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Ozturk S, Kosebent EG, Talibova G, Bilmez Y, Tire B, Can A. Embryonic poly(A)-binding protein interacts with translation-related proteins and undergoes phosphorylation on the serine, threonine, and tyrosine residues in the mouse oocytes and early embryos. J Assist Reprod Genet 2023; 40:929-941. [PMID: 36823316 PMCID: PMC10224904 DOI: 10.1007/s10815-023-02746-7] [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: 09/19/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Expression of the embryonic poly(A)-binding protein (EPAB) in frog, mouse, and human oocytes and early-stage embryos is maintained at high levels until embryonic genome activation (EGA) after which a significant decrease occurs in EPAB levels. Studies on the vertebrate oocytes and early embryos revealed that EPAB plays key roles in the translational regulation, stabilization, and protection of maternal mRNAs during oocyte maturation and early embryogenesis. However, it remains elusive whether EPAB interacts with other cellular proteins and undergoes phosphorylation to perform these roles. For this purpose, we identified a group of Epab-interacting proteins and its phosphorylation status in mouse germinal vesicle (GV)- and metaphase II (MII)-stage oocytes, and in 1-cell, 2-cell, and 4-cell preimplantation embryos. In the oocytes and early preimplantation embryos, Epab-interacting proteins were found to play roles in the translation and transcription processes, intracellular signaling and transport, maintenance of structural integrity, metabolism, posttranslational modifications, and chromatin remodeling. Moreover, we discovered that Epab undergoes phosphorylation on the serine, threonine, and tyrosine residues, which are localized in the RNA recognition motifs 2, 3, and 4 or C-terminal. Conclusively, these findings suggest that Epab not only functions in the translational control of maternal mRNAs through binding to their poly(A) tails but also participates in various cellular events through interacting with certain group proteins. Most likely, Epab undergoes a dynamic phosphorylation during the oocyte maturation and the early embryo development to carry out these functions.
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Affiliation(s)
- Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, Antalya, 07070, Turkey.
| | - Esra Gozde Kosebent
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, Antalya, 07070, Turkey
| | - Gunel Talibova
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, Antalya, 07070, Turkey
| | - Yesim Bilmez
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, Antalya, 07070, Turkey
| | - Betul Tire
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, Antalya, 07070, Turkey
| | - Alp Can
- Department of Histology and Embryology, Ankara University School of Medicine, Ankara, 06410, Turkey
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Fasano M, Alberio T. Neurodegenerative disorders: From clinicopathology convergence to systems biology divergence. HANDBOOK OF CLINICAL NEUROLOGY 2023; 192:73-86. [PMID: 36796949 DOI: 10.1016/b978-0-323-85538-9.00007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Neurodegenerative diseases are multifactorial. This means that several genetic, epigenetic, and environmental factors contribute to their emergence. Therefore, for the future management of these highly prevalent diseases, it is necessary to change perspective. If a holistic viewpoint is assumed, the phenotype (the clinicopathological convergence) emerges from the perturbation of a complex system of functional interactions among proteins (systems biology divergence). The systems biology top-down approach starts with the unbiased collection of sets of data generated through one or more -omics techniques and has the aim to identify the networks and the components that participate in the generation of a phenotype (disease), often without any available a priori knowledge. The principle behind the top-down method is that the molecular components that respond similarly to experimental perturbations are somehow functionally related. This allows the study of complex and relatively poorly characterized diseases without requiring extensive knowledge of the processes under investigation. In this chapter, the use of a global approach will be applied to the comprehension of neurodegeneration, with a particular focus on the two most prevalent ones, Alzheimer's and Parkinson's diseases. The final purpose is to distinguish disease subtypes (even with similar clinical manifestations) to launch a future of precision medicine for patients with these disorders.
