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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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2
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Chi Y, Yuan H, Fan Q, Wang Z, Niu Z, Yu J, Yuan D. Clinical-Molecular characteristics and Post-Translational modifications of colorectal cancer in north China: Implications for future targeted therapies. Gene 2024; 899:148134. [PMID: 38185290 DOI: 10.1016/j.gene.2024.148134] [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: 09/11/2023] [Revised: 12/12/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
This study delineated the elucidate molecular changes and their post-translational modifications (PTMs) in heterogenetic colorectal cancer (CRC) for a deeper understanding of the CRC pathophysiology and identifying potential therapeutic targets. In this retrospective study, the profiles of 13 hot spot gene mutations were analyzed and the microsatellite instability (MSI) status was determined.Employing the Circulating Single-Molecule Amplification and Resequencing Technology (cSMART) assay, the clinical-pathological features of CRC were characterized in 249 Chinese patients. PTMs were quantified online.Among the patients with CRC, the mutation frequencies of KRAS, NRAS, BRAF, PIK3CA, TP53, and APC genes were 47.8%, 3.6%, 4.8%, 13.7%, 55.8%, and 36.9%, respectively. The proportion of MSI-high (MSI-H) was 7.8%.Subsequent multiple logistic regression analysis showed significant associations including a link between lung metastasis and KRAS mutation, between liver metastasis and lymph node metastasis, between MSI-H and early-onset CRC (EOCRC) and KRAS mutation, between right-sided colon cancer and peritoneal metastasis, and between PIK3CA mutation and PTEN mutation. Patients with KRAS mutation presented with MSI-H, lung metastasis, and PIK3CA mutation. MSI-H, BRAF mutation, and PTEN mutation were more frequent in EOCRC. Phosphorylation and ubiquitylation were found in KRAS, BRAF, PTEN, and SMAD4; SUMOylation and ubiquitylation were observed in HRAS and NRAS; while phosphorylation was obvious in APC, P53, and MLH1. Notably, Phosphorylation and ubiquitylation were the two most common PTMs. The biological characteristics of CRC in Chinese patients have some unique clinical features, which can be explained by the genetic mutation profile, correlations among gene mutations and clinical characteristics. These distinctions set the Chinese patient population apart from their Western counterparts.
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Affiliation(s)
- Yajing Chi
- School of Medicine, Nankai University, Tianjin, China; Cancer Center, The General Hospital of the People's Liberation Army, Beijing, China
| | - Hongtu Yuan
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Qing Fan
- Department of Pharmacy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Zhendan Wang
- Department of Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Zuoxing Niu
- Department of Gastroenterology Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Dandan Yuan
- Department of Gastroenterology Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
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Bashyal A, Brodbelt JS. Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation. MASS SPECTROMETRY REVIEWS 2024; 43:289-326. [PMID: 36165040 PMCID: PMC10040477 DOI: 10.1002/mas.21811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
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Li N, Desiderio DM, Zhan X. The use of mass spectrometry in a proteome-centered multiomics study of human pituitary adenomas. MASS SPECTROMETRY REVIEWS 2022; 41:964-1013. [PMID: 34109661 DOI: 10.1002/mas.21710] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
A pituitary adenoma (PA) is a common intracranial neoplasm, and is a complex, chronic, and whole-body disease with multicausing factors, multiprocesses, and multiconsequences. It is very difficult to clarify molecular mechanism and treat PAs from the single-factor strategy model. The rapid development of multiomics and systems biology changed the paradigms from a traditional single-factor strategy to a multiparameter systematic strategy for effective management of PAs. A series of molecular alterations at the genome, transcriptome, proteome, peptidome, metabolome, and radiome levels are involved in pituitary tumorigenesis, and mutually associate into a complex molecular network system. Also, the center of multiomics is moving from structural genomics to phenomics, including proteomics and metabolomics in the medical sciences. Mass spectrometry (MS) has been extensively used in phenomics studies of human PAs to clarify molecular mechanisms, and to discover biomarkers and therapeutic targets/drugs. MS-based proteomics and proteoform studies play central roles in the multiomics strategy of PAs. This article reviews the status of multiomics, multiomics-based molecular pathway networks, molecular pathway network-based pattern biomarkers and therapeutic targets/drugs, and future perspectives for personalized, predeictive, and preventive (3P) medicine in PAs.
