1
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Ning J, Sala M, Reina J, Kalagiri R, Hunter T, McCullough BS. Histidine Phosphorylation: Protein Kinases and Phosphatases. Int J Mol Sci 2024; 25:7975. [PMID: 39063217 PMCID: PMC11277029 DOI: 10.3390/ijms25147975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Phosphohistidine (pHis) is a reversible protein post-translational modification (PTM) that is currently poorly understood. The P-N bond in pHis is heat and acid-sensitive, making it more challenging to study than the canonical phosphoamino acids pSer, pThr, and pTyr. As advancements in the development of tools to study pHis have been made, the roles of pHis in cells are slowly being revealed. To date, a handful of enzymes responsible for controlling this modification have been identified, including the histidine kinases NME1 and NME2, as well as the phosphohistidine phosphatases PHPT1, LHPP, and PGAM5. These tools have also identified the substrates of these enzymes, granting new insights into previously unknown regulatory mechanisms. Here, we discuss the cellular function of pHis and how it is regulated on known pHis-containing proteins, as well as cellular mechanisms that regulate the activity of the pHis kinases and phosphatases themselves. We further discuss the role of the pHis kinases and phosphatases as potential tumor promoters or suppressors. Finally, we give an overview of various tools and methods currently used to study pHis biology. Given their breadth of functions, unraveling the role of pHis in mammalian systems promises radical new insights into existing and unexplored areas of cell biology.
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Affiliation(s)
- Jia Ning
- Correspondence: (J.N.); (B.S.M.)
| | | | | | | | | | - Brandon S. McCullough
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (M.S.); (J.R.); (R.K.); (T.H.)
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2
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Ren Z, Zhang H, Yu H, Zhu X, Lin J. Roles of four targets in the pathogenesis of graves' orbitopathy. Heliyon 2023; 9:e19250. [PMID: 37810014 PMCID: PMC10558314 DOI: 10.1016/j.heliyon.2023.e19250] [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: 12/20/2022] [Revised: 06/29/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023] Open
Abstract
Graves' orbitopathy (GO) is an autoimmune disease that involves complex immune systems. The mainstays of clinical management for this disease are surgery, targeted drugs therapy, and no-targeted drugs drug therapy. targeted drugs can improve therapeutic efficacy and enhance the quality of life for GO patients. However, as a second-line treatment for GO, targeted drugs such as tocilizumab and rituximab have very limited therapeutic effects and may be accompanied by side effects. The introduction of Teprotumumab, which targets IGF-IR, has made significant progress in the clinical management of GO. The pathophysiology of GO still remains uncertain as it involves a variety of immune cells and fibroblast interactions as well as immune responses to relevant disease targets of action. Therfore, learning more about immune response feedback pathways and potential targets of action will assist in the treatment of GO. In this discussion, we explore the pathogenesis of GO and relevant work, and highlight four potential targets for GO: Interleukin-23 receptor (IL-23 R), Leptin receptor (LepR), Orbital fibroblast activating factors, and Plasminogen activator inhibitor-1 (PAI-1). A deeper understanding of the pathogenesis of GO and the role of potential target signaling pathways is crucial for effective treatment of this disease.
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Affiliation(s)
- Ziqiang Ren
- College of Life Sciences, Yantai University, Shandong, China
- Fengjin Biomedical Co., Ltd, Shandong, China
| | - Hailing Zhang
- College of Life Sciences, Yantai University, Shandong, China
| | - Haiwen Yu
- College of Life Sciences, Yantai University, Shandong, China
| | - Xiqiang Zhu
- Fengjin Biomedical Co., Ltd, Shandong, China
| | - Jian Lin
- College of Life Sciences, Yantai University, Shandong, China
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3
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Beacon TH, Davie JR. Chicken Erythrocyte: Epigenomic Regulation of Gene Activity. Int J Mol Sci 2023; 24:ijms24098287. [PMID: 37175991 PMCID: PMC10179511 DOI: 10.3390/ijms24098287] [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: 02/22/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The chicken genome is one-third the size of the human genome and has a similarity of sixty percent when it comes to gene content. Harboring similar genome sequences, chickens' gene arrangement is closer to the human genomic organization than it is to rodents. Chickens have been used as model organisms to study evolution, epigenome, and diseases. The chicken nucleated erythrocyte's physiological function is to carry oxygen to the tissues and remove carbon dioxide. The erythrocyte also supports the innate immune response in protecting the chicken from pathogens. Among the highly studied aspects in the field of epigenetics are modifications of DNA, histones, and their variants. In understanding the organization of transcriptionally active chromatin, studies on the chicken nucleated erythrocyte have been important. Through the application of a variety of epigenomic approaches, we and others have determined the chromatin structure of expressed/poised genes involved in the physiological functions of the erythrocyte. As the chicken erythrocyte has a nucleus and is readily isolated from the animal, the chicken erythrocyte epigenome has been studied as a biomarker of an animal's long-term exposure to stress. In this review, epigenomic features that allow erythroid gene expression in a highly repressive chromatin background are presented.
