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Qiu T, Shi W, Chen J, Li J. Haloketones: A class of unregulated priority DBPs with high contribution to drinking water cytotoxicity. WATER RESEARCH 2024; 259:121866. [PMID: 38852393 DOI: 10.1016/j.watres.2024.121866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/24/2024] [Accepted: 06/01/2024] [Indexed: 06/11/2024]
Abstract
Although unregulated aliphatic disinfection byproducts (DBPs) had a much higher concentration and cytotoxicity than known aromatic DBPs, a recent study indicated that seven classes of regulated and unregulated priority DBPs (one and two-carbon-atom DBPs) just accounted for 16.2% of disinfected water cytotoxicity in the U.S., meaning some of the highly toxic aliphatic DBPs may be overlooked. Haloketones (HKs) are an essential class of priority DBPs with a 1-100 µg/L concentration in drinking water but lack cytotoxicity data. This study investigated the cytotoxicity of seven HKs using Chinese hamster ovary (CHO) cells. The order for cytotoxicity of HKs from most to least toxic was: 1,3-dichloroacetone (LC50: 1.0 ± 0.20 μM) ≈ 1,3-dibromoacetone (1.5 ± 0.19 μM) ≈ bromoacetone (1.9 ± 0.49 μM) > chloroacetone (4.3 ± 0.22 μM) > 1,1,3-trichloropropanone (6.6 ± 0.46 μM) > 1,1,1-trichloroacetone (222 ± 7.7 μM) > hexachloroacetone (3269 ± 344 μM). The cytotoxicity of HKs was higher than most regulated and priority aliphatic DBPs in mono-halogenated, di-halogenated, and tri-halogenated categories. A prediction model of HK cytotoxicity was developed based on the quantitative structure-activity relationship (QSAR), optimizing structures and computing descriptors with Gaussian 09 W. The average concentrations of HKs in representative drinking water samples from South Carolina (U.S.) and Suzhou (China) were 12.4 and 0.9 μg/L, respectively, accounting for 18.8% and 1.7% of their specific total DBPs measured (i.e. not TOX). For South Carolina drinking water, their contributions to total calculated additive cytotoxicity of aliphatic DBPs and overall drinking water cytotoxicity were 86.7% and 14.0%, respectively, demonstrating that HKs are an essential class of overlooked DBPs with a high contribution to drinking water cytotoxicity. Our study can help to explain the conflict that why regulated and priority DBPs (except HKs) just accounted for 16% of chlorinated drinking water cytotoxicity even enough they had much higher concentration and cytotoxicity than known aromatic DBPs.
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Affiliation(s)
- Tian Qiu
- School of Public Health, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College, Soochow University, Suzhou, 215123, China
| | - Wenshan Shi
- School of Public Health, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College, Soochow University, Suzhou, 215123, China
| | - Jingsi Chen
- School of Public Health, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College, Soochow University, Suzhou, 215123, China
| | - Jiafu Li
- School of Public Health, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College, Soochow University, Suzhou, 215123, China.
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2
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Alhujaily M. Glyoxalase System in Breast and Ovarian Cancers: Role of MEK/ERK/SMAD1 Pathway. Biomolecules 2024; 14:584. [PMID: 38785990 PMCID: PMC11117840 DOI: 10.3390/biom14050584] [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: 03/26/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
The glyoxalase system, comprising GLO1 and GLO2 enzymes, is integral in detoxifying methylglyoxal (MGO) generated during glycolysis, with dysregulation implicated in various cancer types. The MEK/ERK/SMAD1 signaling pathway, crucial in cellular processes, influences tumorigenesis, metastasis, and angiogenesis. Altered GLO1 expression in cancer showcases its complex role in cellular adaptation and cancer aggressiveness. GLO2 exhibits context-dependent functions, contributing to both proapoptotic and antiapoptotic effects in different cancer scenarios. Research highlights the interconnected nature of these systems, particularly in ovarian cancer and breast cancer. The glyoxalase system's involvement in drug resistance and its impact on the MEK/ERK/SMAD1 signaling cascade underscore their clinical significance. Furthermore, this review delves into the urgent need for effective biomarkers, exemplified in ovarian cancer, where the RAGE-ligand pathway emerges as a potential diagnostic tool. While therapeutic strategies targeting these pathways hold promise, this review emphasizes the challenges posed by context-dependent effects and intricate crosstalk within the cellular milieu. Insights into the molecular intricacies of these pathways offer a foundation for developing innovative therapeutic approaches, providing hope for enhanced cancer diagnostics and tailored treatment strategies.
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Affiliation(s)
- Muhanad Alhujaily
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
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3
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Sultana R, Butterfield DA. Protein Oxidation in Aging and Alzheimer's Disease Brain. Antioxidants (Basel) 2024; 13:574. [PMID: 38790679 PMCID: PMC11117785 DOI: 10.3390/antiox13050574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Proteins are essential molecules that play crucial roles in maintaining cellular homeostasis and carrying out biological functions such as catalyzing biochemical reactions, structural proteins, immune response, etc. However, proteins also are highly susceptible to damage by reactive oxygen species (ROS) and reactive nitrogen species (RNS). In this review, we summarize the role of protein oxidation in normal aging and Alzheimer's disease (AD). The major emphasis of this review article is on the carbonylation and nitration of proteins in AD and mild cognitive impairment (MCI). The oxidatively modified proteins showed a strong correlation with the reported changes in brain structure, carbohydrate metabolism, synaptic transmission, cellular energetics, etc., of both MCI and AD brains compared to the controls. Some proteins were found to be common targets of oxidation and were observed during the early stages of AD, suggesting that those changes might be critical in the onset of symptoms and/or formation of the pathological hallmarks of AD. Further studies are required to fully elucidate the role of protein oxidation and nitration in the progression and pathogenesis of AD.
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Affiliation(s)
- Rukhsana Sultana
- Department of Neuroscience, School of Behavioral and Brain Sciences, The University of Texas at Dallas, 800 West Campbell Rd., Richardson, TX 75080, USA;
| | - D. Allan Butterfield
- Department of Chemistry, and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
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4
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Teixeira EB, Khayat AS, Assumpção PP, Casseb SM, Moreira-Nunes CA, Moreira FC. EndoGeneAnalyzer: A tool for selection and validation of reference genes. PLoS One 2024; 19:e0299993. [PMID: 38568963 PMCID: PMC10990236 DOI: 10.1371/journal.pone.0299993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024] Open
Abstract
The selection of proper reference genes is critical for accurate gene expression analysis in all fields of biological and medical research, mainly because there are many distinctions between different tissues and specimens. Given this variability, even in known classic reference genes, demands of a comprehensive analysis platform is needed to identify the most suitable genes for each study. For this purpose, we present an analysis tool for assisting in decision-making in the analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) data. EndoGeneAnalyzer, an open-source web tool for reference gene analysis in RT-qPCR studies, was used to compare the groups/conditions under investigation. This interactive application offers an easy-to-use interface that allows efficient exploration of datasets. Through statistical and stability analyses, EndoGeneAnalyzer assists in the select of the most appropriate reference gene or set of genes for each condition. It also allows researchers to identify and remove unwanted outliers. Moreover, EndoGeneAnalyzer provides a graphical interface to compare the evaluated groups, providing a visually informative differential analysis.
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Affiliation(s)
| | - André Salim Khayat
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Caroline Aquino Moreira-Nunes
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
- Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Department of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Clementino Fraga Group, Central Unity, Molecular Biology Laboratory, Fortaleza, CE, Brazil
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5
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Hernández-Prieto JH, Martini VP, Iulek J. Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii in complex with an aldonic sugar acid. Biochimie 2024; 218:20-33. [PMID: 37709188 DOI: 10.1016/j.biochi.2023.09.013] [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: 02/19/2023] [Revised: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The pathogen Paracoccidioides lutzii (Pb01) is found in South America countries Colombia, Ecuador, Venezuela and Brazil, especially in the central, west, and north regions of the latter. It belongs to the Ajellomycetaceae family, Onygenales order, and is typically thermodimorphic, presenting yeast cells when it grows in animal tissues, but mycelia when in the environment, where it produces the infectious propagule. This fungus is one of the etiologic agents of Paracoccidioidomycosis (PCM), the most important endemic fungal infection in Latin America. Investigations on its genome have contributed to a better understanding about its metabolism and revealed the complexity of several metabolic glycolytic pathways. Glyceraldehyde-3-Phosphate Dehydrogenase from Paracoccidioides lutzii (PlGAPDH) is considered a moonlighting protein and participates in several biological processes of this pathogen. The enzyme was expressed and purified, as seen in SDS-PAGE gel, crystallized and had its three dimensional structure (3D) determined in complex with NAD+, a sulphate ion and d-galactonic acid, therefore, a type of 'GAA site'. It is the first GAPDH structure to show this chemical type in this site and how this protein can bind an acid derived from oxidation of a linear hexose.
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Affiliation(s)
| | | | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil.