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Affiliation(s)
- Na Li
- Shandong Key Laboratory of Radiation Oncology, Cancer Hospital of Shandong First Medical University, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, Shandong, China
| | - Dominic M Desiderio
- The Charles B. Stout Neuroscience Mass Spectrometry Laboratory, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Cancer Hospital of Shandong First Medical University, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, Shandong, China
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The comparison between 2DE‐MS and bottom‐up LC‐MS demands high‐end techniques for both technologies. Electrophoresis 2022; 43:1242-1245. [DOI: 10.1002/elps.202200036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 11/07/2022]
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HSP60 Regulates Lipid Metabolism in Human Ovarian Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6610529. [PMID: 34557266 PMCID: PMC8452972 DOI: 10.1155/2021/6610529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 07/08/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Accumulating evidence demonstrates that cancer is an oxidative stress-related disease, and oxidative stress is closely linked with heat shock proteins (HSPs). Lipid oxidative stress is derived from lipid metabolism dysregulation that is closely associated with the development and progression of malignancies. This study sought to investigate regulatory roles of HSPs in fatty acid metabolism abnormality in ovarian cancer. Pathway network analysis of 5115 mitochondrial expressed proteins in ovarian cancer revealed various lipid metabolism pathway alterations, including fatty acid degradation, fatty acid metabolism, butanoate metabolism, and propanoate metabolism. HSP60 regulated the expressions of lipid metabolism proteins in these lipid metabolism pathways, including ADH5, ECHS1, EHHADH, HIBCH, SREBP1, ACC1, and ALDH2. Further, interfering HSP60 expression inhibited migration, proliferation, and cell cycle and induced apoptosis of ovarian cancer cells in vitro. In addition, mitochondrial phosphoproteomics and immunoprecipitation-western blot experiments identified and confirmed that phosphorylation occurred at residue Ser70 in protein HSP60, which might regulate protein folding of ALDH2 and ACADS in ovarian cancers. These findings clearly demonstrated that lipid metabolism abnormality occurred in oxidative stress-related ovarian cancer and that HSP60 and its phosphorylation might regulate this lipid metabolism abnormality in ovarian cancer. It opens a novel vision in the lipid metabolism reprogramming in human ovarian cancer.
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Nilamyani AN, Auliah FN, Moni MA, Shoombuatong W, Hasan MM, Kurata H. PredNTS: Improved and Robust Prediction of Nitrotyrosine Sites by Integrating Multiple Sequence Features. Int J Mol Sci 2021; 22:2704. [PMID: 33800121 PMCID: PMC7962192 DOI: 10.3390/ijms22052704] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Nitrotyrosine, which is generated by numerous reactive nitrogen species, is a type of protein post-translational modification. Identification of site-specific nitration modification on tyrosine is a prerequisite to understanding the molecular function of nitrated proteins. Thanks to the progress of machine learning, computational prediction can play a vital role before the biological experimentation. Herein, we developed a computational predictor PredNTS by integrating multiple sequence features including K-mer, composition of k-spaced amino acid pairs (CKSAAP), AAindex, and binary encoding schemes. The important features were selected by the recursive feature elimination approach using a random forest classifier. Finally, we linearly combined the successive random forest (RF) probability scores generated by the different, single encoding-employing RF models. The resultant PredNTS predictor achieved an area under a curve (AUC) of 0.910 using five-fold cross validation. It outperformed the existing predictors on a comprehensive and independent dataset. Furthermore, we investigated several machine learning algorithms to demonstrate the superiority of the employed RF algorithm. The PredNTS is a useful computational resource for the prediction of nitrotyrosine sites. The web-application with the curated datasets of the PredNTS is publicly available.
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Affiliation(s)
- Andi Nur Nilamyani
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; (A.N.N.); (F.N.A.)
| | - Firda Nurul Auliah
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; (A.N.N.); (F.N.A.)
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia;
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand;
| | - Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; (A.N.N.); (F.N.A.)
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; (A.N.N.); (F.N.A.)
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Li J, Zhan X. Mass spectrometry-based proteomics analyses of post-translational modifications and proteoforms in human pituitary adenomas. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140584. [PMID: 33321259 DOI: 10.1016/j.bbapap.2020.140584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
Pituitary adenoma (PA) is a common intracranial neoplasm, which affects the hypothalamus-pituitary-target organ axis systems, and is hazardous to human health. Post-translational modifications (PTMs), including phosphorylation, ubiquitination, nitration, and sumoylation, are vitally important in the PA pathogenesis. The large-scale analysis of PTMs could provide a global view of molecular mechanisms for PA. Proteoforms, which are used to define various protein structural and functional forms originated from the same gene, are the future direction of proteomics research. The global studies of different proteoforms and PTMs of hypophyseal hormones such as growth hormone (GH) and prolactin (PRL) and the proportion change of different GH proteoforms or PRL proteoforms in human pituitary tissue could provide new insights into the clinical value of pituitary hormones in PAs. Multiple quantitative proteomics methods, including mass spectrometry (MS)-based label-free and stable isotope-labeled strategies in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides increase the feasibility for researchers to study PA proteomes. This article reviews the research status of PTMs and proteoforms in PAs, including the enrichment method, technical limitation, quantitative proteomics strategies, and the future perspectives, to achieve the goals of in-depth understanding its molecular pathogenesis, and discovering effective biomarkers and clinical therapeutic targets for predictive, preventive, and personalized treatment of PA patients.
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Affiliation(s)
- Jiajia Li
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
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9
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The challenge of detecting modifications on proteins. Essays Biochem 2020; 64:135-153. [PMID: 31957791 DOI: 10.1042/ebc20190055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.