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Affiliation(s)
- Tasnim H Beacon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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4
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Yang Q, Chen Y, Guo R, Dai Y, Tang L, Zhao Y, Wu X, Li M, Du F, Shen J, Yi T, Xiao Z, Wen Q. Interaction of ncRNA and Epigenetic Modifications in Gastric Cancer: Focus on Histone Modification. Front Oncol 2022; 11:822745. [PMID: 35155211 PMCID: PMC8826423 DOI: 10.3389/fonc.2021.822745] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 12/28/2021] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer has developed as a very common gastrointestinal tumors, with recent effective advancements in the diagnosis and treatment of early gastric cancer. However, the prognosis for gastric cancer remains poor. As a result, there is in sore need of better understanding the mechanisms of gastric cancer development and progression to improve existing diagnostic and treatment options. In recent years, epigenetics has been recognized as an important contributor on tumor progression. Epigenetic changes in cancer include chromatin remodeling, DNA methylation and histone modifications. An increasing number of studies demonstrated that noncoding RNAs (ncRNAs) are associated with epigenetic changes in gastric cancer. Herein, we describe the molecular interactions of histone modifications and ncRNAs in epigenetics. We focus on ncRNA-mediated histone modifications of gene expression associated with tumorigenesis and progression in gastric cancer. This molecular mechanism will contribute to our deeper understanding of gastric carcinogenesis and progression, thus providing innovations in gastric cancer diagnosis and treatment strategies.
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Affiliation(s)
- Qingfan Yang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yu Chen
- South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, China
| | - Rui Guo
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China
| | - Yalan Dai
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Liyao Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, China
| | - Yueshui Zhao
- South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, China
| | - Xu Wu
- South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, China
| | - Mingxing Li
- South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, China
| | - Fukuan Du
- South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, China
| | - Jing Shen
- South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, China
| | - Tao Yi
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong SAR, China
| | - Zhangang Xiao
- South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
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5
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Tang SY, Zhou PJ, Meng Y, Zeng FR, Deng GT. Gastric cancer: An epigenetic view. World J Gastrointest Oncol 2022; 14:90-109. [PMID: 35116105 PMCID: PMC8790429 DOI: 10.4251/wjgo.v14.i1.90] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/17/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) poses a serious threat worldwide with unfavorable prognosis mainly due to late diagnosis and limited therapies. Therefore, precise molecular classification and search for potential targets are required for diagnosis and treatment, as GC is complicated and heterogeneous in nature. Accumulating evidence indicates that epigenetics plays a vital role in gastric carcinogenesis and progression, including histone modifications, DNA methylation and non-coding RNAs. Epigenetic biomarkers and drugs are currently under intensive evaluations to ensure efficient clinical utility in GC. In this review, key epigenetic alterations and related functions and mechanisms are summarized in GC. We focus on integration of existing epigenetic findings in GC for the bench-to-bedside translation of some pivotal epigenetic alterations into clinical practice and also describe the vacant field waiting for investigation.
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Affiliation(s)
- Si-Yuan Tang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Pei-Jun Zhou
- Cancer Research Institute, School of Basic Medicine Science, Central South University, School of Basic Medicine Science, Central South University 410008, Hunan Province, China
| | - Yu Meng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Fu-Rong Zeng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Guang-Tong Deng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
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6
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Dong Y, Han H, Li Y, Guo L. [Roles of Histidine Kinases and Histidine Phosphatases in Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2021; 24:646-652. [PMID: 34455734 PMCID: PMC8503980 DOI: 10.3779/j.issn.1009-3419.2021.102.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
蛋白磷酸化修饰是最常见、最重要的蛋白质翻译后修饰方式。磷酸化修饰在细胞的增殖、分化、发育和代谢等生物学过程中发挥了重要的调控功能,与肿瘤的发生和发展也密切相关。蛋白激酶和磷酸酶对蛋白磷酸化修饰具有普遍的开/关调控作用。真核生物的蛋白磷酸化主要发生在丝氨酸、苏氨酸和酪氨酸残基,他们在肿瘤发生和发展中的作用已经得到了广泛的研究。但关于组氨酸磷酸化的研究受限于质谱分析和富集技术的发展研究较少。近年来,随着相关技术的快速发展和新的组氨酸磷酸酶的发现,使得研究人员越来越多关注到组氨酸磷酸化在肿瘤中的作用。因此,本文旨在对组氨酸磷酸化调控相关的组氨酸激酶和组氨酸磷酸酶在肿瘤中的作用作一综述。
