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Hung SK, Yu CC, Lin HY, Chiou WY, Lee MS, Lin RI, Lu MC. Targeting PADI2 as a potential therapeutic strategy against metastasis in oral cancer via suppressing EMT-mediated migration and invasion and CCL3/5-induced angiogenesis. Clin Exp Metastasis 2024:10.1007/s10585-024-10310-5. [PMID: 39215870 DOI: 10.1007/s10585-024-10310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Oral squamous cell carcinoma (OSCC) is a prevalent and aggressive malignancy, with metastasis being the leading cause of death in patients. Unfortunately, therapeutic options for metastatic OSCC remain limited. Peptidylarginine deiminases (PADI) are implicated in various tumorigenesis and metastasis processes across multiple cancers. However, the role of PADI2, a type of PADI, in OSCC is not well understood. This study aimed to explore the impact of PADI2 on epithelial-mesenchymal transition (EMT), angiogenesis, and OSCC metastasis. The effect of PADI2 on EMT was evaluated using cell lines by Western blot analysis with shRNA targeting PADI2. In addition, the selective PADI2 inhibitor AFM32a was used to assess the effect of PADI2 on cancer metastasis and angiogenesis in animal models. Our findings indicated that PADI2 expression correlated with EMT changes, and PADI2 knockdown reversed these changes, reducing cell proliferation, cell migration, and invasion. PADI2 inhibition also diminished tube formation in HUVECs and decreased secretion of angiogenesis-related chemokines CCL3, CCL5 and CCL20. In a mouse model, AFM32a markedly reduced lung metastasis and production of CCL3 and CCL5. Our in vitro and in vivo studies suggested inhibiting PADI2 could prevent OSCC metastasis by impeding EMT and angiogenesis via AKT/mTOR signaling pathway. These results highlight PADI2 as a potential therapeutic target for combating OSCC metastasis.
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Affiliation(s)
- Shih-Kai Hung
- Department of Radiation Oncology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Chih-Chia Yu
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Hon-Yi Lin
- Department of Radiation Oncology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Wen-Yen Chiou
- Department of Radiation Oncology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Moon-Sing Lee
- Department of Radiation Oncology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Ru-Inn Lin
- Department of Radiation Oncology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Ming-Chi Lu
- School of Medicine, Tzu Chi University, Hualien, Taiwan.
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan.
- Division of Allergy, Immunology and Rheumatology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 2, Min-Sheng Road, Dalin, Chiayi, 62247, Taiwan.
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2
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Hejnova L, Hronova A, Drastichova Z, Novotny J. Long-term administration of morphine specifically alters the level of protein expression in different brain regions and affects the redox state. Open Life Sci 2024; 19:20220858. [PMID: 38681734 PMCID: PMC11049758 DOI: 10.1515/biol-2022-0858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/06/2024] [Accepted: 03/17/2024] [Indexed: 05/01/2024] Open
Abstract
We investigated the changes in redox state and protein expression in selected parts of the rat brain induced by a 4 week administration of morphine (10 mg/kg/day). We found a significant reduction in lipid peroxidation that mostly persisted for 1 week after morphine withdrawal. Morphine treatment led to a significant increase in complex II in the cerebral cortex (Crt), which was accompanied by increased protein carbonylation, in contrast to the other brain regions studied. Glutathione levels were altered differently in the different brain regions after morphine treatment. Using label-free quantitative proteomic analysis, we found some specific changes in protein expression profiles in the Crt, hippocampus, striatum, and cerebellum on the day after morphine withdrawal and 1 week later. A common feature was the upregulation of anti-apoptotic proteins and dysregulation of the extracellular matrix. Our results indicate that the tested protocol of morphine administration has no significant toxic effect on the rat brain. On the contrary, it led to a decrease in lipid peroxidation and activation of anti-apoptotic proteins. Furthermore, our data suggest that long-term treatment with morphine acts specifically on different brain regions and that a 1 week drug withdrawal is not sufficient to normalize cellular redox state and protein levels.
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Affiliation(s)
- Lucie Hejnova
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Anna Hronova
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Zdenka Drastichova
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
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3
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Villanueva-Cañas JL, Fernandez-Fuentes N, Saul D, Kosinsky RL, Teyssier C, Rogalska ME, Pérez FP, Oliva B, Notredame C, Beato M, Sharma P. Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation. iScience 2024; 27:109584. [PMID: 38623337 PMCID: PMC11016909 DOI: 10.1016/j.isci.2024.109584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/13/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Peptidyl arginine deiminases (PADIs) catalyze protein citrullination, a post-translational conversion of arginine to citrulline. The most widely expressed member of this family, PADI2, regulates cellular processes that impact several diseases. We hypothesized that we could gain new insights into PADI2 function through a systematic evolutionary and structural analysis. Here, we identify 20 positively selected PADI2 residues, 16 of which are structurally exposed and maintain PADI2 interactions with cognate proteins. Many of these selected residues reside in non-catalytic regions of PADI2. We validate the importance of a prominent loop in the middle domain that encompasses PADI2 L162, a residue under positive selection. This site is essential for interaction with the transcription elongation factor (P-TEFb) and mediates the active transcription of the oncogenes c-MYC, and CCNB1, as well as impacting cellular proliferation. These insights could be key to understanding and addressing the role of the PADI2 c-MYC axis in cancer progression.
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Affiliation(s)
- José Luis Villanueva-Cañas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - Dominik Saul
- Division of Endocrinology, Mayo Clinic, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Trauma and Reconstructive Surgery, BG Clinic, University of Tübingen, Tübingen, Germany
| | | | - Catherine Teyssier
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut Du Cancer de Montpellier (ICM), F-34298 Montpellier, France
| | - Malgorzata Ewa Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ferran Pegenaute Pérez
- Live-Cell Structural Biology Laboratory, Department of Medicine and Life Sciences, E-08005 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Baldomero Oliva
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Bioinformatics Laboratory (GRIB-IMIM), Department of Medicine and Life Sciences, E-08003 Barcelona, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Priyanka Sharma
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
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4
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Albano C, Biolatti M, Mazibrada J, Pasquero S, Gugliesi F, Lo Cigno I, Calati F, Bajetto G, Riva G, Griffante G, Landolfo S, Gariglio M, De Andrea M, Dell’Oste V. PAD-mediated citrullination is a novel candidate diagnostic marker and druggable target for HPV-associated cervical cancer. Front Cell Infect Microbiol 2024; 14:1359367. [PMID: 38529474 PMCID: PMC10961408 DOI: 10.3389/fcimb.2024.1359367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
Citrullination is an emerging post-translational modification catalyzed by peptidyl-arginine deiminases (PADs) that convert peptidyl-arginine into peptidyl-citrulline. In humans, the PAD family consists of five isozymes (PADs 1-4, 6) involved in multiple diseases, including cancer. Given that high-risk (hr) human papillomaviruses (HPVs) are the etiological agents of cervical cancer, in this study, we sought to determine whether PAD-mediated protein citrullination would play a functional role in the HPV-driven transformation of epithelial cells. Here we show that both total protein citrullination and PAD4 expression levels are significantly associated with cervical cancer progression. Specifically, epithelial immunostaining for PAD4 revealed an increasingly higher histoscore from low-grade (CIN1) to high-grade (CIN2, CIN3) cervical intraepithelial neoplasia, and invasive squamous cell carcinoma (SCC) lesions, raising the attractive possibility that PAD4 may be used as tumor staging markers. Furthermore, taking advantage of the epidermoid cervical cancer cell line CaSki, which harbors multiple copies of the integrated HPV16 genome, we show that the expression of E6 and E7 HPV oncoproteins is impaired by treatment with the pharmacological pan-PAD inhibitor BB-Cl-amidine. Consistently, p53 and p21, two targets of HPV oncoproteins, are upregulated by the PAD inhibitor, which undergoes cell growth arrest and apoptosis. Altogether, these findings highlight a novel mechanism by which hrHPVs alter host regulatory pathways involved in cell cycle and survival to gain viral fitness, raising the possibility that PADs may represent an attractive target for developing novel host-targeting antivirals effective in preventing cervical cancer progression.