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Li N, Zhan X. MASS SPECTROMETRY-BASED MITOCHONDRIAL PROTEOMICS IN HUMAN OVARIAN CANCERS. MASS SPECTROMETRY REVIEWS 2020; 39:471-498. [PMID: 32020673 DOI: 10.1002/mas.21618] [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: 12/10/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The prominent characteristics of mitochondria are highly dynamic and regulatory, which have crucial roles in cell metabolism, biosynthetic, senescence, apoptosis, and signaling pathways. Mitochondrial dysfunction might lead to multiple serious diseases, including cancer. Therefore, identification of mitochondrial proteins in cancer could provide a global view of tumorigenesis and progression. Mass spectrometry-based quantitative mitochondrial proteomics fulfils this task by enabling systems-wide, accurate, and quantitative analysis of mitochondrial protein abundance, and mitochondrial protein posttranslational modifications (PTMs). Multiple quantitative proteomics techniques, including isotope-coded affinity tag, stable isotope labeling with amino acids in cell culture, isobaric tags for relative and absolute quantification, tandem mass tags, and label-free quantification, in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides, increase flexibility for researchers to study mitochondrial proteomes. This article reviews isolation and purification of mitochondria, quantitative mitochondrial proteomics, quantitative mitochondrial phosphoproteomics, mitochondrial protein-involved signaling pathway networks, mitochondrial phosphoprotein-involved signaling pathway networks, integration of mitochondrial proteomic and phosphoproteomic data with whole tissue proteomic and transcriptomic data and clinical information in ovarian cancers (OC) to in-depth understand its molecular mechanisms, and discover effective mitochondrial biomarkers and therapeutic targets for predictive, preventive, and personalized treatment of OC. This proof-of-principle model about OC mitochondrial proteomics is easily implementable to other cancer types. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Na Li
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- Department of Oncology, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
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Naryzhny S, Klopov N, Ronzhina N, Zorina E, Zgoda V, Kleyst O, Belyakova N, Legina O. A database for inventory of proteoform profiles: "2DE-pattern". Electrophoresis 2020; 41:1118-1124. [PMID: 32307725 DOI: 10.1002/elps.201900468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 01/01/2023]
Abstract
The human proteome is composed of a diverse and heterogeneous range of gene products/proteoforms/protein species. Because of the growing amount of information about proteoforms generated by different methods, we need a convenient approach to make an inventory of the data. Here, we present a database of proteoforms that is based on information obtained by separation of proteoforms using 2DE followed by shotgun ESI-LC-MS/MS. The database's principles and structure are described. The database is called "2DE-pattern" as it contains multiple isoform-centric patterns of proteoforms separated according to 2DE principles. The database can be freely used at http://2de-pattern.pnpi.nrcki.ru.
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Affiliation(s)
- Stanislav Naryzhny
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.,B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Nikolay Klopov
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Natalia Ronzhina
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Elena Zorina
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia
| | - Victor Zgoda
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia
| | - Olga Kleyst
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Natalia Belyakova
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Olga Legina
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Gatchina, Russia
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Ghantasala S, Gollapalli K, Epari S, Moiyadi A, Srivastava S. Glioma tumor proteomics: clinically useful protein biomarkers and future perspectives. Expert Rev Proteomics 2020; 17:221-232. [PMID: 32067544 DOI: 10.1080/14789450.2020.1731310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Introduction: Despite being rare cancers, gliomas account for a significant number of cancer-related deaths. Identification and treatment of these tumors at an early stage would greatly improve the therapeutic outcomes. There is an urgent need for diagnostic and prognostic markers, which can identify disease early and discriminate the subtypes of these tumors thereby improving the existing treatment modalities.Areas covered: In this article, we have reviewed published literature on proteomics biomarkers for gliomas and their importance in diagnosis or prognosis. Proteomic studies for the discovery of protein, autoantibody biomarkers, and biological pathway alterations in serum, CSF and tumor biopsies have been discussed in this review.Expert opinion: The rapid development in the field of mass spectrometry and increased sensitivity and reproducibility in assays has led to the identification and quantification of large number of proteins very precisely. Though genomic markers are the prime focus in the classification of gliomas, incorporating protein markers would further improve the existing classification. In this regard, data mining and studies on large cohorts of glioma patients would help in the identification of diagnostic and prognostic markers ultimately translating to the clinics.
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Affiliation(s)
- Saicharan Ghantasala
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, India
| | - Kishore Gollapalli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.,Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA.,Center for Motor Neuron Biology & Disease, Columbia University Medical Center, New York, NY, USA
| | - Sridhar Epari
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Aliasgar Moiyadi
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level. Proteomes 2019; 7:proteomes7040036. [PMID: 31671630 PMCID: PMC6958347 DOI: 10.3390/proteomes7040036] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/15/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Two-dimensional gel electrophoresis (2DE) is an important and well-established technical platform enabling extensive top-down proteomic analysis. However, the long-held but now largely outdated conventional concepts of 2DE have clearly impacted its application to in-depth investigations of proteomes at the level of protein species/proteoforms. It is time to popularize a new concept of 2DE for proteomics. With the development and enrichment of the proteome concept, any given “protein” is now recognized to consist of a series of proteoforms. Thus, it is the proteoform, rather than the canonical protein, that is the basic unit of a proteome, and each proteoform has a specific isoelectric point (pI) and relative mass (Mr). Accordingly, using 2DE, each proteoform can routinely be resolved and arrayed according to its different pI and Mr. Each detectable spot contains multiple proteoforms derived from the same gene, as well as from different genes. Proteoforms derived from the same gene are distributed into different spots in a 2DE pattern. High-resolution 2DE is thus actually an initial level of separation to address proteome complexity and is effectively a pre-fractionation method prior to analysis using mass spectrometry (MS). Furthermore, stable isotope-labeled 2DE coupled with high-sensitivity liquid chromatography-tandem MS (LC-MS/MS) has tremendous potential for the large-scale detection, identification, and quantification of the proteoforms that constitute proteomes.