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6
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Bhuvaneshwar K, Gusev Y. Translational bioinformatics and data science for biomarker discovery in mental health: an analytical review. Brief Bioinform 2024; 25:bbae098. [PMID: 38493340 PMCID: PMC10944574 DOI: 10.1093/bib/bbae098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/23/2024] [Accepted: 02/18/2024] [Indexed: 03/18/2024] Open
Abstract
Translational bioinformatics and data science play a crucial role in biomarker discovery as it enables translational research and helps to bridge the gap between the bench research and the bedside clinical applications. Thanks to newer and faster molecular profiling technologies and reducing costs, there are many opportunities for researchers to explore the molecular and physiological mechanisms of diseases. Biomarker discovery enables researchers to better characterize patients, enables early detection and intervention/prevention and predicts treatment responses. Due to increasing prevalence and rising treatment costs, mental health (MH) disorders have become an important venue for biomarker discovery with the goal of improved patient diagnostics, treatment and care. Exploration of underlying biological mechanisms is the key to the understanding of pathogenesis and pathophysiology of MH disorders. In an effort to better understand the underlying mechanisms of MH disorders, we reviewed the major accomplishments in the MH space from a bioinformatics and data science perspective, summarized existing knowledge derived from molecular and cellular data and described challenges and areas of opportunities in this space.
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Affiliation(s)
- Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington DC, 20007, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington DC, 20007, USA
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7
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Piccirillo S, Preziuso A, Cerqueni G, Serfilippi T, Terenzi V, Vinciguerra A, Amoroso S, Lariccia V, Magi S. A strategic tool to improve the study of molecular determinants of Alzheimer's disease: The role of glyceraldehyde. Biochem Pharmacol 2023; 218:115869. [PMID: 37871878 DOI: 10.1016/j.bcp.2023.115869] [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: 08/20/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia and is characterized by progressive neurodegeneration leading to severe cognitive, memory, and behavioral impairments. The onset of AD involves a complex interplay among various factors, including age, genetics, chronic inflammation, and impaired energy metabolism. Despite significant efforts, there are currently no effective therapies capable of modifying the course of AD, likely owing to an excessive focus on the amyloid hypothesis and a limited consideration of other intracellular pathways. In the present review, we emphasize the emerging concept of AD as a metabolic disease, where alterations in energy metabolism play a critical role in its development and progression. Notably, glucose metabolism impairment is associated with mitochondrial dysfunction, oxidative stress, Ca2+ dyshomeostasis, and protein misfolding, forming interconnected processes that perpetuate a detrimental self-feeding loop sustaining AD progression. Advanced glycation end products (AGEs), neurotoxic compounds that accumulate in AD, are considered an important consequence of glucose metabolism disruption, and glyceraldehyde (GA), a glycolytic intermediate, is a key contributor to AGEs formation in both neurons and astrocytes. Exploring the impact of GA-induced glucose metabolism impairment opens up exciting possibilities for creating an easy-to-handle in vitro model that recapitulates the early stage of the disease. This model holds great potential for advancing the development of novel therapeutics targeting various intracellular pathways implicated in AD pathogenesis. In conclusion, looking beyond the conventional amyloid hypothesis could lead researchers to discover promising targets for intervention, offering the possibility of addressing the existing medical gaps in AD treatment.
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Affiliation(s)
- Silvia Piccirillo
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
| | - Alessandra Preziuso
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
| | - Giorgia Cerqueni
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
| | - Tiziano Serfilippi
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
| | - Valentina Terenzi
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
| | - Antonio Vinciguerra
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
| | - Salvatore Amoroso
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
| | - Vincenzo Lariccia
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
| | - Simona Magi
- Department of Biomedical Sciences and Public Health, School of Medicine, University "Politecnica delle Marche", Via Tronto 10/A, 60126 Ancona, Italy.
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8
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García-Bermúdez MY, Vohra R, Freude K, van Wijngaarden P, Martin K, Thomsen MS, Aldana BI, Kolko M. Potential Retinal Biomarkers in Alzheimer's Disease. Int J Mol Sci 2023; 24:15834. [PMID: 37958816 PMCID: PMC10649108 DOI: 10.3390/ijms242115834] [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: 09/01/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Alzheimer's disease (AD) represents a major diagnostic challenge, as early detection is crucial for effective intervention. This review examines the diagnostic challenges facing current AD evaluations and explores the emerging field of retinal alterations as early indicators. Recognizing the potential of the retina as a noninvasive window to the brain, we emphasize the importance of identifying retinal biomarkers in the early stages of AD. However, the examination of AD is not without its challenges, as the similarities shared with other retinal diseases introduce complexity in the search for AD-specific markers. In this review, we address the relevance of using the retina for the early diagnosis of AD and the complex challenges associated with the search for AD-specific retinal biomarkers. We provide a comprehensive overview of the current landscape and highlight avenues for progress in AD diagnosis by retinal examination.
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Affiliation(s)
| | - Rupali Vohra
- Eye Translational Research Unit, Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark
| | - Kristine Freude
- Group of Stem Cell Models and Embryology, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Peter van Wijngaarden
- Center for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Keith Martin
- Center for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Maj Schneider Thomsen
- Neurobiology Research and Drug Delivery, Department of Health, Science and Technology, Aalborg University, 9220 Aalborg, Denmark
| | - Blanca Irene Aldana
- Neurometabolism Research Group, Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Miriam Kolko
- Eye Translational Research Unit, Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark
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9
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Malnar Črnigoj M, Čerček U, Yin X, Ho MT, Repic Lampret B, Neumann M, Hermann A, Rouleau G, Suter B, Mayr M, Rogelj B. Phenylalanine-tRNA aminoacylation is compromised by ALS/FTD-associated C9orf72 C4G2 repeat RNA. Nat Commun 2023; 14:5764. [PMID: 37717009 PMCID: PMC10505166 DOI: 10.1038/s41467-023-41511-3] [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: 10/14/2022] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
The expanded hexanucleotide GGGGCC repeat mutation in the C9orf72 gene is the main genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Under one disease mechanism, sense and antisense transcripts of the repeat are predicted to bind various RNA-binding proteins, compromise their function and cause cytotoxicity. Here we identify phenylalanine-tRNA synthetase (FARS) subunit alpha (FARSA) as the main interactor of the CCCCGG antisense repeat RNA in cytosol. The aminoacylation of tRNAPhe by FARS is inhibited by antisense RNA, leading to decreased levels of charged tRNAPhe. Remarkably, this is associated with global reduction of phenylalanine incorporation in the proteome and decrease in expression of phenylalanine-rich proteins in cellular models and patient tissues. In conclusion, this study reveals functional inhibition of FARSA in the presence of antisense RNA repeats. Compromised aminoacylation of tRNA could lead to impairments in protein synthesis and further contribute to C9orf72 mutation-associated pathology.
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Affiliation(s)
- Mirjana Malnar Črnigoj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Urša Čerček
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, 1000, Slovenia
- Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Xiaoke Yin
- King's BHF Centre, King's College London, London, SE5 9NU, UK
| | - Manh Tin Ho
- Institute of Cell Biology, University of Bern, Bern, 3012, Switzerland
| | - Barbka Repic Lampret
- Clinical Institute of Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
| | - Manuela Neumann
- Molecular Neuropathology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Tübingen, 72076, Germany
- Department of Neuropathology, University Hospital of Tübingen, Tübingen, 72076, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology and Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147, Rostock, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Rostock/Greifswald, 18147, Rostock, Germany
| | - Guy Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, H3A 0G4, Canada
| | - Beat Suter
- Institute of Cell Biology, University of Bern, Bern, 3012, Switzerland
| | - Manuel Mayr
- King's BHF Centre, King's College London, London, SE5 9NU, UK
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, 1000, Slovenia.
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, 1000, Slovenia.
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Georgiev SV, Rizzoli SO. The long-loop recycling (LLR) of synaptic components as a question of economics. Mol Cell Neurosci 2023; 126:103862. [PMID: 37236414 DOI: 10.1016/j.mcn.2023.103862] [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: 02/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
The pre- and post-synaptic compartments contain a variety of molecules that are known to recycle between the plasma membrane and intracellular organelles. The recycling steps have been amply described in functional terms, with, for example, synaptic vesicle recycling being essential for neurotransmitter release, and postsynaptic receptor recycling being a fundamental feature of synaptic plasticity. However, synaptic protein recycling may also serve a more prosaic role, simply ensuring the repeated use of specific components, thereby minimizing the energy expenditure on the synthesis of synaptic proteins. This type of process has been recently described for components of the extracellular matrix, which undergo long-loop recycling (LLR), to and from the cell body. Here we suggest that the energy-saving recycling of synaptic components may be more widespread than is generally acknowledged, potentially playing a role in both synaptic vesicle protein usage and postsynaptic receptor metabolism.
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Affiliation(s)
- Svilen Veselinov Georgiev
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Germany; International Max Planck Research School for Neuroscience, Göttingen, Germany.
| | - Silvio O Rizzoli
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Germany; Biostructural Imaging of Neurodegeneration (BIN) Center, Göttingen, Germany; Excellence Cluster Multiscale Bioimaging, Göttingen, Germany.