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Affiliation(s)
- Yafang Dong
- Key Laboratory of Kidney Disease, precision Medicine Center, The Shanxi Provincial People' s Hospital, Shanxi Medical University, Taiyuan 030000, China
| | - Huimin Han
- Key Laboratory of Kidney Disease, precision Medicine Center, The Shanxi Provincial People' s Hospital, Shanxi Medical University, Taiyuan 030000, China
| | - Yafeng Li
- Key Laboratory of Kidney Disease, precision Medicine Center, The Shanxi Provincial People' s Hospital, Shanxi Medical University, Taiyuan 030000, China
| | - Lili Guo
- Key Laboratory of Kidney Disease, precision Medicine Center, The Shanxi Provincial People' s Hospital, Shanxi Medical University, Taiyuan 030000, China
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7
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Bothrops Jararaca Snake Venom Modulates Key Cancer-Related Proteins in Breast Tumor Cell Lines. Toxins (Basel) 2021; 13:toxins13080519. [PMID: 34437390 PMCID: PMC8402457 DOI: 10.3390/toxins13080519] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer is characterized by the development of abnormal cells that divide in an uncontrolled way and may spread into other tissues where they may infiltrate and destroy normal body tissue. Several previous reports have described biochemical anti-tumorigenic properties of crude snake venom or its components, including their capability of inhibiting cell proliferation and promoting cell death. However, to the best of our knowledge, there is no work describing cancer cell proteomic changes following treatment with snake venoms. In this work we describe the quantitative changes in proteomics of MCF7 and MDA-MB-231 breast tumor cell lines following treatment with Bothrops jararaca snake venom, as well as the functional implications of the proteomic changes. Cell lines were treated with sub-toxic doses at either 0.63 μg/mL (low) or 2.5 μg/mL (high) of B. jararaca venom for 24 h, conditions that cause no cell death per se. Proteomics analysis was conducted on a nano-scale liquid chromatography coupled on-line with mass spectrometry (nLC-MS/MS). More than 1000 proteins were identified and evaluated from each cell line treated with either the low or high dose of the snake venom. Protein profiling upon venom treatment showed differential expression of several proteins related to cancer cell metabolism, immune response, and inflammation. Among the identified proteins we highlight histone H3, SNX3, HEL-S-156an, MTCH2, RPS, MCC2, IGF2BP1, and GSTM3. These data suggest that sub-toxic doses of B. jararaca venom have potential to modulate cancer-development related protein targets in cancer cells. This work illustrates a novel biochemical strategy to identify therapeutic targets against cancer cell growth and survival.
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8
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Harjivan SG, Charneira C, Martins IL, Pereira SA, Espadas G, Sabidó E, Beland FA, Marques MM, Antunes AMM. Covalent Histone Modification by an Electrophilic Derivative of the Anti-HIV Drug Nevirapine. Molecules 2021; 26:1349. [PMID: 33802579 PMCID: PMC7961589 DOI: 10.3390/molecules26051349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
Nevirapine (NVP), a non-nucleoside reverse transcriptase inhibitor widely used in combined antiretroviral therapy and to prevent mother-to-child transmission of the human immunodeficiency virus type 1, is associated with several adverse side effects. Using 12-mesyloxy-nevirapine, a model electrophile of the reactive metabolites derived from the NVP Phase I metabolite, 12-hydroxy-NVP, we demonstrate that the nucleophilic core and C-terminal residues of histones are targets for covalent adduct formation. We identified multiple NVP-modification sites at lysine (e.g., H2BK47, H4K32), histidine (e.g., H2BH110, H4H76), and serine (e.g., H2BS33) residues of the four histones using a mass spectrometry-based bottom-up proteomic analysis. In particular, H2BK47, H2BH110, H2AH83, and H4H76 were found to be potential hot spots for NVP incorporation. Notably, a remarkable selectivity to the imidazole ring of histidine was observed, with modification by NVP detected in three out of the 11 histidine residues of histones. This suggests that NVP-modified histidine residues of histones are prospective markers of the drug's bioactivation and/or toxicity. Importantly, NVP-derived modifications were identified at sites known to determine chromatin structure (e.g., H4H76) or that can undergo multiple types of post-translational modifications (e.g., H2BK47, H4H76). These results open new insights into the molecular mechanisms of drug-induced adverse reactions.
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Affiliation(s)
- Shrika G. Harjivan
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
| | - Catarina Charneira
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
| | - Inês L. Martins
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
| | - Sofia A. Pereira
- Centro de Estudos de Doenças Crónicas (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisbon, Portugal;
| | - Guadalupe Espadas
- Proteomics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; (G.E.); (E.S.)
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; (G.E.); (E.S.)