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Affiliation(s)
- Camilla Albano
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Jasenka Mazibrada
- Department of Cellular Pathology, The Cotman Centre Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | - Selina Pasquero
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Francesca Gugliesi
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Irene Lo Cigno
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Federica Calati
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Greta Bajetto
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, Novara, Italy
| | - Giuseppe Riva
- Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Gloria Griffante
- IIGM Foundation – Italian Institute for Genomic Medicine, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Marisa Gariglio
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Marco De Andrea
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, Novara, Italy
| | - Valentina Dell’Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
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5
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Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [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: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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6
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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: 3] [Impact Index Per Article: 3.0] [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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7
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Stachowicz A, Sadiq A, Walker B, Sundararaman N, Fert-Bober J. Treatment of human cardiac fibroblasts with the protein arginine deiminase inhibitor BB-Cl-amidine activates the Nrf2/HO-1 signaling pathway. Biomed Pharmacother 2023; 167:115443. [PMID: 37703660 DOI: 10.1016/j.biopha.2023.115443] [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: 05/26/2023] [Revised: 08/27/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Cardiac fibrosis contributes to end-stage extracellular matrix remodeling and heart failure (HF). Cardiac fibroblasts (CFs) differentiate into myofibroblasts (myoFbs) to preserve the structural integrity of the heart; however, the molecular mechanisms regulating CF transdifferentiation remain poorly understood. Protein arginine deiminase (PAD), which converts arginine to citrulline, has been shown to play a role in myocardial infarction, fibrosis, and HF. This study aimed to investigate the role of PAD in CF differentiation to myoFbs and identify the citrullinated proteins that were associated with phenotypic changes in CFs. RESULTS Gene expression analysis showed that PAD1 and PAD2 isoforms, but not PAD4 isoforms, were abundant in both CFs and myoFbs, and PAD1 was significantly upregulated in myoFbs. The pan-PAD inhibitor BB-Cl-amidine (BB-Cl) downregulated the mRNA expression of PAD1 and PAD2 as well as the protein expression of the fibrosis marker COL1A1 in CFs and myoFbs. Interestingly, a proteomic approach pointed to the activation of the Nrf2/HO-1 signaling pathway upon BB-Cl treatment in CFs and myoFbs. BB-Cl administration resulted in the upregulation of HO-1 at both the gene and protein levels in CFs and myoFbs. Importantly, the protein citrullination landscape of CFs consisting of 86 novel citrullination sites associated with focal adhesion (FN1(R1054)), inflammation (TAGLN(R12)) and DNA replication (EEF2(R767)) pathways was identified. CONCLUSIONS In summary, we revealed that BB-Cl treatment resulted in increased HO-1 expression via the Nrf2 pathway, which could prevent excessive tissue damage, thereby leading to substantial clinical benefits for the treatment of cardiac fibrosis.
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Affiliation(s)
- Aneta Stachowicz
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland; Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alia Sadiq
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brian Walker
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Niveda Sundararaman
- Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Justyna Fert-Bober
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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8
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El-Baba C, Ayache Z, Goli M, Hayar B, Kawtharani Z, Pisano C, Kobeissy F, Mechref Y, Darwiche N. The Antitumor Effect of the DNA Polymerase Alpha Inhibitor ST1926 in Glioblastoma: A Proteomics Approach. Int J Mol Sci 2023; 24:14069. [PMID: 37762371 PMCID: PMC10531065 DOI: 10.3390/ijms241814069] [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: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Glioblastoma Multiforme (GBM) is the most aggressive form of malignant brain tumor. The median survival rate does not exceed two years, indicating an imminent need to develop novel therapies. The atypical adamantyl retinoid ST1926 induces apoptosis and growth inhibition in different cancer types. We have shown that ST1926 is an inhibitor of the catalytic subunit of DNA polymerase alpha (POLA1), which is involved in initiating DNA synthesis in eukaryotic cells. POLA1 levels are elevated in GBM versus normal brain tissues. Therefore, we studied the antitumor effects of ST1926 in several human GBM cell lines. We further explored the global protein expression profiles in GBM cell lines using liquid chromatography coupled with tandem mass spectrometry to identify new targets of ST1926. Low sub-micromolar concentrations of ST1926 potently decreased cell viability, induced cell damage and apoptosis, and reduced POLA1 protein levels in GBM cells. The proteomics profiles revealed 197 proteins significantly differentially altered upon ST1926 treatment of GBM cells involved in various cellular processes. We explored the differential gene and protein expression of significantly altered proteins in GBM compared to normal brain tissues.
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Affiliation(s)
- Chirine El-Baba
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
| | - Zeinab Ayache
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Berthe Hayar
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
| | - Zeinab Kawtharani
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
| | - Claudio Pisano
- Biogem, Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy;
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
- Department of Neurobiology, Center for Neurotrauma, Multiomics and Biomarkers (CNMB), Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Nadine Darwiche
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
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9
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Teng Y, Chen Y, Tang X, Wang S, Yin K. PAD2: A potential target for tumor therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188931. [PMID: 37315720 DOI: 10.1016/j.bbcan.2023.188931] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
Peptide arginine deiminase 2(PAD2) catalyzes the conversion of arginine residues on target proteins to citrulline residues in the presence of calcium ions. This particular posttranslational modification is called citrullination. PAD2 can regulate the transcriptional activity of genes through histone citrullination and nonhistone citrullination. In this review, we summarize the evidence from recent decades and systematically illustrate the role of PAD2-mediated citrullination in tumor pathology and the regulation of tumor-associated immune cells such as neutrophils, monocytes, macrophages and T cells. Several PAD2-specific inhibitors are also presented to discuss the feasibility of anti-PAD2 therapy to treat tumors and the urgent problems to be solved. Finally, we review some recent developments in the development of PAD2 inhibitors.
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Affiliation(s)
- Yi Teng
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yuhang Chen
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xinyi Tang
- Department of Laboratory Medicine, the Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Shengjun Wang
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China; Department of Laboratory Medicine, the Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.
| | - Kai Yin
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
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10
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Lin HY, Yu CC, Chi CL, Wei CK, Yin WY, Tseng CE, Li SC. Peptidylarginine Deiminase Type 2 Predicts Tumor Progression and Poor Prognosis in Patients with Curatively Resected Biliary Tract Cancer. Cancers (Basel) 2023; 15:4131. [PMID: 37627159 PMCID: PMC10452823 DOI: 10.3390/cancers15164131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Background: PADI2 is a post-translational modification (PTM) enzyme that catalyzes citrullination, which then triggers autoimmune disease and cancer. This study aimed to evaluate the prognostic value of peptidylarginine deiminase 2 (PADI2) protein expression in biliary tract cancer (BTC) patients. (2) Methods: Using immunohistochemistry, the PADI2 protein expression in BTC tissues was analyzed. The correlations between PADI2 protein expression and clinicopathologic characteristics were analyzed using Chi-square tests. The Kaplan-Meier procedure was used for comparing survival distributions. We used Cox proportional hazards regression for univariate and multivariate analyses. From 2014 to 2020, 30 resected BTC patients were enrolled in this study. (3) Results: Patients with high PADI2 protein expression were associated with shorter progress-free survival (PFS; p = 0.041), disease-specific survival (DSS; p = 0.025), and overall survival (OS; p = 0.017) than patients with low PADI2 protein expression. (4) Conclusions: The results indicated that PADI2 protein expression was an independent poor prognostic factor for BTC patients regarding PFS, DSS, and OS.
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Affiliation(s)
- Hon-Yi Lin
- Department of Radiation Oncology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi 62247, Taiwan;
- School of Medicine, Tzu Chi University, Hualian 97004, Taiwan; (C.-K.W.); (W.-Y.Y.); (C.-E.T.)
| | - Chih-Chia Yu
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi 62247, Taiwan;
| | - Chen-Lin Chi
- Department of Pathology, Chiayi Chang Gung Memorial Hospital, Chia-Yi 61303, Taiwan;
| | - Chang-Kuo Wei
- School of Medicine, Tzu Chi University, Hualian 97004, Taiwan; (C.-K.W.); (W.-Y.Y.); (C.-E.T.)
- Department of General Surgery, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi 62247, Taiwan
| | - Wen-Yao Yin
- School of Medicine, Tzu Chi University, Hualian 97004, Taiwan; (C.-K.W.); (W.-Y.Y.); (C.-E.T.)
- Metabolic Surgery and Allied Care Center, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi 62247, Taiwan
| | - Chih-En Tseng
- School of Medicine, Tzu Chi University, Hualian 97004, Taiwan; (C.-K.W.); (W.-Y.Y.); (C.-E.T.)
- Department of Anatomic Pathology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi 62247, Taiwan
| | - Szu-Chin Li
- School of Medicine, Tzu Chi University, Hualian 97004, Taiwan; (C.-K.W.); (W.-Y.Y.); (C.-E.T.)
- Division of Hematology-Oncology, Department of Internal Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi 62247, Taiwan
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11
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Behura A, Naik L, Patel S, Das M, Kumar A, Mishra A, Nayak DK, Manna D, Mishra A, Dhiman R. Involvement of epigenetics in affecting host immunity during SARS-CoV-2 infection. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166634. [PMID: 36577469 PMCID: PMC9790847 DOI: 10.1016/j.bbadis.2022.166634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/26/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022]
Abstract
Coronavirus disease 19 (COVID-19) is caused by a highly contagious RNA virus Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2), originated in December 2019 in Wuhan, China. Since then, it has become a global public health concern and leads the disease table with the highest mortality rate, highlighting the necessity for a thorough understanding of its biological properties. The intricate interaction between the virus and the host immune system gives rise to diverse implications of COVID-19. RNA viruses are known to hijack the host epigenetic mechanisms of immune cells to regulate antiviral defence. Epigenetics involves processes that alter gene expression without changing the DNA sequence, leading to heritable phenotypic changes. The epigenetic landscape consists of reversible modifications like chromatin remodelling, DNA/RNA methylation, and histone methylation/acetylation that regulates gene expression. The epigenetic machinery contributes to many aspects of SARS-CoV-2 pathogenesis, like global DNA methylation and receptor angiotensin-converting enzyme 2 (ACE2) methylation determines the viral entry inside the host, viral replication, and infection efficiency. Further, it is also reported to epigenetically regulate the expression of different host cytokines affecting antiviral response. The viral proteins of SARS-CoV-2 interact with various host epigenetic enzymes like histone deacetylases (HDACs) and bromodomain-containing proteins to antagonize cellular signalling. The central role of epigenetic factors in SARS-CoV-2 pathogenesis is now exploited as promising biomarkers and therapeutic targets against COVID-19. This review article highlights the ability of SARS-CoV-2 in regulating the host epigenetic landscape during infection leading to immune evasion. It also discusses the ongoing therapeutic approaches to curtail and control the viral outbreak.
