (EV) release, a critical part of cellular communication. As little is known about PAD-mediated mechanisms in reptile immunology, this study was aimed at profiling EVs and protein deimination in Alligator mississippiensis. Alligator plasma EVs were found to be polydispersed in a 50-400-nm size range. Key immune, metabolic, and gene regulatory proteins were identified to be posttranslationally deiminated in plasma and plasma EVs, with some overlapping hits, while some were unique to either plasma or plasma EVs. In whole plasma, 112 target proteins were identified to be deiminated, while 77 proteins were found as deiminated protein hits in plasma EVs, whereof 31 were specific for EVs only, including proteins specific for gene regulatory functions (e.g., histones). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed KEGG pathways specific to deiminated proteins in whole plasma related to adipocytokine signaling, while KEGG pathways of deiminated proteins specific to EVs included ribosome, biosynthesis of amino acids, and glycolysis/gluconeogenesis pathways as well as core histones. This highlights roles for EV-mediated export of deiminated protein cargo with roles in metabolism and gene regulation, also related to cancer. The identification of posttranslational deimination and EV-mediated communication in alligator plasma revealed here contributes to current understanding of protein moonlighting functions and EV-mediated communication in these ancient reptiles, providing novel insight into their unusual immune systems and physiological traits. In addition, our findings may shed light on pathways underlying cancer resistance, antibacterial and antiviral resistance, with translatable value to human pathologies.
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Affiliation(s)
- Michael F. Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, United States
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, United Kingdom
| | - Lene H. Petersen
- Department of Marine Biology, Texas A&M University at Galvestone, Galveston, TX, United States
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, United Kingdom
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15
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Abstract
PURPOSE OF REVIEW Dysregulated citrullination is a key element that drives the production and maintenance of antibodies to citrullinated proteins, a hallmark in rheumatoid arthritis (RA). This article reviews recent literature on the origin of citrullinated antigens in RA. RECENT FINDINGS The study of synovial fluid from patients with RA has provided important insights into the identity of citrullinated proteins that accumulate in the RA joint (the RA citrullinome) and mechanisms that control their generation. SUMMARY Citrullinating enzymes (peptidylarginine deiminases, PADs) are tightly controlled to limit their hyperactivation. Calcium and redox conditions are important regulators of PAD activity. Studies suggest that citrullination is dysregulated both intra- and extracellularly in RA. In neutrophils, host (i.e., perforin and the membrane attack complex) and bacterial (i.e., toxins) pore-forming proteins induce prominent calcium influx, cytolysis, and hyperactivation of PADs. These factors likely drive hypercitrullination in the RA joint and at extraarticular sites of disease initiation, respectively. As oxidizing conditions present in the extracellular environment are known to inactivate PADs, extracellular citrullination in RA probably requires the constant release of active enzymes from dying cells and may be accelerated by autoantibodies that activate PADs.
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Affiliation(s)
- Erika Darrah
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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16
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Konig MF, Andrade F. A Critical Reappraisal of Neutrophil Extracellular Traps and NETosis Mimics Based on Differential Requirements for Protein Citrullination. Front Immunol 2016; 7:461. [PMID: 27867381 PMCID: PMC5095114 DOI: 10.3389/fimmu.2016.00461] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/14/2016] [Indexed: 12/18/2022] Open
Abstract
NETosis, an antimicrobial form of neutrophil cell death, is considered a primary source of citrullinated autoantigens in rheumatoid arthritis (RA) and immunogenic DNA in systemic lupus erythematosus (SLE). Activation of the citrullinating enzyme peptidylarginine deiminase type 4 (PAD4) is believed to be essential for neutrophil extracellular trap (NET) formation and NETosis. PAD4 is therefore viewed as a promising therapeutic target to inhibit the formation of NETs in both diseases. In this review, we examine the evidence for PAD4 activation during NETosis and provide experimental data to suggest that protein citrullination is not a universal feature of NETs. We delineate two distinct biological processes, leukotoxic hypercitrullination (LTH) and defective mitophagy, which have been erroneously classified as “NETosis.” While these NETosis mimics share morphological similarities with NETosis (i.e., extracellular DNA release), they are biologically distinct. As such, these processes can be readily classified by their stimuli, activation of distinct biochemical pathways, the presence of hypercitrullination, and antimicrobial effector function. NETosis is an antimicrobial form of cell death that is NADPH oxidase-dependent and not associated with hypercitrullination. In contrast, LTH is NADPH oxidase-independent and not bactericidal. Rather, LTH represents a bacterial strategy to achieve immune evasion. It is triggered by pore-forming pathways and equivalent signals that cumulate in calcium-dependent hyperactivation of PADs, protein hypercitrullination, and neutrophil death. The generation of citrullinated autoantigens in RA is likely driven by LTH, but not NETosis. Mitochondrial DNA (mtDNA) expulsion, the result of a constitutive defect in mitophagy, represents a second NETosis mimic. In the presence of interferon-α and immune complexes, this process can generate highly interferogenic oxidized mtDNA, which has previously been mistaken for NETosis in SLE. Distinguishing NETosis from LTH and defective mitophagy is paramount to understanding the role of neutrophil damage in immunity and the pathogenesis of human diseases. This provides a framework to design specific inhibitors of these distinct biological processes in human disease.