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Frederick A. Beland
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA;
| | - M. Matilde Marques
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
| | - Alexandra M. M. Antunes
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
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9
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Zhang Q, Feng Z, Gao M, Guo L. Determining novel candidate anti-hepatocellular carcinoma drugs using interaction networks and molecular docking between drug targets and natural compounds of SiNiSan. PeerJ 2021; 9:e10745. [PMID: 33628636 PMCID: PMC7894118 DOI: 10.7717/peerj.10745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND SiNiSan (SNS) is an ancient traditional Chinese medicine (TCM) used to treat liver and spleen deficiencies. We studied the unique advantages of using SNS to treat hepatocellular carcinoma (HCC) with multiple components and targets to determine its potential mechanism of action. METHODS The active compounds from the individual herbs in the SNS formula and their targets were mined from Traditional Chinese Medicine Systems Pharmacology Database (TCMSP). HCC-associated targets were collected from the TCGA and GEO databases and samples were collected from patients with stage III hepatocellular carcinoma. A compound-disease target network was constructed, visualized, and analyzed using Cytoscape software. We built a protein-protein interaction (PPI) network using the String database. We enriched and analyzed key targets using GSEA, GO, and KEGG in order to explore their functions. Autodock software was used to simulate the process of SNS molecules acting on HCC targets. RESULTS A total of 113 candidate compounds were taken from SNS, and 64 of the same targets were chosen from HCC and SNS. The predominant targets genes were PTGS2, ESR1, CHEK1, CCNA2, NOS2 and AR; kaempferol and quercetin from SNS were the principal ingredients in HCC treatment. The compounds may work against HCC due to a cellular response to steroid hormones and histone phosphorylation. The P53 signaling pathway was significantly enriched in the gene set GSEA enrichment analysis and differential gene KEGG enrichment analysis. CONCLUSIONS Our results showed that the SNS component has a large number of stage III HCC targets. Among the targets, the sex hormone receptors, the AR and ESR1 genes, are the core targets of SNS component and the most active proteins in the PPI network. In addition, quercetin, which has the most targets, can act on the main targets (BAX, CDK1, CCNB1, SERPINE1, CHEK2, and IGFBP3) of the P53 pathway to treat HCC.
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Affiliation(s)
- Qin Zhang
- The Fourth Hospital of Hebei Medical University, Department of General Medicine, Shijiazhuang, Hebei, China
| | - Zhangying Feng
- The Fourth Hospital of Hebei Medical University, Department of Clinical Pharmacology, Shijiazhuang, Hebei, China
| | - Mengxi Gao
- The Fourth Hospital of Hebei Medical University, Department of General Medicine, Shijiazhuang, Hebei, China
| | - Liru Guo
- The Fourth Hospital of Hebei Medical University, Department of General Medicine, Shijiazhuang, Hebei, China
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10
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Liu Y, Xia C, Fan Z, Jiao F, Gao F, Xie Y, He Z, Zhang W, Zhang Y, Shen Y, Qian X, Qin W. Novel Two-Dimensional MoS 2-Ti 4+ Nanomaterial for Efficient Enrichment of Phosphopeptides and Large-Scale Identification of Histidine Phosphorylation by Mass Spectrometry. Anal Chem 2020; 92:12801-12808. [PMID: 32966065 DOI: 10.1021/acs.analchem.0c00618] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Due to its key roles in regulating the occurrence and development of cancer, protein histidine phosphorylation has been increasingly recognized as an important form of post-translational modification in recent years. However, large-scale analysis of histidine phosphorylation is much more challenging than that of serine/threonine or tyrosine phosphorylation, mainly because of its acid lability. In this study, MoS2-Ti4+ nanomaterials were synthesized using a solvothermal method and taking advantage of the electrostatic adsorption between MoS2 nanosheets and Ti4+. The MoS2-Ti4+ nanomaterials have the advantage of the combined affinity of Ti4+ and Mo toward phosphorylation under medium acidic conditions (pH = 3), which is crucial for preventing hydrolysis and loss of histidine phosphorylation during enrichment. The feasibility of using the MoS2-Ti4+ nanomaterial for phosphopeptide enrichment was demonstrated using mixtures of β-casein and bovine serum albumin (BSA). Further evaluation revealed that the MoS2-Ti4+ nanomaterial is capable of enriching synthetic histidine phosphopeptides from 1000 times excess tryptic-digested HeLa cell lysate. Application of the MoS2-Ti4+ nanomaterials for large-scale phosphopeptide enrichment results in the identification of 10 345 serine, threonine, and tyrosine phosphosites and the successful mapping of 159 histidine phosphosites in HeLa cell lysates, therefore indicating great potential for deciphering the vital biological roles of protein (histidine) phosphorylation.