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Affiliation(s)
- Assirbad Behura
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Lincoln Naik
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Salina Patel
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Mousumi Das
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ashish Kumar
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Abtar Mishra
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Dev Kiran Nayak
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Debraj Manna
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342011, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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12
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Selective inhibition of peptidyl-arginine deiminase (PAD): can it control multiple inflammatory disorders as a promising therapeutic strategy? Inflammopharmacology 2023; 31:731-744. [PMID: 36806957 DOI: 10.1007/s10787-023-01149-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/19/2023] [Indexed: 02/19/2023]
Abstract
Peptidyl arginine deiminases (PADs) are a family of post-translational modification enzymes that irreversibly citrullinate (deiminate) arginine residues of protein and convert them to a non-classical amino acid citrulline in the presence of calcium ions. It has five isotypes, such as PAD1, PAD2, PAD3, PAD4, and PAD6, found in mammalian species. It has been suggested that increased PAD expression in various tissues contributes to the development of multiple inflammatory diseases, including rheumatoid arthritis (RA), cancer, diabetes, and neurological disorders. Elevation of PAD enzyme expression depends on several factors like rising intracellular Ca2+ levels, oxidative stress, and proinflammatory cytokines. PAD inhibitors originating from natural or synthetic sources can be used as a novel therapeutic approach concerning inflammatory disorders. Here, we review the pathological role of PAD in several inflammatory disorders, factors that trigger PAD expression, epigenetic role and finally, decipher the therapeutic approach of PAD inhibitors in multiple inflammatory disorders.
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13
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Uhm S, Cho YA, Choe JY, Park JW, Kim MJ, Han WH, Lee J, Lee JW, Shin DW, Soh JS, Lim H, Kang HS, Moon SH, Kim SE. Expression of Peptidyl Arginine Deiminase 2 Is Closely Associated with Recurrence in Patients with Hepatocellular Carcinoma. Diagnostics (Basel) 2023; 13:659. [PMID: 36832148 PMCID: PMC9955443 DOI: 10.3390/diagnostics13040659] [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: 01/04/2023] [Revised: 01/27/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023] Open
Abstract
Peptidyl arginine deiminases (PAD) enzymes have been investigated in various cancers. Recently, PAD enzyme, in particular PAD2, has been further implicated in cancers. Although the expression of PAD2 was significantly higher in hepatocellular carcinoma (HCC) tissue, its diagnostic or prognostic role of PAD2 in HCC patients is unknown. This study investigated whether the expression of PAD2 affects recurrence and survival in HCC patients who underwent hepatic resection. One hundred and twenty-two HCC patients after hepatic resection were enrolled. The median follow-up was 41 months (range 1-213 months) in enrolled patients. To investigate an association between PAD2 expression level and the clinical characteristics of enrolled patients, the recurrence of HCC following surgical resection and survival of the patients were examined. Ninety-eight cases (80.3%) of HCC demonstrated a higher expression of PAD2. The expression of PAD2 was correlated with age, hepatitis B virus positivity, hypertension, and higher alpha-fetoprotein level. There was no association between PAD2 expression and sex, diabetes mellitus, Child-Pugh class, major portal vein invasion, HCC size or number. The recurrence rates in patients with lower PAD2 expression were higher than those with higher PAD2 expression. The cumulative survival rates of patients with higher PAD2 expression were better than those of patients with lower PAD2 expression, but it was not statistically significant. In conclusion, PAD2 expression is closely associated with recurrence of HCC patients following surgical resection.
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Affiliation(s)
- Sunho Uhm
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Yoon Ah Cho
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Ji-Young Choe
- Anatomic Pathology Reference Lab, Seegene Medical Foundation, Seoul 04805, Republic of Korea
| | - Ji Won Park
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Republic of Korea
| | - Min-Jeong Kim
- Department of Radiology, Hallym University Sacred Heart Hospital, Anyang 14068, Republic of Korea
| | - Won-Ho Han
- Department of Anesthesiology and Pain Medicine, Seoul Medical Center, Seoul 02053, Republic of Korea
| | - Junyong Lee
- Department of Anesthesiology and Pain Medicine, Seoul Medical Center, Seoul 02053, Republic of Korea
| | - Jung Woo Lee
- Department of Surgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Dong Woo Shin
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Jae Seung Soh
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Hyun Lim
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Ho Suk Kang
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Sung-Hoon Moon
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Sung-Eun Kim
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Republic of Korea
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14
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Identification of the Inner Cell Mass and the Trophectoderm Responses after an In Vitro Exposure to Glucose and Insulin during the Preimplantation Period in the Rabbit Embryo. Cells 2022; 11:cells11233766. [PMID: 36497026 PMCID: PMC9736044 DOI: 10.3390/cells11233766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/26/2022] Open
Abstract
The prevalence of metabolic diseases is increasing, leading to more women entering pregnancy with alterations in the glucose-insulin axis. The aim of this work was to investigate the effect of a hyperglycemic and/or hyperinsulinemic environment on the development of the preimplantation embryo. In rabbit embryos developed in vitro in the presence of high insulin (HI), high glucose (HG), or both (HGI), we determined the transcriptomes of the inner cell mass (ICM) and the trophectoderm (TE). HI induced 10 differentially expressed genes (DEG) in ICM and 1 in TE. HG ICM exhibited 41 DEGs involved in oxidative phosphorylation (OXPHOS) and cell number regulation. In HG ICM, proliferation was decreased (p < 0.01) and apoptosis increased (p < 0.001). HG TE displayed 132 DEG linked to mTOR signaling and regulation of cell number. In HG TE, proliferation was increased (p < 0.001) and apoptosis decreased (p < 0.001). HGI ICM presented 39 DEG involved in OXPHOS and no differences in proliferation and apoptosis. HGI TE showed 16 DEG linked to OXPHOS and cell number regulation and exhibited increased proliferation (p < 0.001). Exposure to HG and HGI during preimplantation development results in common and specific ICM and TE responses that could compromise the development of the future individual and placenta.
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15
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Li X, Ye Y, Peng K, Zeng Z, Chen L, Zeng Y. Histones: The critical players in innate immunity. Front Immunol 2022; 13:1030610. [PMID: 36479112 PMCID: PMC9720293 DOI: 10.3389/fimmu.2022.1030610] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/07/2022] [Indexed: 11/22/2022] Open
Abstract
The highly conserved histones in different species seem to represent a very ancient and universal innate host defense system against microorganisms in the biological world. Histones are the essential part of nuclear matter and act as a control switch for DNA transcription. However, histones are also found in the cytoplasm, cell membranes, and extracellular fluid, where they function as host defenses and promote inflammatory responses. In some cases, extracellular histones can act as damage-associated molecular patterns (DAMPs) and bind to pattern recognition receptors (PRRs), thereby triggering innate immune responses and causing initial organ damage. Histones and their fragments serve as antimicrobial peptides (AMPs) to directly eliminate bacteria, viruses, fungi, and parasites in vitro and in vivo. Histones are also involved in phagocytes-related innate immune response as components of neutrophil extracellular traps (NETs), neutrophil activators, and plasminogen receptors. In addition, as a considerable part of epigenetic regulation, histone modifications play a vital role in regulating the innate immune response and expression of corresponding defense genes. Here, we review the regulatory role of histones in innate immune response, which provides a new strategy for the development of antibiotics and the use of histones as therapeutic targets for inflammatory diseases, sepsis, autoimmune diseases, and COVID-19.
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Affiliation(s)
- Xia Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Youyuan Ye
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Kailan Peng
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Zhuo Zeng
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Li Chen
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Yanhua Zeng
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China,Department of Dermatology and Venereology, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China,*Correspondence: Yanhua Zeng, ;
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16
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Delshad M, Sanaei MJ, Pourbagheri-Sigaroodi A, Bashash D. Host genetic diversity and genetic variations of SARS-CoV-2 in COVID-19 pathogenesis and the effectiveness of vaccination. Int Immunopharmacol 2022; 111:109128. [PMID: 35963158 PMCID: PMC9359488 DOI: 10.1016/j.intimp.2022.109128] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/15/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the outbreak of coronavirus disease 2019 (COVID-19), has shown a vast range of clinical manifestations from asymptomatic to life-threatening symptoms. To figure out the cause of this heterogeneity, studies demonstrated the trace of genetic diversities whether in the hosts or the virus itself. With this regard, this review provides a comprehensive overview of how host genetic such as those related to the entry of the virus, the immune-related genes, gender-related genes, disease-related genes, and also host epigenetic could influence the severity of COVID-19. Besides, the mutations in the genome of SARS-CoV-2 __leading to emerging of new variants__ per se affect the affinity of the virus to the host cells and enhance the immune escape capacity. The current review discusses these variants and also the latest data about vaccination effectiveness facing the most important variants.