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Li N, Qian S, Li B, Zhan X. Quantitative analysis of the human ovarian carcinoma mitochondrial phosphoproteome. Aging (Albany NY) 2019; 11:6449-6468. [PMID: 31442208 PMCID: PMC6738437 DOI: 10.18632/aging.102199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/10/2019] [Indexed: 05/02/2023]
Abstract
To investigate the existence and their potential biological roles of mitochondrial phosphoproteins (mtPPs) in human ovarian carcinoma (OC), mitochondria purified from OC and control tissues were analyzed with TiO2 enrichment-based iTRAQ quantitative proteomics. Totally 67 mtPPs with 124 phosphorylation sites were identified, which of them included 48 differential mtPPs (mtDPPs). Eighteen mtPPs were reported previously in OCs, and they were consistent in this study compared to previous literature. GO analysis revealed those mtPPs were involved in multiple cellular processes. PPI network indicated that those mtPPs were correlated mutually, and some mtPPs acted as hub molecules, such as EIF2S2, RPLP0, RPLP2, CFL1, MYH10, HSP90, HSPD1, PSMA3, TMX1, VDAC2, VDAC3, TOMM22, and TOMM20. Totally 32 mtPP-pathway systems (p<0.05) were enriched and clustered into 15 groups, including mitophagy, apoptosis, deubiquitination, signaling by VEGF, RHO-GTPase effectors, mitochondrial protein import, translation initiation, RNA transport, cellular responses to stress, and c-MYC transcriptional activation. Totally 29 mtPPs contained a certain protein domains. Upstream regulation analysis showed that TP53, TGFB1, dexamethasone, and thapsigargin might act as inhibitors, and L-dopa and forskolin might act as activators. This study provided novel insights into mitochondrial protein phosphorylations and their potential roles in OC pathogenesis and offered new biomarker resource for OCs.
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Affiliation(s)
- Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Shehua Qian
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Biao Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
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15
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Möller MN, Rios N, Trujillo M, Radi R, Denicola A, Alvarez B. Detection and quantification of nitric oxide-derived oxidants in biological systems. J Biol Chem 2019; 294:14776-14802. [PMID: 31409645 DOI: 10.1074/jbc.rev119.006136] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The free radical nitric oxide (NO•) exerts biological effects through the direct and reversible interaction with specific targets (e.g. soluble guanylate cyclase) or through the generation of secondary species, many of which can oxidize, nitrosate or nitrate biomolecules. The NO•-derived reactive species are typically short-lived, and their preferential fates depend on kinetic and compartmentalization aspects. Their detection and quantification are technically challenging. In general, the strategies employed are based either on the detection of relatively stable end products or on the use of synthetic probes, and they are not always selective for a particular species. In this study, we describe the biologically relevant characteristics of the reactive species formed downstream from NO•, and we discuss the approaches currently available for the analysis of NO•, nitrogen dioxide (NO2 •), dinitrogen trioxide (N2O3), nitroxyl (HNO), and peroxynitrite (ONOO-/ONOOH), as well as peroxynitrite-derived hydroxyl (HO•) and carbonate anion (CO3 •-) radicals. We also discuss the biological origins of and analytical tools for detecting nitrite (NO2 -), nitrate (NO3 -), nitrosyl-metal complexes, S-nitrosothiols, and 3-nitrotyrosine. Moreover, we highlight state-of-the-art methods, alert readers to caveats of widely used techniques, and encourage retirement of approaches that have been supplanted by more reliable and selective tools for detecting and measuring NO•-derived oxidants. We emphasize that the use of appropriate analytical methods needs to be strongly grounded in a chemical and biochemical understanding of the species and mechanistic pathways involved.
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Affiliation(s)
- Matías N Möller
- Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.,Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Natalia Rios
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.,Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay .,Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
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16
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Proteomic Advances in Glial Tumors through Mass Spectrometry Approaches. ACTA ACUST UNITED AC 2019; 55:medicina55080412. [PMID: 31357616 PMCID: PMC6722920 DOI: 10.3390/medicina55080412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/25/2023]
Abstract
Being the fourth leading cause of cancer-related death, glial tumors are highly diverse tumor entities characterized by important heterogeneity regarding tumor malignancy and prognosis. However, despite the identification of important alterations in the genome of the glial tumors, there remains a gap in understanding the mechanisms involved in glioma malignancy. Previous research focused on decoding the genomic alterations in these tumors, but due to intricate cellular mechanisms, the genomic findings do not correlate with the functional proteins expressed at the cellular level. The development of mass spectrometry (MS) based proteomics allowed researchers to study proteins expressed at the cellular level or in serum that may provide new insights on the proteins involved in the proliferation, invasiveness, metastasis and resistance to therapy in glial tumors. The integration of data provided by genomic and proteomic approaches into clinical practice could allow for the identification of new predictive, diagnostic and prognostic biomarkers that will improve the clinical management of patients with glial tumors. This paper aims to provide an updated review of the recent proteomic findings, possible clinical applications, and future research perspectives in diffuse astrocytic and oligodendroglial tumors, pilocytic astrocytomas, and ependymomas.