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Affiliation(s)
- Yuanyuan Liu
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130118, China.,State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Chaoshuang Xia
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China.,Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Zhiya Fan
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Fenglong Jiao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Fangyuan Gao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yuping Xie
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Zhongmei He
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130118, China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Yehua Shen
- Key Laboratory of Synthetic and Natural Function Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
| | - Weijie Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China
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11
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López-Martínez A, Azuara-Pugliese V, Sánchez-Macias A, Sosa-Mendoza G, Dibildox-Alvarado E, Grajales-Lagunes A. High protein and low-fat chips (snack) made out of a legume mixture. CYTA - JOURNAL OF FOOD 2019. [DOI: 10.1080/19476337.2019.1617353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Araceli López-Martínez
- Coordinación Académica Región Altiplano Oeste de la Universidad Autónoma de San Luis Potosí, Salinas de Hidalgo, S.L.P, México
| | - Virginia Azuara-Pugliese
- Coordinación Académica Región Altiplano Oeste de la Universidad Autónoma de San Luis Potosí, Salinas de Hidalgo, S.L.P, México
| | - Armando Sánchez-Macias
- Coordinación Académica Región Altiplano Oeste de la Universidad Autónoma de San Luis Potosí, Salinas de Hidalgo, S.L.P, México
| | - Gloria Sosa-Mendoza
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Elena Dibildox-Alvarado
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Alicia Grajales-Lagunes
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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Hardman G, Perkins S, Brownridge PJ, Clarke CJ, Byrne DP, Campbell AE, Kalyuzhnyy A, Myall A, Eyers PA, Jones AR, Eyers CE. Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation. EMBO J 2019; 38:e100847. [PMID: 31433507 PMCID: PMC6826212 DOI: 10.15252/embj.2018100847] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 07/24/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022] Open
Abstract
Phosphorylation is a key regulator of protein function under (patho)physiological conditions, and defining site-specific phosphorylation is essential to understand basic and disease biology. In vertebrates, the investigative focus has primarily been on serine, threonine and tyrosine phosphorylation, but mounting evidence suggests that phosphorylation of other "non-canonical" amino acids also regulates critical aspects of cell biology. However, standard methods of phosphoprotein characterisation are largely unsuitable for the analysis of non-canonical phosphorylation due to their relative instability under acidic conditions and/or elevated temperature. Consequently, the complete landscape of phosphorylation remains unexplored. Here, we report an unbiased phosphopeptide enrichment strategy based on strong anion exchange (SAX) chromatography (UPAX), which permits identification of histidine (His), arginine (Arg), lysine (Lys), aspartate (Asp), glutamate (Glu) and cysteine (Cys) phosphorylation sites on human proteins by mass spectrometry-based phosphoproteomics. Remarkably, under basal conditions, and having accounted for false site localisation probabilities, the number of unique non-canonical phosphosites is approximately one-third of the number of observed canonical phosphosites. Our resource reveals the previously unappreciated diversity of protein phosphorylation in human cells, and opens up avenues for high-throughput exploration of non-canonical phosphorylation in all organisms.
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Affiliation(s)
- Gemma Hardman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Simon Perkins
- Department of Comparative and Functional Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Philip J Brownridge
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Amy E Campbell
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anton Kalyuzhnyy
- Department of Comparative and Functional Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ashleigh Myall
- Department of Comparative and Functional Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Andrew R Jones
- Department of Comparative and Functional Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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13
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Zhang J, Gelman IH, Katsuta E, Liang Y, Wang X, Li J, Qu J, Yan L, Takabe K, Hochwald SN. Glucose Drives Growth Factor-Independent Esophageal Cancer Proliferation via Phosphohistidine-Focal Adhesion Kinase Signaling. Cell Mol Gastroenterol Hepatol 2019; 8:37-60. [PMID: 30836148 PMCID: PMC6518323 DOI: 10.1016/j.jcmgh.2019.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Most targeted therapies against cancer are designed to block growth factor-stimulated oncogenic growth. However, response rates are low, and resistance to therapy is high. One mechanism might relate to the ability of tumor cells to induce growth factor-independent proliferation (GFIP). This project aims to understand how (1) cancer cells preferentially derive a major growth advantage by using critical metabolic products of glucose, such as phosphoenolpyruvate (PEP), to drive proliferation and (2) esophageal squamous cell carcinoma (ESCC) cells, but not esophageal adenocarcinoma cells, can induce GFIP by using glycolysis to activate phosphohistidine (poHis)-mediated signaling through focal adhesion kinase (FAK). METHODS The hypothesis to be tested is that ESCC GFIP induced by glucose is facilitated by PEP-mediated histidine phosphorylation (poHis) of FAK, leading to the possibility that ESCC progression can be targeted by blocking poHis signaling. Biochemical, molecular biological, and in vivo experiments including bromodeoxyuridine/5-ethynyl-2'-deoxyuridine labeling, radioisotope tracing, CRISPR gene editing, and analysis of signaling gene sets in human cancer tissues and xenograft models were performed to define the mechanisms underlying ESCC GFIP. RESULTS Glucose promotes growth factor-independent DNA replication and accumulation of PEP in ESCC cells. PEP is the direct phospho-donor to poHis58-FAK within a known "HG" motif for histidine phosphorylation. Glucose-induced poHis58 promotes growth factor-independent FAK-mediated proliferation. Furthermore, glucose activates phosphatidylinositol-3'-kinase/AKT via poHis58-FAK signaling. Non-phosphorylatable His58A-FAK reduces xenograft growth. CONCLUSIONS Glucose induces ESCC, but not esophageal adenocarcinoma GFIP via PEP-His58-FAK-AKT signaling. ESCC progression is controlled by actionable growth factor-independent, glucose-induced pathways that regulate proliferation through novel histidine phosphorylation of FAK.