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Affiliation(s)
- Mahda Delshad
- Department of Laboratory Sciences, School of Allied Medical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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17
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Bhat S, Rishi P, Chadha VD. Understanding the epigenetic mechanisms in SARS CoV-2 infection and potential therapeutic approaches. Virus Res 2022; 318:198853. [PMID: 35777502 PMCID: PMC9236910 DOI: 10.1016/j.virusres.2022.198853] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/14/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
Abstract
COVID-19 pandemic caused by the Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) has inflicted a global health challenge. Although the overwhelming escalation of mortality seen during the initial phase of the pandemic has reduced, emerging variants of SARS-CoV-2 continue to impact communities worldwide. Several studies have highlighted the association of gene specific epigenetic modifications in host cells with the pathogenesis and severity of the disease. Therefore, alongside the investigations into the virology and pathogenesis of SARS-CoV-2 infection, understanding the epigenetic mechanisms related to the disease is crucial for the rational design of effective targeted therapies. Here, we discuss the interaction of SARS-CoV-2 with the various epigenetic regulators and their subsequent contribution to the risk of disease severity and dysfunctional immune responses. Finally, we also highlight the use of epigenetically targeted drugs for the potential therapeutic interventions capable of eliminating viral infection and/or build effective immunity against it.
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Affiliation(s)
- Swati Bhat
- Center for Nuclear Medicine (U.I.E.A.S.T), South Campus, Panjab University, Sector 25, Chandigarh 160014, India.
| | - Praveen Rishi
- Department of Microbiology, South Campus, Panjab University, Sector 25, Chandigarh 160014, India.
| | - Vijayta D Chadha
- Center for Nuclear Medicine (U.I.E.A.S.T), South Campus, Panjab University, Sector 25, Chandigarh 160014, India.
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18
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Padi2/3 Deficiency Alters the Epigenomic Landscape and Causes Premature Differentiation of Mouse Trophoblast Stem Cells. Cells 2022; 11:cells11162466. [PMID: 36010543 PMCID: PMC9406452 DOI: 10.3390/cells11162466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/02/2022] [Accepted: 08/06/2022] [Indexed: 11/17/2022] Open
Abstract
Histone citrullination is a relatively poorly studied epigenetic modification that involves the irreversible conversion of arginine residues into citrulline. It is conferred by a small family of enzymes known as protein arginine deiminases (PADIs). PADI function supports the pluripotent state of embryonic stem cells, but in other contexts, also promotes efficient cellular differentiation. In the current study, we sought to gain deeper insights into the possible roles of PADIs in mouse trophoblast stem cells (TSCs). We show that Padi2 and Padi3 are the most highly expressed PADI family members in TSCs and are rapidly down-regulated upon differentiation. Padi2/3 double knockout (DKO) TSCs express lower levels of stem cell transcription factors CDX2 and SOX2 and are prone to differentiate into extremely large trophoblast giant cells, an effect that may be mediated by centrosome duplication defects. Interestingly, Padi2/3 DKO TSCs display alterations to their epigenomic landscape, with fewer H3K9me3-marked chromocentric foci and globally reduced 5-methylcytosine levels. DNA methylation profiling identifies that this effect is specifically evident at CpG islands of critical trophoblast genes, such as Gata3, Peg3, Socs3 and Hand1. As a consequence of the hypomethylated state, these factors are up-regulated in Padi2/3 DKO TSCs, driving their premature differentiation. Our data uncover a critical epigenetic role for PADI2/3 in safeguarding the stem cell state of TSCs by modulating the DNA methylation landscape to restrict precocious trophoblast differentiation.
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Inal JM, Hristova M, Lange S. A Pilot Study on Peptidylarginine Deiminases and Protein Deimination in Animal Cancers across Vertebrate Species. Int J Mol Sci 2022; 23:ijms23158697. [PMID: 35955829 PMCID: PMC9368843 DOI: 10.3390/ijms23158697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 02/04/2023] Open
Abstract
PADs are a group of calcium-dependent enzymes that play key roles in inflammatory pathologies and have diverse roles in cancers. PADs cause irreversible post-translational modification of arginine to citrulline, leading to changes in protein function in different cellular compartments. PAD isozyme diversity differs throughout phylogeny in chordates, with five PAD isozymes in mammals, three in birds, and one in fish. While the roles for PADs in various human cancers are mounting (both in regards to cancer progression and epigenetic regulation), investigations into animal cancers are scarce. The current pilot-study therefore aimed at assessing PAD isozymes in a range of animal cancers across the phylogeny tree. In addition, the tissue samples were assessed for total protein deimination and histone H3 deimination (CitH3), which is strongly associated with human cancers and also indicative of gene regulatory changes and neutrophil extracellular trap formation (NETosis). Cancers were selected from a range of vertebrate species: horse, cow, reindeer, sheep, pig, dog, cat, rabbit, mink, hamster, parrot, and duck. The cancers chosen included lymphoma, kidney, lung, testicular, neuroendocrine, anaplastic, papilloma, and granulosa cell tumour. Immunohistochemical analysis revealed that CitH3 was strongly detected in all of the cancers assessed, while pan-deimination detection was overall low. Both PAD2 and PAD3 were the most predominantly expressed PADs across all of the cancers assessed, while PAD1, PAD4, and PAD6 were overall expressed at lower, albeit varying, levels. The findings from this pilot study provide novel insights into PAD-mediated roles in different cancers across a range of vertebrate species and may aid in the understanding of cancer heterogeneity and cancer evolution.
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Affiliation(s)
- Jameel M. Inal
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK
| | - Mariya Hristova
- Perinatal Brain Repair Group, Department of Neonatology, UCL Institute for Women’s Health, London WC1E 6HU, UK
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
- Correspondence: ; Tel.: +44-(0)207-911-5000 (ext. 64832)
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20
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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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21
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Maronek M, Gardlik R. The Citrullination-Neutrophil Extracellular Trap Axis in Chronic Diseases. J Innate Immun 2022; 14:393-417. [PMID: 35263752 PMCID: PMC9485962 DOI: 10.1159/000522331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/25/2022] [Indexed: 11/19/2022] Open
Abstract
Citrullination of proteins is crucial for the formation of neutrophil extracellular traps (NETs) − strands of nuclear DNA expulsed in the extracellular environment along with antimicrobial proteins in order to halt the spread of pathogens. Paradoxically, NETs may be immunogenic and contribute to inflammation. It is known that for the externalization of DNA, a group of enzymes called peptidyl arginine deiminases (PADs) is required. Current research often looks at citrullination, NET formation, PAD overexpression, and extracellular DNA (ecDNA) accumulation in chronic diseases as separate events. In contrast, we propose that citrullination can be viewed as the primary mechanism of autoimmunity, for instance by the formation of anti-citrullinated protein antibodies (ACPAs) but also as a process contributing to chronic inflammation. Therefore, citrullination could be at the center, connecting and impacting multiple inflammatory diseases in which ACPAs, NETs, or ecDNA have already been documented. In this review, we aimed to highlight the importance of citrullination in the etiopathogenesis of a number of chronic diseases and to explore the diagnostic, prognostic, and therapeutic potential of the citrullination-NET axis.
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Affiliation(s)
- Martin Maronek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Roman Gardlik
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
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22
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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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Gaitskell-Phillips G, Martín-Cano FE, Ortiz-Rodríguez JM, Silva-Rodríguez A, da Silva-Álvarez E, Gil MC, Ortega-Ferrusola C, Peña FJ. The seminal plasma proteins Peptidyl arginine deaminase 2, rRNA adenine N (6)-methyltransferase and KIAA0825 are linked to better motility post thaw in stallions. Theriogenology 2022; 177:94-102. [PMID: 34687941 DOI: 10.1016/j.theriogenology.2021.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023]
Abstract
Seminal plasma plays an important role in sperm physiology. Seminal plasma proteins vehiculated in microvesicles, carry RNAs and proteins with a potential role in early embryo development. Additionally, proteins present in seminal plasma participate in redox regulation and energy metabolism. In view of these facts, we hypothesized that differences in protein composition of the seminal plasma among stallions may help to explain differences in freeze-ability seen among them. Three independent ejaculates from 10 different stallions of varying breeds were frozen using standard protocols in our laboratory. Aliquots of the ejaculate were separated and stored at -80 °C until further proteomic analysis. Semen analysis was performed using computer assisted sperm analysis and flow cytometry. Significant differences in proteome composition of seminal plasma were observed in the group of stallions showing better motility post thaw. 3116 proteins were identified, and of these, 34 were differentially expressed in stallions with better motility post thaw, 4 of them were also differentially expressed in stallions with different percentages of linearly motile sperm post thaw and 1 protein, Midasin, was expressed in stallions showing high circular velocity post thaw. Seminal plasma proteins may play a major role in sperm functionality; being vehiculated through extracellular vesicles and participating in sperm physiology. Bioinformatic analysis identifies discriminant proteins able to predict the outcome of cryopreservation, identifying potential new biomarkers to assess ejaculate quality.