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Affiliation(s)
- Mauro Fasano
- Department of Science and High Technology, University of Insubria, Busto Arsizio and Como, Italy; Center of Neuroscience, University of Insubria, Busto Arsizio and Como, Italy.
| | - Tiziana Alberio
- Department of Science and High Technology, University of Insubria, Busto Arsizio and Como, Italy; Center of Neuroscience, University of Insubria, Busto Arsizio and Como, Italy
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Dowling P, Bazou D. Identification of Ubiquitination-Associated Proteins Using 2D-DIGE. Methods Mol Biol 2023; 2596:83-96. [PMID: 36378432 DOI: 10.1007/978-1-0716-2831-7_6] [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] [Indexed: 06/16/2023]
Abstract
Ubiquitination is a post-translational modification, in which a small regulatory protein (~8.6 kDa) is tagged as a single moiety or as a chain to target proteins. Ubiquitination is the most versatile cellular regulatory mechanism, essential to the physiological and pathophysiological cellular events that regulate protein turnover, gene transcription, cell cycle progression, DNA repair, apoptosis, viral budding, and receptor-mediated endocytosis. Changes and abnormalities within the ubiquitination process can result in a plethora of diseases, including various cancers. The ubiquitination process is tightly controlled in a stepwise manner by four enzymes: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, E3 ubiquitin-ligating enzymes, and deubiquitinating proteases. Using fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) to detect and quantitate cellular proteins associated with the ubiquitination process will facilitate the evaluation of this post-translational modification associated with the pathophysiological phenotype.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, Dublin, Ireland.
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Kara B, Uyguner O, Maraş Genç H, İşlek EE, Kasap M, Toksoy G, Akpınar G, Uyur Yalçın E, Anık Y, Üstek D. BEND4 as a Candidate Gene for an Infection-Induced Acute Encephalopathy Characterized by a Cyst and Calcification of the Pons and Cerebellar Atrophy. Mol Syndromol 2021; 13:12-22. [DOI: 10.1159/000517541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
Three siblings born to Turkish parents from the same village had normal brain development until acute neurological deterioration between 12 months and 8 years of age. Consequent loss of all acquired motor, social, and language functions following infections was associated with a pontine cyst, calcification, and cerebellar atrophy. Exome sequencing revealed a homozygous c.1297G>A (p.Gly433Ser) alteration in <i>BEND4</i>, which was predicted to be deleterious in in silico analysis tools and segregated in multiple affected individuals in the family. <i>BEND4</i> has not been associated with any existing disease. Immunofluorescence microscopy analysis of wild-type and mutant BEND4 expressing Vero cells showed nuclear and cytoplasmic localization. Wild-type BEND4 displayed a network-like distribution, whereas mutant BEND4 showed a juxtanuclear distribution pattern. Differential proteome analysis of Vero cells expressing BEND4 revealed that mutant BEND4 expression caused selective increase in reticulocalbin-1 and endoplasmic reticulum resident protein-29. Both proteins are associated with the endoplasmic reticulum and are primarily involved in protein processing and folding pathways. Any defect or stress in protein folding creates stress on cells and may cause chronic damage. This is the first study showing that pathogenic <i>BEND4</i> variants may lead to an infection-induced acute necrotizing encephalopathy as demonstrated in characteristic neuroimaging findings.