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11
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Bhattacharya R, Alam MR, Kamal MA, Seo KJ, Singh LR. AGE-RAGE axis culminates into multiple pathogenic processes: a central road to neurodegeneration. Front Mol Neurosci 2023; 16:1155175. [PMID: 37266370 PMCID: PMC10230046 DOI: 10.3389/fnmol.2023.1155175] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/27/2023] [Indexed: 06/03/2023] Open
Abstract
Advanced glycation end-products (AGEs; e.g., glyoxal, methylglyoxal or carboxymethyl-lysine) are heterogenous group of toxic compounds synthesized in the body through both exogenous and endogenous pathways. AGEs are known to covalently modify proteins bringing about loss of functional alteration in the proteins. AGEs also interact with their receptor, receptor for AGE (RAGE) and such interactions influence different biological processes including oxidative stress and apoptosis. Previously, AGE-RAGE axis has long been considered to be the maligning factor for various human diseases including, diabetes, obesity, cardiovascular, aging, etc. Recent developments have revealed the involvement of AGE-RAGE axis in different pathological consequences associated with the onset of neurodegeneration including, disruption of blood brain barrier, neuroinflammation, remodeling of extracellular matrix, dysregulation of polyol pathway and antioxidant enzymes, etc. In the present article, we attempted to describe a new avenue that AGE-RAGE axis culminates to different pathological consequences in brain and therefore, is a central instigating component to several neurodegenerative diseases (NGDs). We also invoke that specific inhibitors of TIR domains of TLR or RAGE receptors are crucial molecules for the therapeutic intervention of NGDs. Clinical perspectives have also been appropriately discussed.
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Affiliation(s)
- Reshmee Bhattacharya
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Mohammad Rizwan Alam
- Department of Hospital Pathology, College of Medicine, Uijeongbu St. Mary’s Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj, Saudi Arabia
| | - Kyung Jin Seo
- Department of Hospital Pathology, College of Medicine, Uijeongbu St. Mary’s Hospital, The Catholic University of Korea, Seoul, Republic of Korea
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12
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Crawford AH, Hildyard JCW, Wells DJ, Piercy RJ. Identification of quantitative polymerase chain reaction reference genes suitable for normalising gene expression in the brain of normal and dystrophic mice and dogs. Wellcome Open Res 2023; 6:84. [PMID: 37942409 PMCID: PMC10628364 DOI: 10.12688/wellcomeopenres.16707.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 11/10/2023] Open
Abstract
Background: In addition to progressive, debilitating muscle degeneration, ~50% of patients with Duchenne muscular dystrophy (DMD) have associated cognitive and behavioural disorders secondary to deficiency of dystrophin protein in the brain. The brain expresses a variety of dystrophin isoforms (Dp427, Dp140 and Dp71) whose functions remain to be fully elucidated. Detailed comparative analysis of gene expression in healthy and dystrophin-deficient brain is fundamental to understanding the functions of each isoform, and the consequences of their deficiency, with animal models representing a key tool in this endeavour. Reverse transcription quantitative real-time PCR (RT-qPCR) is a widely used method to study gene expression. However, accurate quantitative assessment requires normalisation of expression data using validated reference genes. The aim of this study was to identify a panel of suitable reference genes that can be used to normalise gene expression in the brain of healthy and dystrophic dogs and mice. Methods: Using the DE50-MD dog and mdx mouse models of DMD we performed RT-qPCR from fresh frozen brain tissue and employed the geNorm, BestKeeper and Normfinder algorithms to determine the stability of expression of a panel of candidate reference genes across healthy and dystrophic animals, and across different brain regions. Results: We show that SDHA, UBC and YWHAZ are suitable reference genes for normalising gene expression in healthy and dystrophic canine brain, and GAPDH, RPL13A and CYC1 in healthy and dystrophic murine brain. Notably, there was no overlap in the highest performing reference genes between the two species. Conclusions: Our findings suggest that gene expression normalisation is possible across six regions of the canine brain, and three regions of the murine brain. Our results should facilitate future work to study gene expression in the brains of normal and dystrophic dogs and mice and thus decipher the transcriptional consequences of dystrophin deficiency in the brain.
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Affiliation(s)
- Abbe H. Crawford
- Clinical Science and Services, Royal Veterinary College, London, UK
| | | | - Dominic J. Wells
- Comparative Biomedical Sciences, Royal Veterinary College, London, UK
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13
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Gupta MN, Uversky VN. Moonlighting enzymes: when cellular context defines specificity. Cell Mol Life Sci 2023; 80:130. [PMID: 37093283 PMCID: PMC11073002 DOI: 10.1007/s00018-023-04781-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 04/15/2023] [Indexed: 04/25/2023]
Abstract
It is not often realized that the absolute protein specificity is an exception rather than a rule. Two major kinds of protein multi-specificities are promiscuity and moonlighting. This review discusses the idea of enzyme specificity and then focusses on moonlighting. Some important examples of protein moonlighting, such as crystallins, ceruloplasmin, metallothioniens, macrophage migration inhibitory factor, and enzymes of carbohydrate metabolism are discussed. How protein plasticity and intrinsic disorder enable the removing the distinction between enzymes and other biologically active proteins are outlined. Finally, information on important roles of moonlighting in human diseases is updated.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612-4799, USA.
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14
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Khan A, Zahid S, Hasan B, Asif AR, Ahmed N. Mass Spectrometry based identification of site-specific proteomic alterations and potential pathways underlying the pathophysiology of schizophrenia. Mol Biol Rep 2023; 50:4931-4943. [PMID: 37076706 DOI: 10.1007/s11033-023-08431-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023]
Abstract
BACKGROUND Schizophrenia (SZ) is a complex multifactorial disorder that affects 1% of the population worldwide with no available effective treatment. Although proteomic alterations are reported in SZ however proteomic expression aberrations among different brain regions are not fully determined. Therefore, the present study aimed spatial differential protein expression profiling of three distinct regions of SZ brain and identification of associated affected biological pathways in SZ progression. METHODS AND RESULTS Comparative protein expression profiling of three distinct autopsied human brain regions (i.e., substantia nigra, hippocampus and prefrontal cortex) of SZ was performed with respective healthy controls. Using two-dimensional electrophoresis (2DE)-based nano liquid chromatography tandem mass spectrometry (Nano-LC MS /MS) analysis, 1443 proteins were identified out of which 58 connote to be significantly dysregulated, representing 26 of substantia nigra,14 of hippocampus and 18 of prefrontal cortex. The 58 differentially expressed proteins were further analyzed using Ingenuity pathway analysis (IPA). The IPA analysis provided protein-protein interaction networks of several proteins including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kb), extracellular signal regulated kinases 1/2 (ERK1/2), alpha serine / Threonine-protein kinase (AKT1), cellular tumor antigen p53 (TP53) and amyloid precursor protein (APP), holding prime positions in networks and interacts with most of the identified proteins and their closely interacting partners. CONCLUSION These findings provide conceptual insights of novel SZ related pathways and the cross talk of co and contra regulated proteins. This spatial proteomic analysis will further broaden the conceptual framework for schizophrenia research in future.
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Affiliation(s)
- Ayesha Khan
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Saadia Zahid
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Beena Hasan
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Abdul R Asif
- Institute of Clinical Chemistry, University Medical Center, Robert-Koch-Str. 40, 37075, Göttingen, Göttingen, Germany
| | - Nikhat Ahmed
- Neurochemistry Research Laboratory, Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan.
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15
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Origin of Elevated S-Glutathionylated GAPDH in Chronic Neurodegenerative Diseases. Int J Mol Sci 2023; 24:ijms24065529. [PMID: 36982600 PMCID: PMC10056234 DOI: 10.3390/ijms24065529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/30/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
H2O2-oxidized glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalytic cysteine residues (Cc(SH) undergo rapid S-glutathionylation. Restoration of the enzyme activity is accomplished by thiol/disulfide SN2 displacement (directly or enzymatically) forming glutathione disulfide (G(SS)G) and active enzyme, a process that should be facile as Cc(SH) reside on the subunit surface. As S-glutathionylated GAPDH accumulates following ischemic and/or oxidative stress, in vitro/silico approaches have been employed to address this paradox. Cc(SH) residues were selectively oxidized and S-glutathionylated. Kinetics of GAPDH dehydrogenase recovery demonstrated that glutathione is an ineffective reactivator of S-glutathionylated GAPDH compared to dithiothreitol. Molecular dynamic simulations (MDS) demonstrated strong binding interactions between local residues and S-glutathione. A second glutathione was accommodated for thiol/disulfide exchange forming a tightly bound glutathione disulfide G(SS)G. The proximal sulfur centers of G(SS)G and Cc(SH) remained within covalent bonding distance for thiol/disulfide exchange resonance. Both these factors predict inhibition of dissociation of G(SS)G, which was verified by biochemical analysis. MDS also revealed that both S-glutathionylation and bound G(SS)G significantly perturbed subunit secondary structure particularly within the S-loop, region which interacts with other cellular proteins and mediates NAD(P)+ binding specificity. Our data provides a molecular rationale for how oxidative stress elevates S-glutathionylated GAPDH in neurodegenerative diseases and implicates novel targets for therapeutic intervention.