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Affiliation(s)
- Gemma Gaitskell-Phillips
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Francisco E Martín-Cano
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - José M Ortiz-Rodríguez
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Antonio Silva-Rodríguez
- Facility of Innovation and Analysis in Animal Source Foodstuffs, University of Extremadura, Cáceres, Spain
| | - Eva da Silva-Álvarez
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Maria C Gil
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Cristina Ortega-Ferrusola
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Fernando J Peña
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain.
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24
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Gutiérrez JR, Salgadoa ARM, Arias MDÁ, Vergara HSJ, Rada WR, Gómez CMM. Epigenetic Modulators as Treatment Alternative to Diverse Types of Cancer. Curr Med Chem 2021; 29:1503-1542. [PMID: 34963430 DOI: 10.2174/0929867329666211228111036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/17/2021] [Accepted: 10/21/2021] [Indexed: 01/10/2023]
Abstract
DNA is packaged in rolls in an octamer of histones forming a complex of DNA and proteins called chromatin. Chromatin as a structural matrix of a chromosome and its modifications are nowadays considered relevant aspects for regulating gene expression, which has become of high interest in understanding genetic mechanisms regulating various diseases, including cancer. In various types of cancer, the main modifications are found to be DNA methylation in the CpG dinucleotide as a silencing mechanism in transcription, post-translational histone modifications such as acetylation, methylation and others that affect the chromatin structure, the ATP-dependent chromatin remodeling and miRNA-mediated gene silencing. In this review we analyze the main alterations in gene expression, the epigenetic modification patterns that cancer cells present, as well as the main modulators and inhibitors of each epigenetic mechanism and the molecular evolution of the most representative inhibitors, which have opened a promising future in the study of HAT, HDAC, non-glycoside DNMT inhibitors and domain inhibitors.
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Affiliation(s)
- Jorseth Rodelo Gutiérrez
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
| | - Arturo René Mendoza Salgadoa
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
| | - Marcio De Ávila Arias
- Department of Medicine, Biotechnology Research Group, Health Sciences Division, Universidad del Norte, Barranquilla, Colombia
| | - Homero San- Juan- Vergara
- Department of Medicine, Biotechnology Research Group, Health Sciences Division, Universidad del Norte, Barranquilla, Colombia
| | - Wendy Rosales Rada
- Advanced Biomedicine Research Group. Faculty of Exact and Natural Sciences, Universidad Libre Seccional, Barranquilla, Colombia
- Advanced Biomedicine Research Group. Faculty of Exact and Natural Sciences, Universidad Libre Seccional, Barranquilla, Colombia
| | - Carlos Mario Meléndez Gómez
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
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25
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Behera S, Reddy RR, Taunk K, Rapole S, Pharande RR, Suryawanshi AR. Delineation of altered brain proteins associated with furious rabies virus infection in dogs by quantitative proteomics. J Proteomics 2021; 253:104463. [PMID: 34954397 DOI: 10.1016/j.jprot.2021.104463] [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: 09/17/2021] [Revised: 12/02/2021] [Accepted: 12/19/2021] [Indexed: 11/24/2022]
Abstract
Rabies is a fatal zoonotic disease caused by rabies virus (RABV). Despite the existence of control measures, dog-transmitted human rabies accounts for ˃95% reported cases due to unavailability of sensitive diagnostic methods, inadequate understanding of disease progression and absence of therapeutics. In addition, host factors and their role in RABV infection are poorly understood. In this study, we used 8-plex iTRAQ coupled with HRMS approach to identify differentially abundant proteins (DAPs) of dog brain associated with furious rabies virus infection. Total 40 DAPs including 26 down-regulated and 14 up-regulated proteins were statistically significant in infected samples. GO annotation and IPA showed that calcium signaling and calcium transport, efficient neuronal function, metabolic pathway associated proteins were mostly altered during this infection. Total 34 proteins including 10 down-regulated proteins pertaining to calcium signaling and calcium transport pathways were successfully verified by qRT-PCR and two proteins were verified by western blot, thereby suggesting these pathways may play an important role in this infection. This study provides the map of altered brain proteins and some insights into the molecular pathophysiology associated with furious rabies virus infection. However, further investigations are required to understand their role in disease mechanism. SIGNIFICANCE: Transmission of rabies by dogs poses the greatest hazard world-wide and the rare survival of post-symptomatic patients as well as severe neurological and immunological problems pose a question to understand the molecular mechanism involved in rabies pathogenesis. However, information regarding host factors and their function in RABV infection is still inadequate. Our study has used an advanced quantitative proteomics approach i.e. 8-plex iTRAQ coupled with HRMS and identified 40 DAPs in furious rabies infected dog brain tissues compared to the controls. Further analysis showed that calcium signaling and transport pathway, efficient neuronal functions and metabolic pathway associated brain proteins were most altered during furious rabies virus infection. This data provides a map of altered brain proteins which may have role in furious rabies virus infection. Hence, this will improve our understanding of the molecular pathogenesis of RABV infection.
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Affiliation(s)
- Suchismita Behera
- Clinical Proteomics, Institute of Life Sciences, Bhubaneswar, Odisha, India; Regional Centre for Biotechnology, Faridabad, India
| | - R Rajendra Reddy
- Clinical Proteomics, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Pune, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Pune, India
| | | | - Amol Ratnakar Suryawanshi
- Clinical Proteomics, Institute of Life Sciences, Bhubaneswar, Odisha, India; Regional Centre for Biotechnology, Faridabad, India.
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26
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Mao L, Mostafa R, Ibili E, Fert-Bober J. Role of protein deimination in cardiovascular diseases: potential new avenues for diagnostic and prognostic biomarkers. Expert Rev Proteomics 2021; 18:1059-1071. [PMID: 34929115 DOI: 10.1080/14789450.2021.2018303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Arginine deimination (citrullination) is a post-translational modification catalyzed by a family of peptidyl arginine deiminase (PAD) enzymes. Cell-based functional studies and animal models have manifested the key role of PADs in various cardiovascular diseases (CVDs). AREA COVERED This review summarizes the latest developments in the role of PADs in CVD pathogenesis. It focuses on the PAD functions and diverse citrullinated proteins in cardiovascular conditions like deep vein thrombosis, ischemia/reperfusion, and atherosclerosis. Identification of PAD isoforms and citrullinated targets are essential for directing diagnosis and clinical intervention. Finally, anti-citrullinated protein antibodies (ACPAs) are addressed as an independent risk factor for cardiovascular events. A search of PubMed biomedical literature from the past ten years was performed with a combination of the following keywords: PAD/PADI, deimination/citrullination, autoimmune, fibrosis, NET, neutrophil, macrophage, inflammation, inflammasome, cardiovascular, heart disease, myocardial infarction, ischemia, atherosclerosis, thrombosis, and aging. Additional papers from retrieved articles were also considered. EXPERT OPINION PADs are unique family of enzymes that converts peptidyl-arginine to -citrulline in protein permanently. Overexpression or increased activity of PAD has been observed in various CVDs with acute and chronic inflammation as the background. Importantly, far beyond being simply involved in forming neutrophil extracellular traps (NETs), accumulating evidence indicated PAD activation as a trigger for numerous processes, such as transcriptional regulation, endothelial dysfunction, and thrombus formation. In summary, the findings so far have testified the important role of deimination in cardiovascular biology, while more basic and translational studies are essential to further exploration.
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Affiliation(s)
- Liqun Mao
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Rowann Mostafa
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Esra Ibili
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Justyna Fert-Bober
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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27
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Arginine and Arginases Modulate Metabolism, Tumor Microenvironment and Prostate Cancer Progression. Nutrients 2021; 13:nu13124503. [PMID: 34960055 PMCID: PMC8704013 DOI: 10.3390/nu13124503] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/05/2021] [Accepted: 12/11/2021] [Indexed: 12/30/2022] Open
Abstract
Arginine availability and activation of arginine-related pathways at cancer sites have profound effects on the tumor microenvironment, far beyond their well-known role in the hepatic urea cycle. Arginine metabolism impacts not only malignant cells but also the surrounding immune cells behavior, modulating growth, survival, and immunosurveillance mechanisms, either through an arginase-mediated effect on polyamines and proline synthesis, or by the arginine/nitric oxide pathway in tumor cells, antitumor T-cells, myeloid-derived suppressor cells, and macrophages. This review presents evidence concerning the impact of arginine metabolism and arginase activity in the prostate cancer microenvironment, highlighting the recent advances in immunotherapy, which might be relevant for prostate cancer. Even though further research is required, arginine deprivation may represent a novel antimetabolite strategy for the treatment of arginine-dependent prostate cancer.