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Affiliation(s)
- Maximilian F Konig
- Division of Rheumatology, Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Felipe Andrade
- Division of Rheumatology, Johns Hopkins University School of Medicine , Baltimore, MD , USA
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17
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Wang F, Chen FF, Gao WB, Wang HY, Zhao NW, Xu M, Gao DY, Yu W, Yan XL, Zhao JN, Li XJ. Identification of citrullinated peptides in the synovial fluid of patients with rheumatoid arthritis using LC-MALDI-TOF/TOF. Clin Rheumatol 2016; 35:2185-94. [PMID: 27060082 PMCID: PMC4989008 DOI: 10.1007/s10067-016-3247-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/11/2016] [Accepted: 03/23/2016] [Indexed: 12/11/2022]
Abstract
The objective of the study is to investigate potential citrullinated autoantigens as targets of anti-citrullinated protein antibodies (ACPAs) response in synovial fluids (SFs) of patients with rheumatoid arthritis (RA). SFs from six RA patients and six osteoarthritis (OA) patients as controls were collected. The citrullinated proteins in SFs were extracted by immunoprecipitation with rabbit anti-citrulline antibodies. Matrix-assisted laser desorption/ionization time of flight mass spectrometry/time of flight mass spectrometry (MALDI-TOF/TOF) mass spectrometry was subsequently performed to discover a characteristic neutral loss to finally determine citrullinated autoantigens. A total of 182 citrullinated peptides and 200 citrullinated sites were identified in RA SFs, while 3 citrullinated peptides and 4 citrullinated sites were identified in OA SFs. The 182 citrullinated peptides from RA SFs and the 3 citrullinated peptides from OA SFs were derived from 83 and 3 autoantigens, respectively. Eighty-three autoantigens except protein-arginine deiminase type-2 (PADI2) and protein-arginine deiminase type-2 (PADI4) were over-citrullinated compared with controls, and the citrullinated sites of PADI2 and PADI4 were different in two groups. Interestingly, citrullinated histone H3.3 (H3F3A) was found in OA controls, but not in RA groups. The differential citrullinated proteins identified in RA SFs suggested potential autoantigens were targeted for ACPAs response and might contribute to the induction and perpetuation of complement activation and joint inflammation in RA.
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Affiliation(s)
- Fei Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - Fang-Fang Chen
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - Wen-Bo Gao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - Hai-Yong Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - Ning-Wei Zhao
- Biomedical Research Laboratory, Shimadzu (China) Co., Ltd., Shanghai, 200052, China
| | - Min Xu
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - De-Yu Gao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - Wei Yu
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - Xiao-Ling Yan
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - Jian-Ning Zhao
- Department of Osteology, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China
| | - Xiao-Jun Li
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, China. .,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, 210093, China.
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18
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Lerner A, Aminov R, Matthias T. Dysbiosis May Trigger Autoimmune Diseases via Inappropriate Post-Translational Modification of Host Proteins. Front Microbiol 2016; 7:84. [PMID: 26903965 PMCID: PMC4742538 DOI: 10.3389/fmicb.2016.00084] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/18/2016] [Indexed: 01/09/2023] Open
Abstract
The gut ecosystem with myriads of microorganisms and the high concentration of immune system cells can be considered as a separate organ on its own. The balanced interaction between the host and microbial cells has been shaped during the long co-evolutionary process. In dysbiotic conditions, however, this balance is compromised and results in abnormal interaction between the host and microbiota. It is hypothesize here that the changed spectrum of microbial enzymes involved in post-translational modification of proteins (PTMP) may contribute to the aberrant modification of host proteins thus generating autoimmune responses by the host, resulting in autoimmune diseases.
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Affiliation(s)
- Aaron Lerner
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of TechnologyHaifa, Israel; AESKU.KIPP InstituteWendelsheim, Germany
| | - Rustam Aminov
- School of Medicine and Dentistry, University of Aberdeen Aberdeen, UK
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