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16
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Tringides ML, Zhang Z, Morgan CE, Su CC, Yu EW. A cryo-electron microscopic approach to elucidate protein structures from human brain microsomes. Life Sci Alliance 2023; 6:6/2/e202201724. [PMID: 36450447 PMCID: PMC9713474 DOI: 10.26508/lsa.202201724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual proteins from a heterogeneous, multiprotein sample. Here we report the use of "Build and Retrieve" to define the composition of a raw human brain microsomal lysate. From this sample, we simultaneously identify and solve cryo-EM structures of five different brain enzymes whose functions affect neurotransmitter recycling, iron metabolism, glycolysis, axonal development, energy homeostasis, and retinoic acid biosynthesis. Interestingly, malfunction of these important proteins has been directly linked to several neurodegenerative disorders, such as Alzheimer's, Huntington's, and Parkinson's diseases. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
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Affiliation(s)
- Marios L Tringides
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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17
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Ahmad I, Singh R, Pal S, Prajapati S, Sachan N, Laiq Y, Husain H. Exploring the Role of Glycolytic Enzymes PFKFB3 and GAPDH in the Modulation of Aβ and Neurodegeneration and Their Potential of Therapeutic Targets in Alzheimer's Disease. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04340-0. [PMID: 36692648 DOI: 10.1007/s12010-023-04340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 01/25/2023]
Abstract
Alzheimer's disease (AD) is presently the 6th major cause of mortality across the globe. However, it is expected to rise rapidly, following cancer and heart disease, as a leading cause of death among the elderly peoples. AD is largely characterized by metabolic changes linked to glucose metabolism and age-induced mitochondrial failure. Recent research suggests that the glycolytic pathway is required for a range of neuronal functions in the brain including synaptic transmission, energy production, and redox balance; however, alteration in glycolytic pathways may play a significant role in the development of AD. Moreover, it is hypothesized that targeting the key enzymes involved in glucose metabolism may help to prevent or reduce the risk of neurodegenerative disorders. One of the major pro-glycolytic enzyme is 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3); it is normally absent in neurons but abundant in astrocytes. Similarly, another key of glycolysis is glyceraldehyde-3-phosphate dehydrogenase (GAPDH) which catalyzes the conversion of aldolase and glyceraldehyde 3 phosphates to 1,3 bisphosphoglycerate. GAPDH has been reported to interact with various neurodegenerative disease-associated proteins, including the amyloid-β protein precursor (AβPP). These findings indicate PFKFB3 and GAPDH as a promising therapeutic target to AD. Current review highlight the contributions of PFKFB3 and GAPDH in the modulation of Aβand AD pathogenesis and further explore the potential of PFKFB3 and GAPDH as therapeutic targets in AD.
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Affiliation(s)
- Imran Ahmad
- Department of Biochemistry, King George's Medical University, Lucknow, 226003, Uttar Pradesh, India.
| | - Ranjana Singh
- Department of Biochemistry, King George's Medical University, Lucknow, 226003, Uttar Pradesh, India.
| | - Saurabh Pal
- Department of Biotechnology, Era's Lucknow Medical College & Hospital, Era University, Lucknow, 226003, Uttar Pradesh, India
| | - Soni Prajapati
- Department of Biochemistry, King George's Medical University, Lucknow, 226003, Uttar Pradesh, India
| | - Nidhi Sachan
- Cell and Neurobiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Yusra Laiq
- Department of Biochemistry, King George's Medical University, Lucknow, 226003, Uttar Pradesh, India
| | - Hadiya Husain
- Department of Zoology, University of Lucknow, Lucknow, 226007, Uttar Pradesh, India
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18
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Mechanism of inactivation of glyceraldehyde-3-phosphate dehydrogenase in the presence of methylglyoxal. Arch Biochem Biophys 2023; 733:109485. [PMID: 36481268 DOI: 10.1016/j.abb.2022.109485] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is known to be one of the targets of methylglyoxal (MGO), a metabolite of glycolysis that increased in diabetes. However, the mechanism of GAPDH inactivation in the presence of MGO is unclear. The purpose of the work was to study the reaction of GAPDH with MGO and to identify the products of the reaction. It was shown that incubation of recombinant human GAPDH with MGO leads to irreversible inactivation of the enzyme, which is accompanied by a decrease in SH-group content by approximately 3.3 per tetramer GAPDH. MALDI-TOF MS analysis showed that the modification of GAPDH with MGO results in the oxidation of the catalytic cysteine residues (Cys152) to form cysteine-sulfinic acid. In addition, 2 arginine residues (R80 and R234) were identified that react with MGO to form hydroimidazolones. Incubation of SH-SY5Y neuroblastoma cells with MGO resulted in the inactivation of GAPDH and inhibition of glycolysis. The mechanism of GAPDH oxidation in the presence of MGO suggests the participation of superoxide anion, which is formed during the reaction of amino groups with methylglyoxal. The role of GAPDH in protection against the damaging effect of ROS in cells in the case of inefficiency of MGO removal by the GSH-dependent glyoxalase system is discussed.
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19
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Homeostasis of carbohydrates and reactive oxygen species is critically changed in the brain of middle-aged mice: molecular mechanisms and functional reasons. BBA ADVANCES 2023; 3:100077. [PMID: 37082254 PMCID: PMC10074963 DOI: 10.1016/j.bbadva.2023.100077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 01/23/2023] Open
Abstract
The brain is an organ that consumes a lot of energy. In the brain, energy is required for synaptic transmission, numerous biosynthetic processes and axonal transport in neurons, and for many supportive functions of glial cells. The main source of energy in the brain is glucose and to a lesser extent lactate and ketone bodies. ATP is formed at glucose catabolism via glycolysis and oxidative phosphorylation in mitochondrial electron transport chain (ETC) within mitochondria being the main source of ATP. With age, brain's energy metabolism is disturbed, involving a decrease in glycolysis and mitochondrial dysfunction. The latter is accompanied by intensified generation of reactive oxygen species (ROS) in ETC leading to oxidative stress. Recently, we have found that crucial changes in energy metabolism and intensity of oxidative stress in the mouse brain occur in middle age with minor progression in old age. In this review, we analyze the metabolic changes and functional causes that lead to these changes in the aging brain.
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20
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Ozguc O, Vonesch S. Finding abundance regulators. eLife 2022; 11:e83907. [PMID: 36326804 PMCID: PMC9633062 DOI: 10.7554/elife.83907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new pooled screening method in yeast allows scientists to probe how protein levels are regulated by mutating thousands of genes at once.
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Affiliation(s)
- Olivia Ozguc
- Center for Microbiology, VIB-KU LeuvenLeuvenBelgium
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU LeuvenLeuvenBelgium
| | - Sibylle Vonesch
- Center for Microbiology, VIB-KU LeuvenLeuvenBelgium
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU LeuvenLeuvenBelgium
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21
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Metabolic and Cellular Compartments of Acetyl-CoA in the Healthy and Diseased Brain. Int J Mol Sci 2022; 23:ijms231710073. [PMID: 36077475 PMCID: PMC9456256 DOI: 10.3390/ijms231710073] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
The human brain is characterised by the most diverse morphological, metabolic and functional structure among all body tissues. This is due to the existence of diverse neurons secreting various neurotransmitters and mutually modulating their own activity through thousands of pre- and postsynaptic interconnections in each neuron. Astroglial, microglial and oligodendroglial cells and neurons reciprocally regulate the metabolism of key energy substrates, thereby exerting several neuroprotective, neurotoxic and regulatory effects on neuronal viability and neurotransmitter functions. Maintenance of the pool of mitochondrial acetyl-CoA derived from glycolytic glucose metabolism is a key factor for neuronal survival. Thus, acetyl-CoA is regarded as a direct energy precursor through the TCA cycle and respiratory chain, thereby affecting brain cell viability. It is also used for hundreds of acetylation reactions, including N-acetyl aspartate synthesis in neuronal mitochondria, acetylcholine synthesis in cholinergic neurons, as well as divergent acetylations of several proteins, peptides, histones and low-molecular-weight species in all cellular compartments. Therefore, acetyl-CoA should be considered as the central point of metabolism maintaining equilibrium between anabolic and catabolic pathways in the brain. This review presents data supporting this thesis.
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22
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Yang X, Wang C, Yang L, Zheng Q, Liu Q, Wawryk NJP, Li XF. Neurotoxicity and transcriptome changes in embryonic zebrafish induced by halobenzoquinone exposure. J Environ Sci (China) 2022; 117:129-140. [PMID: 35725065 DOI: 10.1016/j.jes.2022.03.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Halobenzoquinones (HBQs) are emerging disinfection byproducts (DBPs) with a widespread presence in drinking water that exhibit much higher cytotoxicity than regulated DBPs. However, the developmental neurotoxicity of HBQs has not been studied in vivo. In this work, we studied the neurotoxicity of HBQs on zebrafish embryos, after exposure to varying concentrations (0-8 µmol/L) of three HBQs, 2,5-dichloro-1,4-benzoquinone (2,5-DCBQ), 2,6-dichloro-1,4-benzoquinone (2,6-DCBQ), and 2,5-dibromo-1,4-benzoquinone (2,5-DBBQ) for 4 to 120 hr post fertilization (hpf). HBQ exposure significantly decreased the locomotor activity of larvae, accompanied by significant reduction of neurotransmitters (dopamine and γ-aminobutyric acid) and acetylcholinesterase activity. Furthermore, the expression of genes involved in neuronal morphogenesis (gfap, α1-tubulin, mbp, and syn-2α) were downregulated by 4.4-, 5.2-, 3.0-, and 4.5-fold in the 5 µmol/L 2,5-DCBQ group and 2.0-, 1.6-, 2.1-, and 2.3-fold in the 5 µmol/L 2,5-DBBQ group, respectively. Transcriptomic analysis revealed that HBQ exposure affected the signaling pathways of neural development. This study demonstrates the significant neurotoxicity of HBQs in embryonic zebrafish and provides molecular evidence for understanding the potential mechanisms of HBQ neurotoxicity.