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Guney Eskiler G, Yanar S, Akpinar G, Kasap M. Proteomic analysis of talazoparib resistance in triple-negative breast cancer cells. J Biochem Mol Toxicol 2020; 35:e22678. [PMID: 33325624 DOI: 10.1002/jbt.22678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/18/2020] [Accepted: 11/26/2020] [Indexed: 12/21/2022]
Abstract
Talazoparib (TAL) has been effectively used for the treatment of gBRCA1/2-mutated HER2-negative metastatic breast cancer. However, acquired resistance to TAL remains a major challenge that impedes the clinical success of TAL treatment. Therefore, elucidation of proteins and pathways that contribute to or are affected by the TAL resistance is urgently needed to improve the treatment response and provide novel treatment strategies for advanced metastatic breast cancers. Herein, we aimed to investigate the altered protein signatures in TAL-resistant triple-negative breast cancer (TNBC) cells by comparing with the TNBC parental cell line via proteomic analysis. After validation of TAL-resistance by WST-1 and Annexin V analysis, two-dimensional gel electrophoresis (2DE)-based proteomic analysis coupled to matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry was performed to identify differentially regulated proteins. The findings revealed the identities of 10 differentially regulated proteins in TAL-resistant TNBC cells whose bioinformatic analysis predicted changes in EGF/FGF signaling pathways as well as in the AMPK signaling pathway. In addition, phosphorylation/dephosphorylation dynamics were predicted to be altered in TAL-resistant cells. The proteins identified in this study might be the targets to overcome TAL resistance for the treatment of TNBC.
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Affiliation(s)
- Gamze Guney Eskiler
- Department of Medical Biology, Faculty of Medicine, Sakarya University, Sakarya, Turkey
| | - Sevinc Yanar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
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Zilocchi M, Fasano M, Alberio T. Mitochondrial Proteins in the Development of Parkinson’s Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:17-44. [DOI: 10.1007/978-981-13-8367-0_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Yoneten KK, Kasap M, Akpinar G, Kanli A, Karaoz E. Comparative Proteomics Analysis of Four Commonly Used Methods for Identification of Novel Plasma Membrane Proteins. J Membr Biol 2019; 252:587-608. [PMID: 31346646 DOI: 10.1007/s00232-019-00084-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 11/25/2022]
Abstract
Plasma membrane proteins perform a variety of important tasks in the cells. These tasks can be diverse as carrying nutrients across the plasma membrane, receiving chemical signals from outside the cell, translating them into intracellular action, and anchoring the cell in a particular location. When these crucial roles of plasma membrane proteins are considered, the need for their characterization becomes inevitable. Certain characteristics of plasma membrane proteins such as hydrophobicity, low solubility, and low abundance limit their detection by proteomic analyses. Here, we presented a comparative proteomics study in which the most commonly used plasma membrane protein enrichment methods were evaluated. The methods that were utilized include biotinylation, selective CyDye labeling, temperature-dependent phase partition, and density-gradient ultracentrifugation. Western blot analysis was performed to assess the level of plasma membrane protein enrichment using plasma membrane and cytoplasmic protein markers. Quantitative evaluation of the level of enrichment was performed by two-dimensional electrophoresis (2-DE) and benzyldimethyl-n-hexadecylammonium chloride/sodium dodecyl sulfate polyacrylamide gel electrophoresis (16-BAC/SDS-PAGE) from which the protein spots were cut and identified. Results from this study demonstrated that density-gradient ultracentrifugation method was superior when coupled with 16-BAC/SDS-PAGE. This work presents a valuable contribution and provides a future direction to the membrane sub-proteome research by evaluating commonly used methods for plasma membrane protein enrichment.
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Affiliation(s)
| | - Murat Kasap
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey.