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28
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Rast JP, D'Alessio S, Kraev I, Lange S. Post-translational protein deimination signatures in sea lamprey (Petromyzon marinus) plasma and plasma-extracellular vesicles. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 125:104225. [PMID: 34358577 DOI: 10.1016/j.dci.2021.104225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Lampreys are a jawless vertebrate species belonging to an ancient vertebrate lineage that diverged from a common ancestor with humans ~500 million years ago. The sea lamprey (Petromyzon marinus) has a filter feeding ammocoete larval stage that metamorphoses into a parasitic adult, feeding both on teleost and elasmobranch fish. Lampreys are a valuable comparative model species for vertebrate immunity and physiology due to their unique phylogenetic position, unusual adaptive immune system, and physiological adaptions such as tolerance to salinity changes and urea. Peptidylarginine deiminases (PADs) are a phylogenetically conserved enzyme family which catalyses post-translational deimination/citrullination in target proteins, enabling proteins to gain new functions (moonlighting). The identification of deiminated protein targets in species across phylogeny may provide novel insights into post-translational regulation of physiological and pathophysiological processes. Extracellular vesicles (EVs) are membrane vesicles released from cells that carry cargos of small molecules and proteins for cellular communication, involved in both normal and pathological processes. The current study identified deimination signatures in proteins of both total plasma and plasma-EVs in sea lamprey and furthermore reports the first characterisation of plasma-EVs in lamprey. EVs were poly-dispersed in the size range of 40-500 nm, similar to what is observed in other taxa, positive for CD63 and Flotillin-1. Plasma-EV morphology was confirmed by transmission electron microscopy. Assessment of deimination/citrullination signatures in lamprey plasma and plasma-EVs, revealed 72 deimination target proteins involved in immunity, metabolism and gene regulation in whole plasma, and 37 target proteins in EVs, whereof 24 were shared targets. Furthermore, the presence of deiminated histone H3, indicative of gene-regulatory mechanisms and also a marker of neutrophil extracellular trap formation (NETosis), was confirmed in lamprey plasma. Functional protein network analysis revealed some differences in KEGG and GO pathways of deiminated proteins in whole plasma compared with plasma-EVs. For example, while common STRING network clusters in plasma and plasma-EVs included Peptide chain elongation, Viral mRNA translation, Glycolysis and gluconeogenesis, STRING network clusters specific for EVs only included: Cellular response to heat stress, Muscle protein and striated muscle thin filament, Nucleosome, Protein processing in endoplasmic reticulum, Nucleosome and histone deacetylase complex. STRING network clusters specific for plasma were: Adipokinetic hormone receptor activity, Fibrinogen alpha/beta chain family, peptidase S1A, Glutathione synthesis and recycling-arginine, Fructose 1,6-bisphosphate metabolic process, Carbon metabolism and lactate dehydrogenase activity, Post-translational protein phosphorylation, Regulation of insulin-like growth factor transport and clotting cascade. Overall, for the EV citrullinome, five STRING network clusters, 10 KEGG pathways, 15 molecular GO pathways and 29 Reactome pathways were identified, compared with nine STRING network clusters, six KEGG pathways, two Molecular GO pathways and one Reactome pathway specific for whole plasma; while further pathways were shared. The reported findings indicate that major pathways relevant for immunity and metabolism are targets of deimination in lamprey plasma and plasma-EVs, with some differences, and may help elucidating roles for the conserved PAD enzyme family in regulation of immune and metabolic function throughout phylogeny.
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Affiliation(s)
- Jonathan P Rast
- Emory University School of Medicine, Pathology & Laboratory Medicine, Atlanta, GA, 30322, USA.
| | - Stefania D'Alessio
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
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29
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Sperling LC, Darling TN. Central centrifugal cicatricial alopecia: A common but under-recognized and under-treated disease finally comes of age. J Cutan Pathol 2021; 49:204-206. [PMID: 34743373 DOI: 10.1111/cup.14164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/19/2021] [Accepted: 10/31/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Leonard C Sperling
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.,Dermatology Service, Walter Reed National Military Medical Center, Bethesda, Maryland, USA.,Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Thomas N Darling
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.,Dermatology Service, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
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30
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D’Alessio S, Buckley KM, Kraev I, Hayes P, Lange S. Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin ( Strongylocentrotus purpuratus) Coelomic Fluid-Novel Insights into Echinodermata Biology. BIOLOGY 2021; 10:866. [PMID: 34571743 PMCID: PMC8464700 DOI: 10.3390/biology10090866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
The purple sea urchin (Strongylocentrotus purpuratus) is a marine invertebrate of the class Echinoidea that serves as an important research model for developmental biology, cell biology, and immunology, as well as for understanding regenerative responses and ageing. Peptidylarginine deiminases (PADs) are calcium-dependent enzymes that mediate post-translational protein deimination/citrullination. These alterations affect protein function and may also play roles in protein moonlighting. Extracellular vesicles (EVs) are membrane-bound vesicles that are released from cells as a means of cellular communication. Their cargo includes a range of protein and RNA molecules. EVs can be isolated from many body fluids and are therefore used as biomarkers in physiological and pathological responses. This study assessed EVs present in the coelomic fluid of the purple sea urchin (Strongylocentrotus purpuratus), and identified both total protein cargo as well as the deiminated protein cargo. Deiminated proteins in coelomic fluid EVs were compared with the total deiminated proteins identified in coelomic fluid to assess putative differences in deiminated protein targets. Functional protein network analysis for deiminated proteins revealed pathways for immune, metabolic, and gene regulatory functions within both total coelomic fluid and EVs. Key KEGG and GO pathways for total EV protein cargo furthermore showed some overlap with deimination-enriched pathways. The findings presented in this study add to current understanding of how post-translational deimination may shape immunity across the phylogeny tree, including possibly via PAD activity from microbiota symbionts. Furthermore, this study provides a platform for research on EVs as biomarkers in sea urchin models.
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Affiliation(s)
- Stefania D’Alessio
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
| | | | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Polly Hayes
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
- UCL EGA Institute for Women’s Health, Maternal and Fetal Medicine, London WC1E 6AU, UK
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31
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Metabolic enzymes function as epigenetic modulators: A Trojan Horse for chromatin regulation and gene expression. Pharmacol Res 2021; 173:105834. [PMID: 34450321 DOI: 10.1016/j.phrs.2021.105834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 02/08/2023]
Abstract
Epigenetic modification is a fundamental biological process in living organisms, which has significant impact on health and behavior. Metabolism refers to a set of life-sustaining chemical reactions, including the uptake of nutrients, the subsequent conversion of nutrients into energy or building blocks for organism growth, and finally the clearance of redundant or toxic substances. It is well established that epigenetic modifications govern the metabolic profile of a cell by modulating the expression of metabolic enzymes. Strikingly, almost all the epigenetic modifications require substrates produced by cellular metabolism, and a large proportion of metabolic enzymes can transfer into nucleus to locally produce substrates for epigenetic modification, thereby providing an alternative link between metabolism, epigenetic modification and gene expression. Here, we summarize the recent literature pertinent to metabolic enzymes functioning as epigenetic modulators in the regulation of chromatin architecture and gene expression.
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32
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Guzmán-Guzmán IP, Ramírez-Vélez CI, Falfán-Valencia R, Navarro-Zarza JE, Gutiérrez-Pérez IA, Zaragoza-García O, Ramírez M, Castro-Alarcón N, Parra-Rojas I. PADI2 Polymorphisms Are Significantly Associated With Rheumatoid Arthritis, Autoantibodies Serologic Status and Joint Damage in Women from Southern Mexico. Front Immunol 2021; 12:718246. [PMID: 34421923 PMCID: PMC8371707 DOI: 10.3389/fimmu.2021.718246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The enzymes of the family peptidylarginine deiminases (PADs) have an important role in the pathogenesis of rheumatoid arthritis (RA) due to their association with the anti-citrullinated protein antibodies (ACPA) production. To evaluate the association between single-nucleotide polymorphisms (SNPs) in the PADI2 gene and RA susceptibility, related clinical parameters, and the serologic status of autoantibodies in a women population with RA from southern Mexico, a case-control study was conducted (case n=229; control n=333). Sociodemographic characteristics were evaluated, along with clinical parameters, inflammation markers, the levels of ACPAs as anti-cyclic citrullinated peptides (anti-CCPs), anti-modified citrullinated vimentin (anti-MCV), and rheumatoid factor (RF). Genomic DNA was extracted from peripheral blood, and three SNPs of the PADI2 gene (rs1005753, rs2057094, and rs2235926) were performed by qPCR using TaqMan probes. The data analysis reveals that the carriers of the T allele for rs2057094 and rs2235926 presented an earlier onset of the disease (β= -3.26; p = 0.03 and β = -4.13; p = 0.015, respectively) while the carriers of the T allele for rs1005753 presented higher levels of anti-CCPs (β= 68.3; p = 0.015). Additionally, the T allele of rs2235926 was associated with a positive RF (OR = 2.90; p = 0.04), anti-MCV (OR = 2.92; p = 0.05), and with the serologic status anti-CCP+/anti-MCV+ (OR = 3.02; p = 0.03), and anti-CCP+/anti-MCV+/RF+ (OR = 3.79; p = 0.004). The haplotypes GTT (OR =1.52; p = 0.027) and TTT (OR = 1.32; p = 0.025) were associated with the presence of RA. In addition, in this study the haplotype TTT is linked to the presence of radiographic joint damage defined by a Sharp-van der Heijde score (SHS) ≥2 (OR = 1.97; p = 0.0021) and SHS ≥3 (OR = 1.94; p = 0.011). The haplotype TTT of SNPs rs1005753, rs2057094, and rs2235926 of the PADI2 gene confers genetic susceptibility to RA and radiographic joint damage in women from southern Mexico. The evidence reveals that SNPs of the PADI2 gene favors the presence of a positive serologic status in multiple autoantibodies and the clinical manifestations of RA at an early onset age.