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17
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Bandookwala M, Thakkar D, Sengupta P. Advancements in the Analytical Quantification of Nitroxidative Stress Biomarker 3-Nitrotyrosine in Biological Matrices. Crit Rev Anal Chem 2019; 50:265-289. [DOI: 10.1080/10408347.2019.1623010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Bandookwala
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat, India
| | - Disha Thakkar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat, India
| | - Pinaki Sengupta
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat, India
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18
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Li Y, Fu Y, Hu X, Sun L, Tang D, Li N, Peng F, Fan XG. The HBx-CTTN interaction promotes cell proliferation and migration of hepatocellular carcinoma via CREB1. Cell Death Dis 2019; 10:405. [PMID: 31138777 PMCID: PMC6538608 DOI: 10.1038/s41419-019-1650-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus-encoded X protein (HBx) acts as a tumor promoter during hepatocellular carcinoma (HCC) development, probably by regulating the expression of host proteins through protein–protein interaction. A proteomics approach was used to identify HBx-interacting proteins involved in HBx-induced hepatocarcinogenesis. We validated the proteomics findings by co-immunoprecipitation and confocal microscopy. We performed cell proliferation, migration assays and cell cycle analyses in HCC cells. Finally, we confirmed the clinical significance of our findings in samples from patients. We found that cortactin (CTTN) is a novel HBx-interacting protein, and HBx regulates the expression of CTTN in the HCC cell lines MHCC-LM3 and HepG2. Mechanistically, by upregulating the expression of cAMP response element-binding protein (CREB1) and its downstream targets, such as cyclin D1 and MMP-9, the effects of the HBx-CTTN interaction on the enhancement of cellular proliferation and migration were maintained by inhibiting cell cycle arrest. In addition, we demonstrated that the levels of CTTN and CREB1 were closely correlated in clinical samples from HBV-infected patients with HCC. Overall, our data suggests that HBx contributes to cell migration and proliferation of HCC cells by interacting with CTTN and regulating the expression of CTTN and CREB1. Therefore, the HBx/CTTN/CREB1 axis is a potential novel therapeutic target in HCC.
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Affiliation(s)
- Yajun Li
- Department of Infectious Diseases and Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China
| | - Yongming Fu
- Department of Infectious Diseases and Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China
| | - Xingwang Hu
- Department of Infectious Diseases and Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China
| | - Lunquan Sun
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ning Li
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China
| | - Fang Peng
- NHC Key Laboratory of Cancer Proteomics, XiangYa Hospital, Central South University, Changsha, China.
| | - Xue-Gong Fan
- Department of Infectious Diseases and Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China.
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19
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Li N, Li H, Cao L, Zhan X. Quantitative analysis of the mitochondrial proteome in human ovarian carcinomas. Endocr Relat Cancer 2018; 25:909-931. [PMID: 29997262 DOI: 10.1530/erc-18-0243] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 12/20/2022]
Abstract
Mitochondria play important roles in growth, signal transduction, division, tumorigenesis and energy metabolism in epithelial ovarian carcinomas (EOCs) without an effective biomarker. To investigate the proteomic profile of EOC mitochondrial proteins, a 6-plex isobaric tag for relative and absolute quantification (iTRAQ) proteomics was used to identify mitochondrial expressed proteins (mtEPs) in EOCs relative to controls, followed by an integrative analysis of the identified mtEPs and the Cancer Genome Atlas (TCGA) data from 419 patients. A total of 5115 quantified proteins were identified from purified mitochondrial samples, and 262 proteins were significantly related to overall survival in EOC patients. Furthermore, 63 proteins were identified as potential biomarkers for the development of an EOC, and our findings were consistent with previous reports on a certain extent. Pathway network analysis identified 70 signaling pathways. Interestingly, the results demonstrated that cancer cells exhibited an increased dependence on mitophagy, such as peroxisome, phagosome, lysosome, valine, leucine and isoleucine degradation and fatty acid degradation pathways, which might play an important role in EOC invasion and metastasis. Five proteins (GLDC, PCK2, IDH2, CPT2 and HMGCS2) located in the mitochondrion and enriched pathways were selected for further analysis in an EOC cell line and tissues, and the results confirmed reliability of iTRAQ proteomics. These findings provide a large-scale mitochondrial proteomic profiling with quantitative information, a certain number of potential protein biomarkers and a novel vision in the mitophagy bio-mechanism of a human ovarian carcinoma.