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Affiliation(s)
- Jianliang Zhang
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Irwin H. Gelman
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Eriko Katsuta
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Yuanzi Liang
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Xue Wang
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Jun Li
- University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, New York
| | - Jun Qu
- University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, New York
| | - Li Yan
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Steven N. Hochwald
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York,Correspondence Address correspondence to: Steven N. Hochwald, MD, Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York 14263. fax: (716) 845-1060.
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14
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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15
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Dissociating effect of salivary gland extract from Ixodes ricinus on human fibroblasts: Potential impact on Borrelia transmission. Ticks Tick Borne Dis 2018; 10:433-441. [PMID: 30595500 DOI: 10.1016/j.ttbdis.2018.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022]
Abstract
Understanding the mechanism of pathogen transmission is essential for the development of strategies to reduce arthropod-borne diseases. The pharmaco- and immunomodulatory properties of insect and acarine saliva play an essential role in the efficiency of pathogen transmission. The skin as the site where arthropod saliva and pathogens are inoculated - represents the key interface in vector-borne diseases. We identified tick molecules potentially involved in pathogen transmission, using micro-HPLC and mass spectrometry, followed by in vitro assays on human skin cells. Histone H4 isolated from Ixodes ricinus salivary gland extract was identified as a molecule with a dissociating effect on human primary fibroblasts. This histone might be involved in the formation of the feeding pool formed around the tick mouthparts and responsible of tissue necrosis in the vertebrate host. Thanks to its selective antimicrobial activity, it may also sterilize the feeding pool and facilitate transmission of pathogens such as Borrelia burgdorferi sensu lato.
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16
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Yang K, Greenberg MM. Histone Tail Sequences Balance Their Role in Genetic Regulation and the Need To Protect DNA against Destruction in Nucleosome Core Particles Containing Abasic Sites. Chembiochem 2018; 20:78-82. [PMID: 30307690 DOI: 10.1002/cbic.201800559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 12/14/2022]
Abstract
Abasic sites (AP) are produced 10 000 times per day in a single cell. Strand cleavage at AP is accelerated ≈100-fold within a nucleosome core particle (NCP) compared to free DNA. The lysine-rich N-terminal tails of histone proteins catalyze single-strand breaks through a mechanism used by base-excision-repair enzymes, despite the general dearth of glutamic acid, aspartic acid, and histidine-the amino acids that are typically responsible for deprotonation of Schiff base intermediates. Incorporating glutamic acid, aspartic acid, or histidine proximal to lysine residues in histone N-terminal tails increases AP reactivity as much as sixfold. The rate acceleration is due to more facile DNA cleavage of Schiff-base intermediates. These observations raise the possibility that histone proteins could have evolved to minimize the presence of histidine, glutamic acid, and aspartic acid in their lysine-rich N-terminal tails to guard against enhancing the toxic effects of DNA damage.
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Affiliation(s)
- Kun Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
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17
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Fuhs SR, Hunter T. pHisphorylation: the emergence of histidine phosphorylation as a reversible regulatory modification. Curr Opin Cell Biol 2017; 45:8-16. [PMID: 28129587 DOI: 10.1016/j.ceb.2016.12.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/31/2016] [Indexed: 12/30/2022]
Abstract
Histidine phosphorylation is crucial for prokaryotic signal transduction and as an intermediate for several metabolic enzymes, yet its role in mammalian cells remains largely uncharted. This is primarily caused by difficulties in studying histidine phosphorylation because of the relative instability of phosphohistidine (pHis) and lack of specific antibodies and methods to preserve and detect it. The recent synthesis of stable pHis analogs has enabled development of pHis-specific antibodies and their use has started to shed light onto this important, yet enigmatic posttranslational modification. We are beginning to understand that pHis has broader roles in protein and cellular function including; cell cycle regulation, phagocytosis, regulation of ion channel activity and metal ion coordination. Two mammalian histidine kinases (NME1 and NME2), two pHis phosphatases (PHPT1 and LHPP), and a handful of substrates were previously identified. These new tools have already led to the discovery of an additional phosphatase (PGAM5) and hundreds of putative substrates. New methodologies are also being developed to probe the pHis phosphoproteome and determine functional consequences, including negative ion mode mass spectroscopy and unnatural amino acid incorporation. These new tools and strategies have the potential to overcome the unique challenges that have been holding back our understanding of pHis in cell biology.