| | - Gurler Akpinar
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey
| | - Aylin Kanli
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey
| | - Erdal Karaoz
- Department of Histology and Embryology, School of Medicine, Istinye University, 34010, Istanbul, Turkey
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Bogetofte H, Jensen P, Ryding M, Schmidt SI, Okarmus J, Ritter L, Worm CS, Hohnholt MC, Azevedo C, Roybon L, Bak LK, Waagepetersen H, Ryan BJ, Wade-Martins R, Larsen MR, Meyer M. PARK2 Mutation Causes Metabolic Disturbances and Impaired Survival of Human iPSC-Derived Neurons. Front Cell Neurosci 2019; 13:297. [PMID: 31333417 PMCID: PMC6624735 DOI: 10.3389/fncel.2019.00297] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022] Open
Abstract
The protein parkin, encoded by the PARK2 gene, is vital for mitochondrial homeostasis, and although it has been implicated in Parkinson’s disease (PD), the disease mechanisms remain unclear. We have applied mass spectrometry-based proteomics to investigate the effects of parkin dysfunction on the mitochondrial proteome in human isogenic induced pluripotent stem cell-derived neurons with and without PARK2 knockout (KO). The proteomic analysis quantified nearly 60% of all mitochondrial proteins, 119 of which were dysregulated in neurons with PARK2 KO. The protein changes indicated disturbances in oxidative stress defense, mitochondrial respiration and morphology, cell cycle control, and cell viability. Structural and functional analyses revealed an increase in mitochondrial area and the presence of elongated mitochondria as well as impaired glycolysis and lactate-supported respiration, leading to an impaired cell survival in PARK2 KO neurons. This adds valuable insight into the effect of parkin dysfunction in human neurons and provides knowledge of disease-related pathways that can potentially be targeted for therapeutic intervention.
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Affiliation(s)
- Helle Bogetofte
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Oxford Parkinson's Disease Centre, Medical Sciences Division, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Pia Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Matias Ryding
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Sissel I Schmidt
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Louise Ritter
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Christina S Worm
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Michaela C Hohnholt
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carla Azevedo
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Laurent Roybon
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Lasse K Bak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helle Waagepetersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brent J Ryan
- Oxford Parkinson's Disease Centre, Medical Sciences Division, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, Medical Sciences Division, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Brain Research - Inter-Disciplinary Guided Excellence, University of Southern Denmark, Odense, Denmark
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Yaprak E, Kasap M, Akpinar G, Islek EE, Sinanoglu A. Abundant proteins in platelet-rich fibrin and their potential contribution to wound healing: An explorative proteomics study and review of the literature. J Dent Sci 2018; 13:386-395. [PMID: 30895150 PMCID: PMC6388803 DOI: 10.1016/j.jds.2018.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/01/2018] [Indexed: 01/12/2023] Open
Abstract
Background/purpose It is well-known that diverse types of blood proteins contribute to healing process via different mechanisms. Presence and potential involvements of blood-derived abundant proteins in the platelet-rich fibrin (PRF) to its regenerative capacity have not been sufficiently emphasized in the literature. The aim of this paper was to analyze the abundant proteome content of PRF and summarize previously reported effects of identified proteins on wound healing via a literature review. Materials and methods The PRF samples obtained from non-smoking, systemically healthy volunteers were subjected to 2D gel electrophoresis after extracting the proteins from fibrin matrices. All matching spots were excised from the gels and identified by MALDI TOF/TOF MS/MS analysis. A literature review was conducted to reveal possible contributions of identified proteins to wound healing. Results Totally, thirty-five blood proteins were commonly identified among all studied samples. These proteins included serine protease inhibitors, such as alpha-1-antitrypsin, alpha-1-antichymotrypsin, alpha-1-acid glycoprotein, inter-alpha-trypsin-inhibitor, protease C1 inhibitor, and complement proteins. In addition, abundant presence of immunoglobulin G was observed. The abundance of albumin, haptoglobin, ceruloplasmin vitronectin, fetuin-A, ficolin-3 and transthyretin was also detected. Conclusion The results of this study indicated that PRF abundantly contains blood-origin actors which were previously reported for their direct contribution to wound healing. Further studies exploring the protein content of PRF are needed to reveal its undisclosed potential roles in the healing process.