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Affiliation(s)
- Xue Yang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Chang Wang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China; Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
| | - Lihua Yang
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Qi Zheng
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Qiongyu Liu
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Nicholas J P Wawryk
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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23
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Hyslop PA, Chaney MO. Mechanism of GAPDH Redox Signaling by H 2O 2 Activation of a Two-Cysteine Switch. Int J Mol Sci 2022; 23:4604. [PMID: 35562998 PMCID: PMC9102624 DOI: 10.3390/ijms23094604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
Oxidation of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) by reactive oxygen species such as H2O2 activate pleiotropic signaling pathways is associated with pathophysiological cell fate decisions. Oxidized GAPDH binds chaperone proteins with translocation of the complex to the nucleus and mitochondria initiating autophagy and cellular apoptosis. In this study, we establish the mechanism by which H2O2-oxidized GAPDH subunits undergo a subunit conformational rearrangement. H2O2 oxidizes both the catalytic cysteine and a vicinal cysteine (four residues downstream) to their respective sulfenic acids. A 'two-cysteine switch' is activated, whereby the sulfenic acids irreversibly condense to an intrachain thiosulfinic ester resulting in a major metastable subunit conformational rearrangement. All four subunits of the homotetramer are uniformly and independently oxidized by H2O2, and the oxidized homotetramer is stabilized at low temperatures. Over time, subunits unfold forming disulfide-linked aggregates with the catalytic cysteine oxidized to a sulfinic acid, resulting from thiosulfinic ester hydrolysis via the highly reactive thiosulfonic ester intermediate. Molecular Dynamic Simulations provide additional mechanistic insights linking GAPDH subunit oxidation with generating a putative signaling conformer. The low-temperature stability of the H2O2-oxidized subunit conformer provides an operable framework to study mechanisms associated with gain-of-function activities of oxidized GAPDH to identify novel targets for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Paul A. Hyslop
- Arkley Research Labs, Arkley BioTek, LLC, 4444 Decatur Blvd., Indianapolis, IN 46241, USA
| | - Michael O. Chaney
- Eli Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN 46285, USA;
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24
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Alteration in the Expression of Genes Involved in Cerebral Glucose Metabolism as a Process of Adaptation to Stressful Conditions. Brain Sci 2022; 12:brainsci12040498. [PMID: 35448030 PMCID: PMC9030173 DOI: 10.3390/brainsci12040498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/05/2023] Open
Abstract
Exposure to chronic stress leads to disturbances in glucose metabolism in the brain, and changes in the functioning of neurons coexisting with the development of depression. The detailed molecular mechanism and cerebral gluconeogenesis during depression are not conclusively established. The aim of the research was to assess the expression of selected genes involved in cerebral glucose metabolism of mice in the validated animal paradigm of chronic stress. To confirm the induction of depression-like disorders, we performed three behavioral tests: sucrose preference test (SPT), forced swim test (FST), and tail suspension test (TST). In order to study the cerebral glucose metabolism of the brain, mRNA levels of the following genes were determined in the prefrontal cortex of mice: Slc2a3, Gapdh, Ldha, Ldhb, and Pkfb3. It has been shown that exogenous, chronic administration of corticosterone developed a model of depression in behavioral tests. There were statistically significant changes in the mRNA level of the Slc2a3, Ldha, Gapdh, and Ldhb genes. The obtained results suggest changes in cerebral glucose metabolism as a process of adaptation to stressful conditions, and may provide the basis for introducing new therapeutic strategies for chronic stress-related depression.
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25
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Defining the Role of Isoeugenol from Ocimum tenuiflorum against Diabetes Mellitus-Linked Alzheimer’s Disease through Network Pharmacology and Computational Methods. Molecules 2022; 27:molecules27082398. [PMID: 35458596 PMCID: PMC9025232 DOI: 10.3390/molecules27082398] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 02/07/2023] Open
Abstract
The present study involves the integrated network pharmacology and phytoinformatics-based investigation of phytocompounds from Ocimum tenuiflorum against diabetes mellitus-linked Alzheimer’s disease. It aims to investigate the mechanism of the Ocimum tenuiflorum phytocompounds in the amelioration of diabetes mellitus-linked Alzheimer’s disease through network pharmacology, druglikeness and pharmacokinetics, molecular docking simulations, GO analysis, molecular dynamics simulations, and binding free energy analyses. A total of 14 predicted genes of the 26 orally bioactive compounds were identified. Among these 14 genes, GAPDH and AKT1 were the most significant. The network analysis revealed the AGE-RAGE signaling pathway to be a prominent pathway linked to GAPDH with 50.53% probability. Upon the molecular docking simulation with GAPDH, isoeugenol was found to possess the most significant binding affinity (−6.0 kcal/mol). The molecular dynamics simulation and binding free energy calculation results also predicted that isoeugenol forms a stable protein–ligand complex with GAPDH, where the phytocompound is predicted to chiefly use van der Waal’s binding energy (−159.277 kj/mol). On the basis of these results, it can be concluded that isoeugenol from Ocimum tenuiflorum could be taken for further in vitro and in vivo analysis, targeting GAPDH inhibition for the amelioration of diabetes mellitus-linked Alzheimer’s disease.
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26
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Gray ALH, Sawaya MR, Acharyya D, Lou J, Edington EM, Best MD, Prosser RA, Eisenberg DS, Do TD. Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices. Protein Sci 2022; 31:716-727. [PMID: 34954854 PMCID: PMC8862425 DOI: 10.1002/pro.4268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Atomic structures of amyloid oligomers that capture the neurodegenerative disease pathology are essential to understand disease-state causes and finding cures. Here we investigate the G6W mutation of the cytotoxic, hexameric amyloid model KV11. The mutation results into an asymmetric dodecamer composed of a pair of 30° twisted antiparallel β-sheets. The complete break between adjacent β-strands is unprecedented among amyloid fibril crystal structures and supports that our structure is an oligomer. The poor shape complementarity between mated sheets reveals an interior channel for binding lipids, suggesting that the toxicity may be due to a perturbation of lipid transport rather than a direct disruption of membrane integrity. Viability assays on mouse suprachiasmatic nucleus, anterior hypothalamus, and cerebral cortex demonstrated selective regional vulnerability consistent with Alzheimer's disease. Neuropeptides released from the brain slices may provide clues to how G6W initiates cellular injury.
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Affiliation(s)
- Amber L. H. Gray
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Michael R. Sawaya
- HHMIUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Biological ChemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Energy Institute for Genomics and ProteomicsUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Debalina Acharyya
- Department of Biochemistry & Cellular and Molecular BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Jinchao Lou
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | | | - Michael D. Best
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Rebecca A. Prosser
- Department of Biochemistry & Cellular and Molecular BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - David S. Eisenberg
- HHMIUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Biological ChemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Energy Institute for Genomics and ProteomicsUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Thanh D. Do
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
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27
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Jung Y, Noda N, Takaya J, Abo M, Toh K, Tajiri K, Cui C, Zhou L, Sato SI, Uesugi M. Discovery of Non-Cysteine-Targeting Covalent Inhibitors by Activity-Based Proteomic Screening with a Cysteine-Reactive Probe. ACS Chem Biol 2022; 17:340-347. [PMID: 35076225 DOI: 10.1021/acschembio.1c00824] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covalent inhibitors of enzymes are increasingly appreciated as pharmaceutical seeds, yet discovering non-cysteine-targeting inhibitors remains challenging. Herein, we report an intriguing experience during our activity-based proteomic screening of 1601 reactive small molecules, in which we monitored the ability of library molecules to compete with a cysteine-reactive iodoacetamide probe. One epoxide molecule, F8, exhibited unexpected enhancement of the probe reactivity for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a rate-limiting glycolysis enzyme. In-depth mechanistic analysis suggests that F8 forms a covalent adduct with an aspartic acid in the active site to displace NAD+, a cofactor of the enzyme, with concomitant enhancement of the probe reaction with the catalytic cysteine. The mechanistic underpinning permitted the identification of an optimized aspartate-reactive GAPDH inhibitor. Our findings exemplify that activity-based proteomic screening with a cysteine-reactive probe can be used for discovering covalent inhibitors that react with non-cysteine residues.