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Affiliation(s)
| | | | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - José Eduardo Navarro-Zarza
- Department of Rheumatology and Internal Medicine, Hospital General de Chilpancingo Dr. Raymundo Abarca Alarcón, Guerrero, Mexico
| | | | - Oscar Zaragoza-García
- Faculty of Chemical-Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Mónica Ramírez
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | | | - Isela Parra-Rojas
- Faculty of Chemical-Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
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33
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Shirvaliloo M. Epigenomics in COVID-19; the link between DNA methylation, histone modifications and SARS-CoV-2 infection. Epigenomics 2021; 13:745-750. [PMID: 33876664 PMCID: PMC8074570 DOI: 10.2217/epi-2021-0057] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/31/2021] [Indexed: 01/23/2023] Open
Affiliation(s)
- Milad Shirvaliloo
- Student Research Committee, Tabriz University of Medical Sciences, 5166 Tabriz, Iran
- Faculty of Medicine, Tabriz University of Medical Sciences, 15731 Tabriz, Iran
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34
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Mohanty V, Subbannayya Y, Patil S, Puttamallesh VN, Najar MA, Datta KK, Pinto SM, Begum S, Mohanty N, Routray S, Abdulla R, Ray JG, Sidransky D, Gowda H, Prasad TSK, Chatterjee A. Molecular alterations in oral cancer using high-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue. J Cell Commun Signal 2021; 15:447-459. [PMID: 33683571 DOI: 10.1007/s12079-021-00609-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 01/04/2023] Open
Abstract
Loss of cell differentiation is a hallmark for the progression of oral squamous cell carcinoma (OSCC). Archival Formalin-Fixed Paraffin-Embedded (FFPE) tissues constitute a valuable resource for studying the differentiation of OSCC and can offer valuable insights into the process of tumor progression. In the current study, we performed LC-MS/MS-based quantitative proteomics of FFPE specimens from pathologically-confirmed well-differentiated, moderately-differentiated, and poorly-differentiated OSCC cases. The data were analyzed in four technical replicates, resulting in the identification of 2376 proteins. Of these, 141 and 109 were differentially expressed in moderately-differentiated and poorly differentiated OSCC cases, respectively, compared to well-differentiated OSCC. The data revealed significant metabolic reprogramming with respect to lipid metabolism and glycolysis with proteins belonging to both these processes downregulated in moderately-differentiated OSCC when compared to well-differentiated OSCC. Signaling pathway analysis indicated the alteration of extracellular matrix organization, muscle contraction, and glucose metabolism pathways across tumor grades. The extracellular matrix organization pathway was upregulated in moderately-differentiated OSCC and downregulated in poorly differentiated OSCC, compared to well-differentiated OSCC. PADI4, an epigenetic enzyme transcriptional regulator, and its transcriptional target HIST1H1B were both found to be upregulated in moderately differentiated and poorly differentiated OSCC, indicating epigenetic events underlying tumor differentiation. In conclusion, the findings support the advantage of using high-resolution mass spectrometry-based FFPE archival blocks for clinical and translational research. The candidate signaling pathways identified in the study could be used to develop potential therapeutic targets for OSCC.
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Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Shankargouda Patil
- Division of Oral Pathology, College of Dentistry, Department of Maxillofacial Surgery and Diagnostic Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Keshava K Datta
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Sameera Begum
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Neeta Mohanty
- Department of Oral Pathology & Microbiology, Institute of Dental Sciences, Siksha'O'Anusandhan University, Bhubaneswar, Odisha, 751003, India
| | - Samapika Routray
- Department of Oral Pathology & Microbiology, Institute of Dental Sciences, Siksha'O'Anusandhan University, Bhubaneswar, Odisha, 751003, India.,Department of Dental Surgery, All India Institute of Medical Sciences, Bhubaneswar, Odisha, 751019, India
| | - Riaz Abdulla
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India
| | - Jay Gopal Ray
- Department of Oral Pathology, Dr. R. Ahmed Dental College & Hospital, Kolkata, West Bengal, 700 014, India.,Department of Pathology, Burdwan Dental College and Hospital, Burdwan, West Bengal, 713101, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, 21231, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India.
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed To Be University), Mangalore, Karnataka, 575018, India. .,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India. .,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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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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Marondedze C, Elia G, Thomas L, Wong A, Gehring C. Citrullination of Proteins as a Specific Response Mechanism in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:638392. [PMID: 33897727 PMCID: PMC8060559 DOI: 10.3389/fpls.2021.638392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/17/2021] [Indexed: 05/19/2023]
Abstract
Arginine deimination, also referred to as citrullination of proteins by L-arginine deiminases, is a post-translational modification affecting histone modifications, epigenetic transcriptional regulation, and proteolysis in animals but has not been reported in higher plants. Here we report, firstly, that Arabidopsis thaliana proteome contains proteins with a specific citrullination signature and that many of the citrullinated proteins have nucleotide-binding regulatory functions. Secondly, we show that changes in the citrullinome occur in response to cold stress, and thirdly, we identify an A. thaliana protein with peptidyl arginine deiminase activity that was shown to be calcium-dependent for many peptide substrates. Taken together, these findings establish this post-translational modification as a hitherto neglected component of cellular reprogramming during stress responses.
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Affiliation(s)
- Claudius Marondedze
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Rijk Zwaan, De Lier, Netherlands
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Gweru, Zimbabwe
- Claudius Marondedze,
| | - Giuliano Elia
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Ludivine Thomas
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center of Wenzhou-Kean University, Wenzhou, China
| | - Chris Gehring
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
- *Correspondence: Chris Gehring,
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37
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Bowden TJ, Kraev I, Lange S. Extracellular Vesicles and Post-Translational Protein Deimination Signatures in Mollusca-The Blue Mussel ( Mytilus edulis), Soft Shell Clam ( Mya arenaria), Eastern Oyster ( Crassostrea virginica) and Atlantic Jacknife Clam ( Ensis leei). BIOLOGY 2020; 9:biology9120416. [PMID: 33255637 PMCID: PMC7760292 DOI: 10.3390/biology9120416] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022]
Abstract
Simple Summary Oysters and clams form an important component of the food chain and food security and are of considerable commercial value worldwide. They are affected by pollution and climate change, as well as a range of infections, some of which are opportunistic. For aquaculture purposes they are furthermore of great commercial value and changes in their immune responses can also serve as indicators of changes in ocean environments. Therefore, studies into understanding new factors in their immune systems may aid new biomarker discovery and are of considerable value. This study assessed new biomarkers relating to changes in protein function in four economically important marine molluscs, the blue mussel, soft shell clam, Eastern oyster, and Atlantic jacknife clam. These findings indicate novel regulatory mechanisms of important metabolic and immunology related pathways in these mollusks. The findings provide new understanding to how these pathways function in diverse ways in different animal species as well as aiding new biomarker discovery for Mollusca aquaculture. Abstract Oysters and clams are important for food security and of commercial value worldwide. They are affected by anthropogenic changes and opportunistic pathogens and can be indicators of changes in ocean environments. Therefore, studies into biomarker discovery are of considerable value. This study aimed at assessing extracellular vesicle (EV) signatures and post-translational protein deimination profiles of hemolymph from four commercially valuable Mollusca species, the blue mussel (Mytilus edulis), soft shell clam (Mya arenaria), Eastern oyster (Crassostrea virginica), and Atlantic jacknife clam (Ensis leei). EVs form part of cellular communication by transporting protein and genetic cargo and play roles in immunity and host–pathogen interactions. Protein deimination is a post-translational modification caused by peptidylarginine deiminases (PADs), and can facilitate protein moonlighting in health and disease. The current study identified hemolymph-EV profiles in the four Mollusca species, revealing some species differences. Deiminated protein candidates differed in hemolymph between the species, with some common targets between all four species (e.g., histone H3 and H4, actin, and GAPDH), while other hits were species-specific; in blue mussel these included heavy metal binding protein, heat shock proteins 60 and 90, 2-phospho-D-glycerate hydrolyase, GTP cyclohydrolase feedback regulatory protein, sodium/potassium-transporting ATPase, and fibrinogen domain containing protein. In soft shell clam specific deimination hits included dynein, MCM3-associated protein, and SCRN. In Eastern oyster specific deimination hits included muscle LIM protein, beta-1,3-glucan-binding protein, myosin heavy chain, thaumatin-like protein, vWFA domain-containing protein, BTB domain-containing protein, amylase, and beta-catenin. Deiminated proteins specific to Atlantic jackknife clam included nacre c1q domain-containing protein and PDZ domain-containing protein In addition, some proteins were common as deiminated targets between two or three of the Bivalvia species under study (e.g., EP protein, C1q domain containing protein, histone H2B, tubulin, elongation factor 1-alpha, dominin, extracellular superoxide dismutase). Protein interaction network analysis for the deiminated protein hits revealed major pathways relevant for immunity and metabolism, providing novel insights into post-translational regulation via deimination. The study contributes to EV characterization in diverse taxa and understanding of roles for PAD-mediated regulation of immune and metabolic pathways throughout phylogeny.