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Affiliation(s)
- Emre Yaprak
- Kocaeli University, Faculty of Dentistry, Department of Periodontology, Kocaeli, Turkey
- Corresponding author. Kocaeli University, Faulty of Dentistry, Department of Periodontology, Yuvacik, Basiskele, Kocaeli, Turkey. Fax: +90 2623442109.
| | - Murat Kasap
- Kocaeli University, Faculty of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Gurler Akpinar
- Kocaeli University, Faculty of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Eylul Ece Islek
- Kocaeli University, Faculty of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Alper Sinanoglu
- Kocaeli University, Faculty of Dentistry, Department of Oral and Maxillofacial Radiology, Oral Diagnosis Clinic, Kocaeli, Turkey
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Kanli A, Kasap M, Yoneten KK, Akpinar G, Gulkac MD. Identification of differentially regulated deceitful proteins in SH-SY5Y cells engineered with Tet-regulated protein expression system. J Cell Biochem 2018; 119:6065-6071. [PMID: 29600520 DOI: 10.1002/jcb.26804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/23/2018] [Indexed: 01/28/2023]
Abstract
Tetracycline regulated protein expression in mammalian cells is a powerful tool to predict the physiological function, cellular localization, and stability of a protein. In addition, to predict metabolic networks affected by the expression of wild-type or mutant forms of proteins, researchers generally produce a single mammalian cell clone that can express the protein of interest under tetracycline control and study the changes occurring in overall proteome before and after expression of a protein of interest. One limitation of tetracycline regulated clonal cell creation, however, is that it sometimes creates clones with changed protein levels even without the expression of the protein of interest due to the nonspecific insertion of the gene encoding the protein of interest into the genome or disruption of a metabolic pathway due to insertional silencing or activation. The aim of this study was to demonstrate the limitation of tetracycline regulated gene expression by creating clonal cell lines expressing the wild-type or the mutant forms of Fat mass and obesity-associated protein. Comparative proteome analysis of the protein extracts by two-dimensional gel electrophoresis coupled to MALDI-TOF/TOF revealed the presence of eight proteins subjected to differential regulation even in the absence of induction. The identified proteins were 14-3-3 protein Epsilon, Vimentin, Heterogeneous nuclear ribonucleoprotein K, Tubulin beta-2C chain, Heat shock protein HSP 90-alpha, Heat shock protein HSP 90-beta, Alpha-enolase, TATA-binding protein-associated factor 2N. An ultimate care should be taken to prevent reporting of deceitful proteins generated from studies utilizing tetracycline regulated gene expression systems.
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Affiliation(s)
- Aylin Kanli
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Kubra K Yoneten
- Department of Biomedical Engineering, Technology Faculty, Kocaeli University, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Mehmet Dogan Gulkac
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
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Yan J, Zhang P, Jiao F, Wang Q, He F, Zhang Q, Zhang Z, Lv Z, Peng X, Cai H, Tian B. Quantitative proteomics in A30P*A53T α-synuclein transgenic mice reveals upregulation of Sel1l. PLoS One 2017; 12:e0182092. [PMID: 28771510 PMCID: PMC5542467 DOI: 10.1371/journal.pone.0182092] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/12/2017] [Indexed: 01/17/2023] Open
Abstract
α-Synuclein is an abundantly expressed neuronal protein that is at the center of focus in understanding a group of neurodegenerative disorders called synucleinopathies, which are characterized by the intracellular presence of aggregated α-synuclein. However, the mechanism of α-synuclein biology in synucleinopathies pathogenesis is not fully understood. In this study, mice overexpressing human A30P*A53T α-synuclein were evaluated by a motor behavior test and count of TH-positive neurons, and then two-dimensional liquid chromatography-tandem mass spectrometry coupled with tandem mass tags (TMTs) labeling was employed to quantitatively identify the differentially expressed proteins of substantia nigra pars compacta (SNpc) tissue samples that were obtained from the α-synuclein transgenic mice and wild type controls. The number of SNpc dopaminergic neurons and the motor behavior were unchanged in A30P*A53T transgenic mice at the age of 6 months. Of the 4,715 proteins identified by proteomic techniques, 271 were differentially expressed, including 249 upregulated and 22 downregulated proteins. These alterations were primarily associated with mitochondrial dysfunction, oxidative stress, ubiquitin-proteasome system impairment, and endoplasmic reticulum (ER) stress. Some obviously changed proteins, which were validated by western blotting and immunofluorescence staining, including Sel1l and Sdhc, may be involved in the α-synuclein pathologies of synucleinopathies. A biological pathway analysis of common related proteins showed that the proteins were linked to a total of 31 KEGG pathways. Our findings suggest that these identified proteins may serve as novel therapeutic targets for synucleinopathies.