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Affiliation(s)
- Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of HealthXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug DesignXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- State Local Joint Engineering Laboratory for Anticancer DrugsXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Huanni Li
- Department of Obstetrics and GynecologyXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Lanqin Cao
- Department of Obstetrics and GynecologyXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of HealthXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug DesignXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- State Local Joint Engineering Laboratory for Anticancer DrugsXiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- The Laboratory of Medical GeneticsCentral South University, Changsha, Hunan, People's Republic of China
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20
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Exploration of variations in proteome and metabolome for predictive diagnostics and personalized treatment algorithms: Innovative approach and examples for potential clinical application. J Proteomics 2018; 188:30-40. [DOI: 10.1016/j.jprot.2017.08.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/06/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022]
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21
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Qian S, Yang Y, Li N, Cheng T, Wang X, Liu J, Li X, Desiderio DM, Zhan X. Prolactin Variants in Human Pituitaries and Pituitary Adenomas Identified With Two-Dimensional Gel Electrophoresis and Mass Spectrometry. Front Endocrinol (Lausanne) 2018; 9:468. [PMID: 30210449 PMCID: PMC6121189 DOI: 10.3389/fendo.2018.00468] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022] Open
Abstract
Human prolactin (hPRL) plays multiple roles in growth, metabolism, development, reproduction, and immunoregulation, which is an important protein synthesized in a pituitary. Two-dimensional gel electrophoresis (2DE) is an effective method in identity of protein variants for in-depth insight into functions of that protein. 2DE, 2DE-based PRL-immunoblot, mass spectrometry, and bioinformatics were used to analyze hPRL variants in human normal (control; n = 8) pituitaries and in five subtypes of pituitary adenomas [NF- (n = 3)-, FSH+ (n = 3)-, LH+ (n = 3)-, FSH+/LH+ (n = 3)-, and PRL+ (n = 3)-adenomas]. Six hPRL variants were identified with different isoelectric point (pI)-relative molecular mass (Mr ) distribution on a 2DE pattern, including variants V1 (pI 6.1; 26.0 kDa), V2 (pI 6.3; 26.4 kDa), V3 (pI 6.3; 27.9 kDa), V4 (pI 6.5; 26.1 kDa), V5 (pI 6.8; 25.9 kDa), and V6 (pI 6.7; 25.9 kDa). Compared to controls, except for variants V2-V6 in PRL-adenomas, V2 in FSH+-adenomas, and V3 in NF--adenomas, the other PRL variants were significantly downregulated in each subtype of pituitary adenomas. Moreover, the pattern of those six PRL variants was significantly different among five subtypes of pituitary adenomas relative to control pituitaries. Different hPRL variants might be involved in different types of PRL receptor-signaling pathways in a given condition. Those findings clearly revealed the existence of six hPRL variants in human pituitaries, and the pattern changes of six hPRL variants among different subtypes of pituitary adenomas, which provide novel clues to further study the functions, and mechanisms of action, of hPRL in human pituitary and in PRL-related diseases, and the potential clinical value in pituitary adenomas.
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Affiliation(s)
- Shehua Qian
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Yongmei Yang
- Geriatric Department of Cadre's Ward, Baoji Traditional Chinese Medicine Hospital, Baoji, China
| | - Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
| | - Tingting Cheng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaowei Wang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Jianping Liu
- Bio-Analytical Chemistry Research Laboratory, Modern Analytical Testing Center, Central South University, Changsha, China
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Dominic M. Desiderio
- The Charles B. Stout Neuroscience Mass Spectrometry Laboratory, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
- The Laboratory of Medical Genetics, Central South University, Changsha, China
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22
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Hasan MM, Khatun MS, Mollah MNH, Yong C, Dianjing G. NTyroSite: Computational Identification of Protein Nitrotyrosine Sites Using Sequence Evolutionary Features. Molecules 2018; 23:E1667. [PMID: 29987232 PMCID: PMC6099560 DOI: 10.3390/molecules23071667] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/28/2018] [Accepted: 06/28/2018] [Indexed: 02/06/2023] Open
Abstract
Nitrotyrosine is a product of tyrosine nitration mediated by reactive nitrogen species. As an indicator of cell damage and inflammation, protein nitrotyrosine serves to reveal biological change associated with various diseases or oxidative stress. Accurate identification of nitrotyrosine site provides the important foundation for further elucidating the mechanism of protein nitrotyrosination. However, experimental identification of nitrotyrosine sites through traditional methods are laborious and expensive. In silico prediction of nitrotyrosine sites based on protein sequence information are thus highly desired. Here, we report a novel predictor, NTyroSite, for accurate prediction of nitrotyrosine sites using sequence evolutionary information. The generated features were optimized using a Wilcoxon-rank sum test. A random forest classifier was then trained using these features to build the predictor. The final NTyroSite predictor achieved an area under a receiver operating characteristics curve (AUC) score of 0.904 in a 10-fold cross-validation test. It also significantly outperformed other existing implementations in an independent test. Meanwhile, for a better understanding of our prediction model, the predominant rules and informative features were extracted from the NTyroSite model to explain the prediction results. We expect that the NTyroSite predictor may serve as a useful computational resource for high-throughput nitrotyrosine site prediction. The online interface of the software is publicly available at https://biocomputer.bio.cuhk.edu.hk/NTyroSite/.
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Affiliation(s)
- Md Mehedi Hasan
- School of Life Sciences and the State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Mst Shamima Khatun
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh.
| | - Md Nurul Haque Mollah
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh.
| | - Cao Yong
- Department of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen Graduate School, Shenzhen 518000, China.
| | - Guo Dianjing
- School of Life Sciences and the State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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23
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Lu M, Zhan X. The crucial role of multiomic approach in cancer research and clinically relevant outcomes. EPMA J 2018; 9:77-102. [PMID: 29515689 PMCID: PMC5833337 DOI: 10.1007/s13167-018-0128-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/29/2018] [Indexed: 02/06/2023]
Abstract
Cancer with heavily economic and social burden is the hot point in the field of medical research. Some remarkable achievements have been made; however, the exact mechanisms of tumor initiation and development remain unclear. Cancer is a complex, whole-body disease that involves multiple abnormalities in the levels of DNA, RNA, protein, metabolite and medical imaging. Biological omics including genomics, transcriptomics, proteomics, metabolomics and radiomics aims to systematically understand carcinogenesis in different biological levels, which is driving the shift of cancer research paradigm from single parameter model to multi-parameter systematical model. The rapid development of various omics technologies is driving one to conveniently get multi-omics data, which accelerates predictive, preventive and personalized medicine (PPPM) practice allowing prediction of response with substantially increased accuracy, stratification of particular patients and eventual personalization of medicine. This review article describes the methodology, advances, and clinically relevant outcomes of different "omics" technologies in cancer research, and especially emphasizes the importance and scientific merit of integrating multi-omics in cancer research and clinically relevant outcomes.