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Affiliation(s)
- Timothy J. Bowden
- Aquaculture Research Institute, School of Food & Agriculture, University of Maine, Orono, ME 04469-5735, USA;
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
- Correspondence: ; Tel.: +44-(0)207-911-5000
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38
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Bowden TJ, Kraev I, Lange S. Extracellular vesicles and post-translational protein deimination signatures in haemolymph of the American lobster (Homarus americanus). FISH & SHELLFISH IMMUNOLOGY 2020; 106:79-102. [PMID: 32731012 DOI: 10.1016/j.fsi.2020.06.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
The American lobster (Homarus americanus) is a commercially important crustacean with an unusual long life span up to 100 years and a comparative animal model of longevity. Therefore, research into its immune system and physiology is of considerable importance both for industry and comparative immunology studies. Peptidylarginine deiminases (PADs) are a phylogenetically conserved enzyme family that catalyses post-translational protein deimination via the conversion of arginine to citrulline. This can lead to structural and functional protein changes, sometimes contributing to protein moonlighting, in health and disease. PADs also regulate the cellular release of extracellular vesicles (EVs), which is an important part of cellular communication, both in normal physiology and in immune responses. Hitherto, studies on EVs in Crustacea are limited and neither PADs nor associated protein deimination have been studied in a Crustacean species. The current study assessed EV and deimination signatures in haemolymph of the American lobster. Lobster EVs were found to be a poly-dispersed population in the 10-500 nm size range, with the majority of smaller EVs, which fell within 22-115 nm. In lobster haemolymph, 9 key immune and metabolic proteins were identified to be post-translationally deiminated, while further 41 deiminated protein hits were identified when searching against a Crustacean database. KEGG (Kyoto encyclopedia of genes and genomes) and GO (gene ontology) enrichment analysis of these deiminated proteins revealed KEGG and GO pathways relating to a number of immune, including anti-pathogenic (viral, bacterial, fungal) and host-pathogen interactions, as well as metabolic pathways, regulation of vesicle and exosome release, mitochondrial function, ATP generation, gene regulation, telomerase homeostasis and developmental processes. The characterisation of EVs, and post-translational deimination signatures, reported in lobster in the current study, and the first time in Crustacea, provides insights into protein moonlighting functions of both species-specific and phylogenetically conserved proteins and EV-mediated communication in this long-lived crustacean. The current study furthermore lays foundation for novel biomarker discovery for lobster aquaculture.
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Affiliation(s)
- Timothy J Bowden
- Aquaculture Research Institute, School of Food & Agriculture, University of Maine, Orono, ME, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science,Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
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39
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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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40
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Yu HC, Tung CH, Huang KY, Huang HB, Lu MC. The Essential Role of Peptidylarginine Deiminases 2 for Cytokines Secretion, Apoptosis, and Cell Adhesion in Macrophage. Int J Mol Sci 2020; 21:ijms21165720. [PMID: 32785008 PMCID: PMC7460808 DOI: 10.3390/ijms21165720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/13/2022] Open
Abstract
Objective: The study aims to investigate the functional roles of peptidylarginine deiminase 2 (PADI2) in macrophages. Methods: The clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein-9 nuclease (Cas9) system was used to knockout PADI2 in U937 cells. U937 cells were introduced to differentiate macrophages and were stimulated with lipopolysaccharides (LPS). The protein expression of PADI2, PADI4, and citrullinated proteins were analyzed by Western blotting. The mRNA and protein levels of interleukin 1 beta (IL-1β), IL-6, and tumor necrosis factor-alpha (TNF-α) were analyzed using RT-PCR and ELISA, respectively. Cell apoptosis was analyzed using flow cytometry. Cell adhesion assay was performed using a commercially available fibrinogen-coated plate. Results: PADI2 knockout could markedly suppress the PADI2 protein expression, but not the PADI4 protein expression. PADI2 knockout decreased the protein levels of citrullinated nuclear factor κB (NF-κB) p65, but not those of citrullinated histone 3, resulting in the decreased mRNA expression levels of IL-1β and TNF-α in the U937 cells and IL-1β and IL-6 in the differentiated macrophages and the macrophages stimulated with LPS. The cytokines levels of IL-1β, IL-6, and TNF-α were all dramatically decreased in the PADI2 knockout group compared with in the controls. PADI2 knockout prevented macrophages apoptosis via the decreased caspase-3, caspase-2, and caspase-9 activation. PADI2 knockout also impaired macrophages adhesion capacity through the decreased protein levels of focal adhesion kinase (FAK), phospho-FAK, paxillin, phospho-paxillin, and p21-activated kinase 1. Conclusion: This study showed that PADI2 could promote IL-1β, IL-6, and TNF-α production in macrophages, promote macrophage apoptosis through caspase-3, caspase-2, and caspase-9 activation and enhance cell adhesion via FAK, paxillin, and PAK1. Therefore, targeting PADI2 could be used as a novel strategy for controlling inflammation caused by macrophages.
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Affiliation(s)
- Hui-Chun Yu
- Division of Allergy, Immunology and Rheumatology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Dalin, Chiayi 62130, Taiwan; (H.-C.Y.); (C.-H.T.); (K.-Y.H.)
| | - Chien-Hsueh Tung
- Division of Allergy, Immunology and Rheumatology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Dalin, Chiayi 62130, Taiwan; (H.-C.Y.); (C.-H.T.); (K.-Y.H.)
- School of Medicine, Tzu Chi University, Hualien City 97071, Taiwan
| | - Kuang-Yung Huang
- Division of Allergy, Immunology and Rheumatology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Dalin, Chiayi 62130, Taiwan; (H.-C.Y.); (C.-H.T.); (K.-Y.H.)
- School of Medicine, Tzu Chi University, Hualien City 97071, Taiwan
| | - Hsien-Bin Huang
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Minxiong, Chiayi 62130, Taiwan;
| | - Ming-Chi Lu
- Division of Allergy, Immunology and Rheumatology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Dalin, Chiayi 62130, Taiwan; (H.-C.Y.); (C.-H.T.); (K.-Y.H.)
- School of Medicine, Tzu Chi University, Hualien City 97071, Taiwan
- Correspondence: ; Tel.: +886-5-2648000 (ext. 3205); Fax: +886-5-2648006
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41
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Criscitiello MF, Kraev I, Lange S. Post-Translational Protein Deimination Signatures in Serum and Serum-Extracellular Vesicles of Bos taurus Reveal Immune, Anti-Pathogenic, Anti-Viral, Metabolic and Cancer-Related Pathways for Deimination. Int J Mol Sci 2020; 21:E2861. [PMID: 32325910 PMCID: PMC7215346 DOI: 10.3390/ijms21082861] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
The bovine immune system is known for its unusual traits relating to immunoglobulin and antiviral responses. Peptidylarginine deiminases (PADs) are phylogenetically conserved enzymes that cause post-translational deimination, contributing to protein moonlighting in health and disease. PADs also regulate extracellular vesicle (EV) release, forming a critical part of cellular communication. As PAD-mediated mechanisms in bovine immunology and physiology remain to be investigated, this study profiled deimination signatures in serum and serum-EVs in Bos taurus. Bos EVs were poly-dispersed in a 70-500 nm size range and showed differences in deiminated protein cargo, compared with whole sera. Key immune, metabolic and gene regulatory proteins were identified to be post-translationally deiminated with some overlapping hits in sera and EVs (e.g., immunoglobulins), while some were unique to either serum or serum-EVs (e.g., histones). Protein-protein interaction network analysis of deiminated proteins revealed KEGG pathways common for serum and serum-EVs, including complement and coagulation cascades, viral infection (enveloped viruses), viral myocarditis, bacterial and parasitic infections, autoimmune disease, immunodeficiency intestinal IgA production, B-cell receptor signalling, natural killer cell mediated cytotoxicity, platelet activation and hematopoiesis, alongside metabolic pathways including ferroptosis, vitamin digestion and absorption, cholesterol metabolism and mineral absorption. KEGG pathways specific to EVs related to HIF-1 signalling, oestrogen signalling and biosynthesis of amino acids. KEGG pathways specific for serum only, related to Epstein-Barr virus infection, transcription mis-regulation in cancer, bladder cancer, Rap1 signalling pathway, calcium signalling pathway and ECM-receptor interaction. This indicates differences in physiological and pathological pathways for deiminated proteins in serum-EVs, compared with serum. Our findings may shed light on pathways underlying a number of pathological and anti-pathogenic (viral, bacterial, parasitic) pathways, with putative translatable value to human pathologies, zoonotic diseases and development of therapies for infections, including anti-viral therapies.
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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 77843, USA;
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843, USA
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6XH, UK
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