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Affiliation(s)
- Yejin Jung
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naotaka Noda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Junichiro Takaya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiro Abo
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kohei Toh
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ken Tajiri
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Changyi Cui
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Lu Zhou
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shin-ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- School of Pharmacy, Fudan University, Shanghai 201203, China
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
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28
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Martinez-Banaclocha M. N-Acetyl-Cysteine: Modulating the Cysteine Redox Proteome in Neurodegenerative Diseases. Antioxidants (Basel) 2022; 11:antiox11020416. [PMID: 35204298 PMCID: PMC8869501 DOI: 10.3390/antiox11020416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 12/14/2022] Open
Abstract
In the last twenty years, significant progress in understanding the pathophysiology of age-associated neurodegenerative diseases has been made. However, the prevention and treatment of these diseases remain without clinically significant therapeutic advancement. While we still hope for some potential genetic therapeutic approaches, the current reality is far from substantial progress. With this state of the issue, emphasis should be placed on early diagnosis and prompt intervention in patients with increased risk of neurodegenerative diseases to slow down their progression, poor prognosis, and decreasing quality of life. Accordingly, it is urgent to implement interventions addressing the psychosocial and biochemical disturbances we know are central in managing the evolution of these disorders. Genomic and proteomic studies have shown the high molecular intricacy in neurodegenerative diseases, involving a broad spectrum of cellular pathways underlying disease progression. Recent investigations indicate that the dysregulation of the sensitive-cysteine proteome may be a concurrent pathogenic mechanism contributing to the pathophysiology of major neurodegenerative diseases, opening new therapeutic opportunities. Considering the incidence and prevalence of these disorders and their already significant burden in Western societies, they will become a real pandemic in the following decades. Therefore, we propose large-scale investigations, in selected groups of people over 40 years of age with decreased blood glutathione levels, comorbidities, and/or mild cognitive impairment, to evaluate supplementation of the diet with low doses of N-acetyl-cysteine, a promising and well-tolerated therapeutic agent suitable for long-term use.
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29
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Metabolic Features of Brain Function with Relevance to Clinical Features of Alzheimer and Parkinson Diseases. Molecules 2022; 27:molecules27030951. [PMID: 35164216 PMCID: PMC8839962 DOI: 10.3390/molecules27030951] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
Brain metabolism is comprised in Alzheimer’s disease (AD) and Parkinson’s disease (PD). Since the brain primarily relies on metabolism of glucose, ketone bodies, and amino acids, aspects of these metabolic processes in these disorders—and particularly how these altered metabolic processes are related to oxidative and/or nitrosative stress and the resulting damaged targets—are reviewed in this paper. Greater understanding of the decreased functions in brain metabolism in AD and PD is posited to lead to potentially important therapeutic strategies to address both of these disorders, which cause relatively long-lasting decreased quality of life in patients.
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30
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Ji Y, Liansheng F, Suchen Q, Han X. Stimuli-Responsive Delivery Strategies for Controllable Gene Editing in Tumor Therapeutics. J Mater Chem B 2022; 10:7694-7707. [DOI: 10.1039/d2tb01055k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CRISPR system has attracted significant interest due to its great potential in tumour therapy. Developing effective, precise and safe delivery vectors is a prerequisite for CRISPR applications. Some disease-related biological...
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31
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Canarelli SE, Swalm BM, Larson ET, Morrison MJ, Weerapana E. Monitoring GAPDH activity and inhibition with cysteine-reactive chemical probes. RSC Chem Biol 2022; 3:972-982. [PMID: 35866162 PMCID: PMC9257626 DOI: 10.1039/d2cb00091a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a central enzyme in glycolysis that regulates the Warburg effect in cancer cells. In addition to its role in metabolism, GAPDH is also implicated in diverse cellular processes, including transcription and apoptosis. Dysregulated GAPDH activity is associated with a variety of pathologies, and GAPDH inhibitors have demonstrated therapeutic potential as anticancer and immunomodulatory agents. Given the critical role of GAPDH in pathophysiology, it is important to have access to tools that enable rapid monitoring of GAPDH activity and inhibition within a complex biological system. Here, we report an electrophilic peptide-based probe, SEC1, which covalently modifies the active-site cysteine, C152, of GAPDH to directly report on GAPDH activity within a proteome. We demonstrate the utility of SEC1 to assess changes in GAPDH activity in response to oncogenic transformation, reactive oxygen species (ROS) and small-molecule GAPDH inhibitors, including Koningic acid (KA). We then further evaluated KA, to determine the detailed mechanism of inhibition. Our mechanistic studies confirm that KA is a highly effective irreversible inhibitor of GAPDH, which acts through a NAD+-uncompetitive and G3P-competitive mechanism. Proteome-wide evaluation of the cysteine targets of KA demonstrated high selectivity for the active-site cysteine of GAPDH over other reactive cysteines within the proteome. Lastly, the therapeutic potential of KA was investigated in an autoimmune model, where treatment with KA resulted in decreased cytokine production by Th1 effector cells. Together, these studies describe methods to evaluate GAPDH activity and inhibition within a proteome, and report on the high potency and selectivity of KA as an irreversible inhibitor of GAPDH. Cysteine-reactive chemical probes can covalently modify the active-site cysteine of GAPDH.![]()
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Affiliation(s)
- Sarah E. Canarelli
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | | | - Eric T. Larson
- Rheos Medicines, Inc, Cambridge, Massachusetts 02142, USA
| | | | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
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32
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Kim Y, Kim S, Im G, Kim YH, Jeong G, Jeon HR, Kim D, Lee H, Park SY, Cho SM, Bhang SH. Area light source-triggered latent angiogenic molecular mechanisms intensify therapeutic efficacy of adult stem cells. Bioeng Transl Med 2022; 7:e10255. [PMID: 35079630 PMCID: PMC8780080 DOI: 10.1002/btm2.10255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/03/2021] [Accepted: 09/05/2021] [Indexed: 12/31/2022] Open
Abstract
Light-based therapy such as photobiomodulation (PBM) reportedly produces beneficial physiological effects in cells and tissues. However, most reports have focused on the immediate and instant effects of light. Considering the physiological effects of natural light exposure in living organisms, the latent reaction period after irradiation should be deliberated. In contrast to previous reports, we examined the latent reaction period after light exposure with optimized irradiating parameters and validated novel therapeutic molecular mechanisms for the first time. we demonstrated an organic light-emitting diode (OLED)-based PBM (OPBM) strategy that enhances the angiogenic efficacy of human adipose-derived stem cells (hADSCs) via direct irradiation with red OLEDs of optimized wavelength, voltage, current, luminance, and duration, and investigated the underlying molecular mechanisms. Our results revealed that the angiogenic paracrine effect, viability, and adhesion of hADSCs were significantly intensified by our OPBM strategy. Following OPBM treatment, significant changes were observed in HIF-1α expression, intracellular reactive oxygen species levels, activation of the receptor tyrosine kinase, and glycolytic pathways in hADSCs. In addition, transplantation of OLED-irradiated hADSCs resulted in significantly enhanced limb salvage ratio in a mouse model of hindlimb ischemia. Our OPBM might serve as a new paradigm for stem cell culture systems to develop cell-based therapies in the future.
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Affiliation(s)
- Yu‐Jin Kim
- School of Chemical EngineeringSungkyunkwan UniversitySuwonRepublic of Korea
| | - Sung‐Won Kim
- School of Chemical EngineeringSungkyunkwan UniversitySuwonRepublic of Korea
| | - Gwang‐Bum Im
- School of Chemical EngineeringSungkyunkwan UniversitySuwonRepublic of Korea
| | - Yeong Hwan Kim
- School of Chemical EngineeringSungkyunkwan UniversitySuwonRepublic of Korea
| | - Gun‐Jae Jeong
- Division of Vascular Surgery, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulRepublic of Korea
| | - Hye Ran Jeon
- Department of Health Sciences and Technology, SAIHSTSungkyunkwan UniversitySeoulRepublic of Korea
| | - Dong‐Ik Kim
- Division of Vascular Surgery, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulRepublic of Korea
| | - Haeshin Lee
- Department of Chemistry, Center for Nature‐Inspired Technology (CNiT)Korea Advanced Institute of Science and Technology (KAIST)DaejeonRepublic of Korea
| | - Sung Young Park
- Department of Chemical and Biological EngineeringKorea National University of TransportationChungjuRepublic of Korea
| | - Sung Min Cho
- School of Chemical EngineeringSungkyunkwan UniversitySuwonRepublic of Korea
| | - Suk Ho Bhang
- School of Chemical EngineeringSungkyunkwan UniversitySuwonRepublic of Korea
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33
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Zhang Y, Chen H, Long X, Xu T. Three-dimensional-engineered bioprinted in vitro human neural stem cell self-assembling culture model constructs of Alzheimer's disease. Bioact Mater 2021; 11:192-205. [PMID: 34938923 PMCID: PMC8665263 DOI: 10.1016/j.bioactmat.2021.09.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 12/31/2022] Open
Abstract
The pathogenic cascade of Alzheimer's disease (AD) characterized by amyloid-β protein accumulation is still poorly understood, partially owing to the limitations of relevant models without in vivo neural tissue microenvironment to recapitulate cell-cell interactions. To better mimic neural tissue microenvironment, three-dimensional (3D) core-shell AD model constructs containing human neural progenitor cells (NSCs) with 2% matrigel as core bioink and 2% alginate as shell bioink have been bioprinted by a co-axial bioprinter, with a suitable shell thickness for nutrient exchange and barrier-free cell interaction cores. These constructs exhibit cell self-clustering and -assembling properties and engineered reproducibility with long-term cell viability and self-renewal, and a higher differentiation level compared to 2D and 3D MIX models. The different effects of 3D bioprinted, 2D, and MIX microenvironments on the growth of NSCs are mainly related to biosynthesis of amino acids and glyoxylate and dicarboxylate metabolism on day 2 and ribosome, biosynthesis of amino acids and proteasome on day 14. Particularly, the model constructs demonstrated Aβ aggregation and higher expression of Aβ and tau isoform genes compared to 2D and MIX controls. AD model constructs will provide a promising strategy to facilitate the development of a 3D in vitro AD model for neurodegeneration research.