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Affiliation(s)
- Miaolong Lu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- The State Key Laboratory of Medical Genetics, Central South University, 88 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
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24
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Zhan X, Yang H, Peng F, Li J, Mu Y, Long Y, Cheng T, Huang Y, Li Z, Lu M, Li N, Li M, Liu J, Jungblut PR. How many proteins can be identified in a 2DE gel spot within an analysis of a complex human cancer tissue proteome? Electrophoresis 2018; 39:965-980. [PMID: 29205401 DOI: 10.1002/elps.201700330] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 11/03/2017] [Accepted: 11/17/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- The State Key Laboratory of Medical Genetics; Central South University; Changsha Hunan P. R. China
| | - Haiyan Yang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Fang Peng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, Hunan University; Changsha Hunan P. R. China
| | - Yun Mu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Ying Long
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Tingting Cheng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Yuda Huang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Zhao Li
- Department of Neurosurgery; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Miaolong Lu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Maoyu Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Jianping Liu
- Bio-Analytical Chemistry Research Laboratory, Modern Analytical Testing Center; Central South University; Changsha Hunan P. R. China
| | - Peter R. Jungblut
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis; Berlin Germany
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25
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Zhao Y, Zhang Y, Sun H, Maroto R, Brasier AR. Selective Affinity Enrichment of Nitrotyrosine-Containing Peptides for Quantitative Analysis in Complex Samples. J Proteome Res 2017; 16:2983-2992. [PMID: 28714690 DOI: 10.1021/acs.jproteome.7b00275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein tyrosine nitration by oxidative and nitrate stress is important in the pathogenesis of many inflammatory or aging-related diseases. Mass spectrometry analysis of protein nitrotyrosine is very challenging because the non-nitrated peptides suppress the signals of the low-abundance nitrotyrosine (NT) peptides. No validated methods for enrichment of NT-peptides are currently available. Here we report an immunoaffinity enrichment of NT-peptides for proteomics analysis. The effectiveness of this approach was evaluated using nitrated protein standards and whole-cell lysates in vitro. A total of 1881 NT sites were identified from a nitrated whole-cell extract, indicating that this immunoaffinity-MS method is a valid approach for the enrichment of NT-peptides, and provides a significant advance for characterizing the nitrotyrosine proteome. We noted that this method had higher affinity to peptides with N-terminal nitrotyrosine relative to peptides with other nitrotyrosine locations, which raises the need for future study to develop a pan-specific nitrotyrosine antibody for unbiased, proteome-wide analysis of tyrosine nitration. We applied this method to quantify the changes in protein tyrosine nitration in mouse lungs after intranasal poly(I:C) treatment and quantified 237 NT sites. This result indicates that the immunoaffinity-MS method can be used for quantitative analysis of protein nitrotyrosines in complex samples.
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Affiliation(s)
- Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Rosario Maroto
- Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
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26
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Qi XT, Zhan JS, Xiao LM, Li L, Xu HX, Fu ZB, Zhang YH, Zhang J, Jia XH, Ge G, Chai RC, Gao K, Yu ACH. The Unwanted Cell Migration in the Brain: Glioma Metastasis. Neurochem Res 2017; 42:1847-1863. [PMID: 28478595 DOI: 10.1007/s11064-017-2272-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/12/2017] [Accepted: 04/17/2017] [Indexed: 12/19/2022]
Abstract
Cell migration is identified as a highly orchestrated process. It is a fundamental and essential phenomenon underlying tissue morphogenesis, wound healing, and immune response. Under dysregulation, it contributes to cancer metastasis. Brain is considered to be the most complex organ in human body containing many types of neural cells with astrocytes playing crucial roles in monitoring both physiological and pathological functions. Astrocytoma originates from astrocytes and its most malignant type is glioblastoma multiforme (WHO Grade IV astrocytoma), which is capable to infiltrate widely into the neighboring brain tissues making a complete resection of tumors impossible. Very recently, we have reviewed the mechanisms for astrocytes in migration. Given the fact that astrocytoma shares many histological features with astrocytes, we therefore attempt to review the mechanisms for glioma cells in migration and compare them to normal astrocytes, hoping to obtain a better insight into the dysregulation of migratory mechanisms contributing to their metastasis in the brain.
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Affiliation(s)
- Xue Tao Qi
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Jiang Shan Zhan
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Li Ming Xiao
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Lina Li
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China.
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China.
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China.
- Hai Kang Life (Beijing) Corporation Ltd., Sino-I Campus No.1, Beijing Economic-Technological Development Area, Beijing, 100176, China.