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Affiliation(s)
- Stephen Rush Fuhs
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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18
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19
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Yang Q, Mas A, Diamond MP, Al-Hendy A. The Mechanism and Function of Epigenetics in Uterine Leiomyoma Development. Reprod Sci 2016; 23:163-75. [PMID: 25922306 PMCID: PMC5933172 DOI: 10.1177/1933719115584449] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Uterine leiomyomas, also known as uterine fibroids, are the most common pelvic tumors, occurring in nearly 70% of all reproductive-aged women and are the leading indication for hysterectomy worldwide. The development of uterine leiomyomas involve a complex and heterogeneous constellation of hormones, growth factors, stem cells, genetic, and epigenetic abnormalities. An increasing body of evidence emphasizes the important contribution of epigenetics in the pathogenesis of leiomyomas. Genome-wide methylation analysis demonstrates that a subset of estrogen receptor (ER) response genes exhibit abnormal hypermethylation levels that are inversely correlated with their RNA expression. Several tumor suppressor genes, including Kruppel-like factor 11 (KLF11), deleted in lung and esophageal cancer 1 (DLEC1), keratin 19 (KRT19), and death-associated protein kinase 1 (DAPK1) also display higher hypermethylation levels in leiomyomas when compared to adjacent normal tissues. The important role of active DNA demethylation was recently identified with regard to the ten-eleven translocation protein 1 and ten-eleven translocation protein 3-mediated elevated levels of 5-hydroxymethylcytosine in leiomyoma. In addition, both histone deacetylase and histone methyltransferase are reported to be involved in the biology of leiomyomas. A number of deregulated microRNAs have been identified in leiomyomas, leading to an altered expression of their targets. More recently, the existence of side population (SP) cells with characteristics of tumor-initiating cells have been characterized in leiomyomas. These SP cells exhibit a tumorigenic capacity in immunodeficient mice when exposed to 17β-estradiol and progesterone, giving rise to fibroid-like tissue in vivo. These new findings will likely enhance our understanding of the crucial role epigenetics plays in the pathogenesis of uterine leiomyomas as well as point the way to novel therapeutic options.
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Affiliation(s)
- Qiwei Yang
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Aymara Mas
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Michael P Diamond
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Ayman Al-Hendy
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
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20
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Fuhs SR, Meisenhelder J, Aslanian A, Ma L, Zagorska A, Stankova M, Binnie A, Al-Obeidi F, Mauger J, Lemke G, Yates JR, Hunter T. Monoclonal 1- and 3-Phosphohistidine Antibodies: New Tools to Study Histidine Phosphorylation. Cell 2015; 162:198-210. [PMID: 26140597 DOI: 10.1016/j.cell.2015.05.046] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/13/2015] [Accepted: 04/20/2015] [Indexed: 01/18/2023]
Abstract
Histidine phosphorylation (pHis) is well studied in bacteria; however, its role in mammalian signaling remains largely unexplored due to the lack of pHis-specific antibodies and the lability of the phosphoramidate (P-N) bond. Both imidazole nitrogens can be phosphorylated, forming 1-phosphohistidine (1-pHis) or 3-phosphohistidine (3-pHis). We have developed monoclonal antibodies (mAbs) that specifically recognize 1-pHis or 3-pHis; they do not cross-react with phosphotyrosine or the other pHis isomer. Assays based on the isomer-specific autophosphorylation of NME1 and phosphoglycerate mutase were used with immunoblotting and sequencing IgG variable domains to screen, select, and characterize anti-1-pHis and anti-3-pHis mAbs. Their sequence independence was determined by blotting synthetic peptide arrays, and they have been tested for immunofluorescence staining and immunoaffinity purification, leading to putative identification of pHis-containing proteins. These reagents should be broadly useful for identification of pHis substrates and functional study of pHis using a variety of immunological, proteomic, and biological assays.
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Affiliation(s)
- Stephen Rush Fuhs
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jill Meisenhelder
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Aaron Aslanian
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Li Ma
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Anna Zagorska
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Alan Binnie
- Tucson Innovation Center, Sanofi, Tucson, AZ 85755, USA
| | | | | | - Greg Lemke
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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21
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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22
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Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
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23
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Ni F, Fu C, Gao X, Liu Y, Xu P, Liu L, Lv Y, Fu S, Sun Y, Han D, Li Y, Zhao Y. N-phosphoryl amino acid models for P-N bonds in prebiotic chemical evolution. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5321-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Bai G, Ren K, Dubner R. Epigenetic regulation of persistent pain. Transl Res 2015; 165:177-99. [PMID: 24948399 PMCID: PMC4247805 DOI: 10.1016/j.trsl.2014.05.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 02/09/2023]
Abstract
Persistent or chronic pain is tightly associated with various environmental changes and linked to abnormal gene expression within cells processing nociceptive signaling. Epigenetic regulation governs gene expression in response to environmental cues. Recent animal model and clinical studies indicate that epigenetic regulation plays an important role in the development or maintenance of persistent pain and possibly the transition of acute pain to chronic pain, thus shedding light in a direction for development of new therapeutics for persistent pain.