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Affiliation(s)
- Yi Zhang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Haiyan Chen
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xiaoyan Long
- East China Institute of Digital Medical Engineering, Shangrao, 334000, China
| | - Tao Xu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.,Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
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34
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Schmalhausen EV, Medvedeva MV, Serebryakova MV, Chagovets VV, Muronetz VI. Products of S-nitrosylation of glyceraldehyde-3-phosphate dehydrogenase: Relation between S-nitrosylation and oxidation. Biochim Biophys Acta Gen Subj 2021; 1866:130032. [PMID: 34627945 DOI: 10.1016/j.bbagen.2021.130032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 10/06/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the major targets of NO in cells, especially in neurodegenerative diseases. S-Nitrosylation of GAPDH is accompanied by its translocation into the nucleus with subsequent apoptosis. The product of GAPDH modification by NO is considered to be S-nitrosylated GAPDH (GAPDH-SNO). However, this has not been confirmed by direct methods. METHODS Products of GAPDH modification in the presence of the NO donor diethylamine NONOate were analyzed by MALDI- and ESI- mass spectrometry methods. RESULTS The adduct between GAPDH and dimedone was detected by MALDI-MS analysis after incubation of S-nitrosylated GAPDH with dimedone, which points to the formation of cysteine-sulfenic acid (GAPDH-SOH) in the protein. Analysis of the protein hydrolysate revealed the incorporation of dimedone into the catalytic residue Cys150. An additional peak that corresponded to GAPDH-SNO was detected by ESI-MS analysis in GAPDH after the incubation with the NO donor. The content of GAPDH-SNO and GAPDH-SOH in the modified GAPDH was evaluated by different approaches and constituted 2.3 and 0.7 mol per mol GAPDH, respectively. A small fraction of GAPDH was irreversibly inactivated after NO treatment, suggesting that a minor part of the products includes cysteine-sulfinic or cysteine-sulfonic acids. CONCLUSIONS The main products of GAPDH modification by NO are GAPDH-SNO and GAPDH-SOH that is presumably formed due to the hydrolysis of GAPDH-SNO. GENERAL SIGNIFICANCE The obtained results are important for understanding the molecular mechanism of redox regulation of cell functions and the role of GAPDH in the development of neurodegenerative disorders.
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Affiliation(s)
- E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - M V Medvedeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - V V Chagovets
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology of Ministry of Healthcare of Russia, Akademika Oparina 4, Moscow 117997, Russia
| | - V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
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35
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Rahman MM, Lendel C. Extracellular protein components of amyloid plaques and their roles in Alzheimer's disease pathology. Mol Neurodegener 2021; 16:59. [PMID: 34454574 PMCID: PMC8400902 DOI: 10.1186/s13024-021-00465-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is pathologically defined by the presence of fibrillar amyloid β (Aβ) peptide in extracellular senile plaques and tau filaments in intracellular neurofibrillary tangles. Extensive research has focused on understanding the assembly mechanisms and neurotoxic effects of Aβ during the last decades but still we only have a brief understanding of the disease associated biological processes. This review highlights the many other constituents that, beside Aβ, are accumulated in the plaques, with the focus on extracellular proteins. All living organisms rely on a delicate network of protein functionality. Deposition of significant amounts of certain proteins in insoluble inclusions will unquestionably lead to disturbances in the network, which may contribute to AD and copathology. This paper provide a comprehensive overview of extracellular proteins that have been shown to interact with Aβ and a discussion of their potential roles in AD pathology. Methods that can expand the knowledge about how the proteins are incorporated in plaques are described. Top-down methods to analyze post-mortem tissue and bottom-up approaches with the potential to provide molecular insights on the organization of plaque-like particles are compared. Finally, a network analysis of Aβ-interacting partners with enriched functional and structural key words is presented.
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Affiliation(s)
- M Mahafuzur Rahman
- Department of Chemistry, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden.
| | - Christofer Lendel
- Department of Chemistry, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden.
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36
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Wang F, Xu CS, Chen WH, Duan SW, Xu SJ, Dai JJ, Wang QW. Identification of Blood-Based Glycolysis Gene Associated with Alzheimer's Disease by Integrated Bioinformatics Analysis. J Alzheimers Dis 2021; 83:163-178. [PMID: 34308907 DOI: 10.3233/jad-210540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is one of many common neurodegenerative diseases without ideal treatment, but early detection and intervention can prevent the disease progression. OBJECTIVE This study aimed to identify AD-related glycolysis gene for AD diagnosis and further investigation by integrated bioinformatics analysis. METHODS 122 subjects were recruited from the affiliated hospitals of Ningbo University between 1 October 2015 and 31 December 2016. Their clinical information and methylation levels of 8 glycolysis genes were assessed. Machine learning algorithms were used to establish an AD prediction model. Receiver operating characteristic curve (AUC) and decision curve analysis (DCA) were used to assess the model. An AD risk factor model was developed by SHapley Additive exPlanations (SHAP) to extract features that had important impacts on AD. Finally, gene expression of AD-related glycolysis genes were validated by AlzData. RESULTS An AD prediction model was developed using random forest algorithm with the best average ROC_AUC (0.969544). The threshold probability of the model was positive in the range of 0∼0.9875 by DCA. Eight glycolysis genes (GAPDHS, PKLR, PFKFB3, LDHC, DLD, ALDOC, LDHB, HK3) were identified by SHAP. Five of these genes (PFKFB3, DLD, ALDOC, LDHB, LDHC) have significant differences in gene expression between AD and control groups by Alzdata, while three of the genes (HK3, ALDOC, PKLR) are related to the pathogenesis of AD. GAPDHS is involved in the regulatory network of AD risk genes. CONCLUSION We identified 8 AD-related glycolysis genes (GAPDHS, PFKFB3, LDHC, HK3, ALDOC, LDHB, PKLR, DLD) as promising candidate biomarkers for early diagnosis of AD by integrated bioinformatics analysis. Machine learning has the advantage in identifying genes.
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Affiliation(s)
- Fng Wang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Zhejiang Pharmaceutical College, Ningbo, China
| | - Chun-Shuang Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Wei-Hua Chen
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Shi-Wei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Shu-Jun Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Jun-Jie Dai
- Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
| | - Qin-Wen Wang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
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37
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Alldred MJ, Penikalapati SC, Lee SH, Heguy A, Roussos P, Ginsberg SD. Profiling Basal Forebrain Cholinergic Neurons Reveals a Molecular Basis for Vulnerability Within the Ts65Dn Model of Down Syndrome and Alzheimer's Disease. Mol Neurobiol 2021; 58:5141-5162. [PMID: 34263425 DOI: 10.1007/s12035-021-02453-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/13/2021] [Indexed: 12/30/2022]
Abstract
Basal forebrain cholinergic neuron (BFCN) degeneration is a hallmark of Down syndrome (DS) and Alzheimer's disease (AD). Current therapeutics have been unsuccessful in slowing disease progression, likely due to complex pathological interactions and dysregulated pathways that are poorly understood. The Ts65Dn trisomic mouse model recapitulates both cognitive and morphological deficits of DS and AD, including BFCN degeneration. We utilized Ts65Dn mice to understand mechanisms underlying BFCN degeneration to identify novel targets for therapeutic intervention. We performed high-throughput, single population RNA sequencing (RNA-seq) to interrogate transcriptomic changes within medial septal nucleus (MSN) BFCNs, using laser capture microdissection to individually isolate ~500 choline acetyltransferase-immunopositive neurons in Ts65Dn and normal disomic (2N) mice at 6 months of age (MO). Ts65Dn mice had unique MSN BFCN transcriptomic profiles at ~6 MO clearly differentiating them from 2N mice. Leveraging Ingenuity Pathway Analysis and KEGG analysis, we linked differentially expressed gene (DEG) changes within MSN BFCNs to several canonical pathways and aberrant physiological functions. The dysregulated transcriptomic profile of trisomic BFCNs provides key information underscoring selective vulnerability within the septohippocampal circuit. We propose both expected and novel therapeutic targets for DS and AD, including specific DEGs within cholinergic, glutamatergic, GABAergic, and neurotrophin pathways, as well as select targets for repairing oxidative phosphorylation status in neurons. We demonstrate and validate this interrogative quantitative bioinformatic analysis of a key dysregulated neuronal population linking single population transcript changes to an established pathological hallmark associated with cognitive decline for therapeutic development in human DS and AD.