- Hai Kang Life Corporation Ltd., Hong Kong Science Park, Shatin, New Territories, Hong Kong, China.
| | - Han Xiao Xu
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Department of Human Anatomy, Guizhou Medical University, Guian New Area, Guiyang, Guizhou, 550025, China
| | - Zi Bing Fu
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Hao Zhang
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
| | - Jing Zhang
- Department of Pathology, Peking University Health Science Center and Peking University Third Hospital, Beijing, 100191, China
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, 98104, USA
| | - Xi Hua Jia
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Hai Kang Life (Beijing) Corporation Ltd., Sino-I Campus No.1, Beijing Economic-Technological Development Area, Beijing, 100176, China
- Hai Kang Life Corporation Ltd., Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Guo Ge
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Department of Human Anatomy, Guizhou Medical University, Guian New Area, Guiyang, Guizhou, 550025, China
| | - Rui Chao Chai
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Hai Kang Life (Beijing) Corporation Ltd., Sino-I Campus No.1, Beijing Economic-Technological Development Area, Beijing, 100176, China
- Hai Kang Life Corporation Ltd., Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Kai Gao
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Albert Cheung Hoi Yu
- Laboratory for Functional Study of Astrocytes, Neuroscience Research Institute, Peking University, 38 Xue Yuan Road, Beijing, 100191, China.
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education, Peking University Health Science Center, Beijing, 100191, China.
- National Health and Family Planning Commission, Peking University Health Science Center, Beijing, 100191, China.
- Hai Kang Life (Beijing) Corporation Ltd., Sino-I Campus No.1, Beijing Economic-Technological Development Area, Beijing, 100176, China.
- Hai Kang Life Corporation Ltd., Hong Kong Science Park, Shatin, New Territories, Hong Kong, China.
- Laboratory of Translational Medicine, Institute of Systems Biomedicine, Peking University, Beijing, 100191, China.
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27
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Batthyány C, Bartesaghi S, Mastrogiovanni M, Lima A, Demicheli V, Radi R. Tyrosine-Nitrated Proteins: Proteomic and Bioanalytical Aspects. Antioxid Redox Signal 2017; 26:313-328. [PMID: 27324931 PMCID: PMC5326983 DOI: 10.1089/ars.2016.6787] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
SIGNIFICANCE "Nitroproteomic" is under active development, as 3-nitrotyrosine in proteins constitutes a footprint left by the reactions of nitric oxide-derived oxidants that are usually associated to oxidative stress conditions. Moreover, protein tyrosine nitration can cause structural and functional changes, which may be of pathophysiological relevance for human disease conditions. Biological protein tyrosine nitration is a free radical process involving the intermediacy of tyrosyl radicals; in spite of being a nonenzymatic process, nitration is selectively directed toward a limited subset of tyrosine residues. Precise identification and quantitation of 3-nitrotyrosine in proteins has represented a "tour de force" for researchers. Recent Advances: A small number of proteins are preferential targets of nitration (usually less than 100 proteins per proteome), contrasting with the large number of proteins modified by other post-translational modifications such as phosphorylation, acetylation, and, notably, S-nitrosation. Proteomic approaches have revealed key features of tyrosine nitration both in vivo and in vitro, including selectivity, site specificity, and effects in protein structure and function. CRITICAL ISSUES Identification of 3-nitrotyrosine-containing proteins and mapping nitrated residues is challenging, due to low abundance of this oxidative modification in biological samples and its unfriendly behavior in mass spectrometry (MS)-based technologies, that is, MALDI, electrospray ionization, and collision-induced dissociation. FUTURE DIRECTIONS The use of (i) classical two-dimensional electrophoresis with immunochemical detection of nitrated proteins followed by protein ID by regular MS/MS in combination with (ii) immuno-enrichment of tyrosine-nitrated peptides and (iii) identification of nitrated peptides by a MIDAS™ experiment is arising as a potent methodology to unambiguously map and quantitate tyrosine-nitrated proteins in vivo. Antioxid. Redox Signal. 26, 313-328.
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Affiliation(s)
- Carlos Batthyány
- 1 Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay .,2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Silvina Bartesaghi
- 3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay .,4 Departamento de Educación Médica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Analía Lima
- 1 Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Verónica Demicheli
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
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28
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Partial Immunoblotting of 2D-Gels: A Novel Method to Identify Post-Translationally Modified Proteins Exemplified for the Myelin Acetylome. Proteomes 2017; 5:proteomes5010003. [PMID: 28248254 PMCID: PMC5372224 DOI: 10.3390/proteomes5010003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/23/2016] [Accepted: 01/04/2017] [Indexed: 11/17/2022] Open
Abstract
Post-translational modifications (PTMs) play a key role in regulating protein function, yet their identification is technically demanding. Here, we present a straightforward workflow to systematically identify post-translationally modified proteins based on two-dimensional gel electrophoresis. Upon colloidal Coomassie staining the proteins are partially transferred, and the investigated PTMs are immunodetected. This strategy allows tracking back the immunopositive antigens to the corresponding spots on the original gel, from which they are excised and mass spectrometrically identified. Candidate proteins are validated on the same membrane by immunodetection using a second fluorescence channel. We exemplify the power of partial immunoblotting with the identification of lysine-acetylated proteins in myelin, the oligodendroglial membrane that insulates neuronal axons. The excellent consistency of the detected fluorescence signals at all levels allows the differential comparison of PTMs across multiple conditions. Beyond PTM screening, our multi-level workflow can be readily adapted to clinical applications such as identifying auto-immune antigens or host-pathogen interactions.
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