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Affiliation(s)
- Guang Bai
- Program in Neuroscience, Department of Neural and Pain Sciences, University of Maryland Dental School, University of Maryland, Baltimore, MD.
| | - Ke Ren
- Program in Neuroscience, Department of Neural and Pain Sciences, University of Maryland Dental School, University of Maryland, Baltimore, MD
| | - Ronald Dubner
- Program in Neuroscience, Department of Neural and Pain Sciences, University of Maryland Dental School, University of Maryland, Baltimore, MD
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25
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A splice variant of the human phosphohistidine phosphatase 1 (PHPT1) is degraded by the proteasome. Int J Biochem Cell Biol 2014; 57:69-75. [PMID: 25450458 DOI: 10.1016/j.biocel.2014.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/17/2014] [Accepted: 10/06/2014] [Indexed: 01/03/2023]
Abstract
Regulation of protein activity by phosphorylation is central in many cellular processes. Phosphorylation of serine, threonine and tyrosine residues is well documented and studied. In addition, other amino acids, like histidine can be phosphorylated, but neither the mechanism nor the function of this modification is well understood. Nevertheless, there is a 14 kDa enzyme with phosphohistidine phosphatase activity, named PHPT1, found in most animals, but not in bacteria, plant or fungi. There are a few splice variant transcripts formed from the human PHPT1 locus and some of them are predicted to form variant proteins, but studies of these proteins are lacking. In order to get insight into the possible function of the variant transcripts encoded at the PHPT1 locus, ectopic expression of PHPT1 transcript variant 6, predicted to be degraded by the non-sense mediated mRNA decay pathway, in HeLa cells was undertaken. In HeLa cells the splice variant protein was degraded by the proteasome, unlike the wild type protein. Using an in silico modeling approach the variant C-terminal end of the proteins were predicted to form different secondary structures that might explain the different properties of the two proteins. The specific degradation of the PHPT1 splice variant indicates that at least for the PHPT1 protein, the quality control and the self-guarding of the cellular system works at two levels, first at the RNA level, aberrant transcripts are degraded by the non-sense mediated mRNA decay pathway, and the small amount of proteins that are formed will be degraded by the proteasome.
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26
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Downey AM, Cairo CW. Synthesis of α-brominated phosphonates and their application as phosphate bioisosteres. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00255e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A review of the synthesis and biological activity of α-bromo-phosphonate groups as phosphate bioisosteres.
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Affiliation(s)
- A. Michael Downey
- Alberta Glycomics Centre
- Department of Chemistry
- University of Alberta
- Edmonton, Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre
- Department of Chemistry
- University of Alberta
- Edmonton, Canada
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27
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Attempting to rewrite History: challenges with the analysis of histidine-phosphorylated peptides. Biochem Soc Trans 2013; 41:1089-95. [DOI: 10.1042/bst20130072] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A significant number of proteins in both eukaryotes and prokaryotes are known to be post-translationally modified by the addition of phosphate, serving as a means of rapidly regulating protein function. Phosphorylation of the amino acids serine, threonine and tyrosine are the focus of the vast majority of studies aimed at elucidating the extent and roles of such modification, yet other amino acids, including histidine and aspartate, are also phosphorylated. Although histidine phosphorylation is known to play extensive roles in signalling in eukaryotes, plants and fungi, roles for phosphohistidine are poorly defined in higher eukaryotes. Characterization of histidine phosphorylation aimed at elucidating such information is problematic due to the acid-labile nature of the phosphoramidate bond, essential for many of its biological functions. Although MS-based strategies have proven extremely useful in the analysis of other types of phosphorylated peptides, the chromatographic procedures essential for such approaches promote rapid hydrolysis of phosphohistidine-containing peptides. Phosphate transfer to non-biologically relevant aspartate residues during MS analysis further complicates the scenario.
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28
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Abstract
It is more than 50 years since protein histidine phosphorylation was first discovered in 1962 by Boyer and co-workers; however, histidine kinases are still much less well recognized than the serine/threonine and tyrosine kinases. The best-known histidine kinases are the two-component signalling kinases that occur in bacteria, fungi and plants. The mechanisms and functions of these kinases, their cognate response regulators and associated phosphorelay proteins are becoming increasingly well understood. When genomes of higher eukaryotes began to be sequenced, it did not appear that they contained two-component histidine kinase system homologues, apart from a couple of related mitochondrial enzymes that were later shown not to function as histidine kinases. However, as a result of the burgeoning sequencing of genomes from a wide variety of eukaryotic organisms, it is clear that there are proteins that correspond to components of the two-component histidine kinase systems in higher eukaryotes and that operational two-component kinase systems are likely to occur in these organisms. There is unequivocal direct evidence that protein histidine phosphorylation does occur in mammals. So far, only nucleoside diphosphate kinases have been shown to be involved in protein histidine phosphorylation, but their mechanisms of action are not well understood. It is clear that other, yet to be identified, histidine kinases also exist in mammals and that protein histidine phosphorylation may play important roles in higher eukaryotes.
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