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Affiliation(s)
- Jianguo Yan
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Pei Zhang
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Fengjuan Jiao
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Qingzhi Wang
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Feng He
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Qian Zhang
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Zheng Zhang
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Zexi Lv
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Xiang Peng
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Hongwei Cai
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
| | - Bo Tian
- Department of Neurobiology, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- Key Laboratory of Neurological Diseases, Ministry of Education, Wuhan, Hubei Province, P. R. China
- Institute for Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei Province, P. R. China
- * E-mail:
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Abstract
INTRODUCTION Parkinson's disease (PD) is an insidious disorder affecting more than 1-2% of the population over the age of 65. Understanding the etiology of PD may create opportunities for developing new treatments. Genomic and transcriptomic studies are useful, but do not provide evidence for the actual status of the disease. Conversely, proteomic studies deal with proteins, which are real time players, and can hence provide information on the dynamic nature of the affected cells. The number of publications relating to the proteomics of PD is vast. Therefore, there is a need to evaluate the current proteomics literature and establish the connections between the past and the present to foresee the future. Areas covered: PubMed and Web of Science were used to retrieve the literature associated with PD proteomics. Studies using human samples, model organisms and cell lines were selected and reviewed to highlight their contributions to PD. Expert commentary: The proteomic studies associated with PD achieved only limited success in facilitating disease diagnosis, monitoring and progression. A global system biology approach using new models is needed. Future research should integrate the findings of proteomics with other omics data to facilitate both early diagnosis and the treatment of PD.
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Affiliation(s)
- Murat Kasap
- a Department of Medical Biology/DEKART Proteomics Laboratory , Kocaeli University Medical School , Kocaeli , Turkey
| | - Gurler Akpinar
- a Department of Medical Biology/DEKART Proteomics Laboratory , Kocaeli University Medical School , Kocaeli , Turkey
| | - Aylin Kanli
- a Department of Medical Biology/DEKART Proteomics Laboratory , Kocaeli University Medical School , Kocaeli , Turkey
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Fasano M, Monti C, Alberio T. A systems biology-led insight into the role of the proteome in neurodegenerative diseases. Expert Rev Proteomics 2016; 13:845-55. [PMID: 27477319 DOI: 10.1080/14789450.2016.1219254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Multifactorial disorders are the result of nonlinear interactions of several factors; therefore, a reductionist approach does not appear to be appropriate. Proteomics is a global approach that can be efficiently used to investigate pathogenetic mechanisms of neurodegenerative diseases. AREAS COVERED Here, we report a general introduction about the systems biology approach and mechanistic insights recently obtained by over-representation analysis of proteomics data of cellular and animal models of Alzheimer's disease, Parkinson's disease and other neurodegenerative disorders, as well as of affected human tissues. Expert commentary: As an inductive method, proteomics is based on unbiased observations that further require validation of generated hypotheses. Pathway databases and over-representation analysis tools allow researchers to assign an expectation value to pathogenetic mechanisms linked to neurodegenerative diseases. The systems biology approach based on omics data may be the key to unravel the complex mechanisms underlying neurodegeneration.
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Affiliation(s)
- Mauro Fasano
- a Department of Science and High Technology and Center of Neuroscience , University of Insubria , Busto Arsizio , Italy
| | - Chiara Monti
- a Department of Science and High Technology and Center of Neuroscience , University of Insubria , Busto Arsizio , Italy
| | - Tiziana Alberio
- a Department of Science and High Technology and Center of Neuroscience , University of Insubria , Busto Arsizio , Italy
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