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Affiliation(s)
- Melissa J Alldred
- Center for Dementia Research, Nathan Kline Institute, 140 Old Orangeburg Road, Orangeburg, NY, 10962, USA.,Departments of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Sai C Penikalapati
- Center for Dementia Research, Nathan Kline Institute, 140 Old Orangeburg Road, Orangeburg, NY, 10962, USA
| | - Sang Han Lee
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute, Orangeburg, NY, USA
| | - Adriana Heguy
- Genome Technology Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Panos Roussos
- Center for Dementia Research, Nathan Kline Institute, 140 Old Orangeburg Road, Orangeburg, NY, 10962, USA.,Departments of Genetics and Genomic Sciences and Psychiatry and the Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, 140 Old Orangeburg Road, Orangeburg, NY, 10962, USA. .,Departments of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA. .,Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY, USA. .,NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
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Chaudhary S, Dhiman A, Patidar A, Malhotra H, Talukdar S, Dilawari R, Chaubey GK, Modanwal R, Raje CI, Raje M. Moonlighting glyceraldehyde-3-phosphate dehydrogenase (GAPDH) modulates protein aggregation. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166202. [PMID: 34144092 DOI: 10.1016/j.bbadis.2021.166202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 11/18/2022]
Abstract
Onset of protein aggregation reflects failure of the cellular folding machinery to keep aggregation-prone protein from misfolding and accumulating into a non-degradable state. FRET based analysis and biochemical data reveal that cytosolic prion (cyPrP) and httQ-103 interact with the multifunctional protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) leading to few detectable aggregates in GAPDH-over expressing cells.The preventive effect of GAPDH suggests that this abundant and long-lived cytoplasmic protein has an active role in the shielding and maintenance, in soluble form of proteins as heterogeneous as huntingtin and cyPrP.
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Affiliation(s)
- Surbhi Chaudhary
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Asmita Dhiman
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Anil Patidar
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Himanshu Malhotra
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Sharmila Talukdar
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Rahul Dilawari
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | | | - Radheshyam Modanwal
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Chaaya Iyengar Raje
- National Institute of Pharmaceutical Education & Research, Phase X, Sector 67, SAS Nagar, Punjab 160062, India
| | - Manoj Raje
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India.
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Tigro H, Kronqvist N, Abelein A, Galan-Acosta L, Chen G, Landreh M, Lyashkov A, Aon MA, Ferrucci L, Shimmo R, Johansson J, Moaddel R. The synthesis and characterization of Bri2 BRICHOS coated magnetic particles and their application to protein fishing: Identification of novel binding proteins. J Pharm Biomed Anal 2021; 198:113996. [PMID: 33690096 PMCID: PMC10644258 DOI: 10.1016/j.jpba.2021.113996] [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: 01/19/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
Human integral membrane protein 2B (ITM2B or Bri2) is a member of the BRICHOS family, proteins that efficiently prevent Aβ42 aggregation via a unique mechanism. The identification of novel Bri2 BRICHOS client proteins could help elucidate signaling pathways and determine novel targets to prevent or cure amyloid diseases. To identify Bri2 BRICHOS interacting partners, we carried out a 'protein fishing' experiment using recombinant human (rh) Bri2 BRICHOS-coated magnetic particles, which exhibit essentially identical ability to inhibit Aβ42 fibril formation as free rh Bri2 BRICHOS, in combination with proteomic analysis on homogenates of SH-SY5Y cells. We identified 70 proteins that had more significant interactions with rh Bri2 BRICHOS relative to the corresponding control particles. Three previously identified Bri2 BRICHOS interacting proteins were also identified in our 'fishing' experiments. The binding affinity of Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), the top 'hit', was calculated and was identified as a strong interacting partner. Enrichment analysis of the retained proteins identified three biological pathways: Rho GTPase, heat stress response and pyruvate, cysteine and methionine metabolism.
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Affiliation(s)
- Helene Tigro
- School of Natural Sciences and Health, Tallinn University, Tallinn, Estonia
| | - Nina Kronqvist
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Lorena Galan-Acosta
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Alexey Lyashkov
- Biomedical Research Centre, National Institute on Aging, NIH, Baltimore, MD, 21224, United States
| | - Miguel A Aon
- Biomedical Research Centre, National Institute on Aging, NIH, Baltimore, MD, 21224, United States
| | - Luigi Ferrucci
- Biomedical Research Centre, National Institute on Aging, NIH, Baltimore, MD, 21224, United States
| | - Ruth Shimmo
- School of Natural Sciences and Health, Tallinn University, Tallinn, Estonia
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Ruin Moaddel
- Biomedical Research Centre, National Institute on Aging, NIH, Baltimore, MD, 21224, United States.
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40
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Selinski J, Scheibe R. Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate. Antioxid Redox Signal 2021; 34:1025-1047. [PMID: 32620064 PMCID: PMC8060724 DOI: 10.1089/ars.2020.8121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Significance: The importance of oxidoreductases in energy metabolism together with the occurrence of enzymes of central metabolism in the nucleus gave rise to the active research field aiming to understand moonlighting enzymes that undergo post-translational modifications (PTMs) before carrying out new tasks. Recent Advances: Cytosolic enzymes were shown to induce gene transcription after PTM and concomitant translocation to the nucleus. Changed properties of the oxidized forms of cytosolic glyceraldehyde 3-phosphate dehydrogenase, and also malate dehydrogenases and others, are the basis for a hypothesis suggesting moonlighting functions that directly link energy metabolism to adaptive responses required for maintenance of redox-homeostasis in all eukaryotes. Critical Issues: Small molecules, such as metabolic intermediates, coenzymes, or reduced glutathione, were shown to fine-tune the redox switches, interlinking redox state, metabolism, and induction of new functions via nuclear gene expression. The cytosol with its metabolic enzymes connecting energy fluxes between the various cell compartments can be seen as a hub for redox signaling, integrating the different signals for graded and directed responses in stressful situations. Future Directions: Enzymes of central metabolism were shown to interact with p53 or the assumed plant homologue suppressor of gamma response 1 (SOG1), an NAM, ATAF, and CUC transcription factor involved in the stress response upon ultraviolet exposure. Metabolic enzymes serve as sensors for imbalances, their inhibition leading to changed energy metabolism, and the adoption of transcriptional coactivator activities. Depending on the intensity of the impact, rerouting of energy metabolism, proliferation, DNA repair, cell cycle arrest, immune responses, or cell death will be induced. Antioxid. Redox Signal. 34, 1025-1047.
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Affiliation(s)
- Jennifer Selinski
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Renate Scheibe
- Department of Plant Physiology, Faculty of Biology/Chemistry, Osnabrueck University, Osnabrueck, Germany
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Hachiya N, Sochocka M, Brzecka A, Shimizu T, Gąsiorowski K, Szczechowiak K, Leszek J. Nuclear Envelope and Nuclear Pore Complexes in Neurodegenerative Diseases-New Perspectives for Therapeutic Interventions. Mol Neurobiol 2021; 58:983-995. [PMID: 33067781 PMCID: PMC7878205 DOI: 10.1007/s12035-020-02168-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022]
Abstract
Transport of proteins, transcription factors, and other signaling molecules between the nucleus and cytoplasm is necessary for signal transduction. The study of these transport phenomena is particularly challenging in neurons because of their highly polarized structure. The bidirectional exchange of molecular cargoes across the nuclear envelope (NE) occurs through nuclear pore complexes (NPCs), which are aqueous channels embedded in the nuclear envelope. The NE and NPCs regulate nuclear transport but are also emerging as relevant regulators of chromatin organization and gene expression. The alterations in nuclear transport are regularly identified in affected neurons associated with human neurodegenerative diseases. This review presents insights into the roles played by nuclear transport defects in neurodegenerative disease, focusing primarily on NE proteins and NPCs. The subcellular mislocalization of proteins might be a very desirable means of therapeutic intervention in neurodegenerative disorders.
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Affiliation(s)
- Naomi Hachiya
- Tokyo Metropolitan Industrial Technology Research Institute, Tokyo, Japan
| | - Marta Sochocka
- Laboratory of Virology, Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anna Brzecka
- Department of Pulmonology and Lung Cancer, Wroclaw Medical University, Wroclaw, Poland
| | - Takuto Shimizu
- Tokyo Metropolitan Industrial Technology Research Institute, Tokyo, Japan
- Laboratory of Biochemistry, School of Veterinary Medicine, Azabu University, Sagamihara, Japan
| | | | | | - Jerzy Leszek
- Department of Psychiatry, Wroclaw Medical University, Wybrzeże L. Pasteura 10, 50-367, Wroclaw, Poland.
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Interplay between bioenergetics and oxidative stress at normal brain aging. Aging as a result of increasing disbalance in the system oxidative stress-energy provision. Pflugers Arch 2021; 473:713-722. [PMID: 33599804 DOI: 10.1007/s00424-021-02531-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/18/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022]
Abstract
At normal aging, the brain exhibits signs of compromised bioenergetic and increased levels of products of interaction between reactive oxygen/nitrogen species (ROS/RNS) and brain constituents. Under normal conditions, steady-state levels of ATP and ROS/RNS fluctuate in certain ranges providing basis for stable homeostasis. However, from time to time these parameters leave a "comfort zone," and at adulthood, organisms are able to cope with these challenges efficiently, whereas at aging, efficiency of the systems maintaining homeostasis declines. That is very true for the brain due to high ATP demands which are mainly covered by mitochondrial oxidative phosphorylation. Such active oxidative metabolism gives rise to intensive ROS generation as side products. The situation is worsened by high brain level of polyunsaturated fatty acids which are substrates for ROS/RNS attack and production of lipid peroxides. In this review, organization of energetic metabolism in the brain with a focus on its interplay with ROS at aging is discussed. The working hypothesis on aging as a disbalance between oxidative stress and energy provision as a reason for brain aging is proposed. From this point of view, normal age-related physiological decline in the brain functions results from increased disbalance between decrease in capability of the brain to control constantly increased incapability to maintain ROS levels and produce ATP due to amplification of vicious cycles intensification of oxidative stress <----> impairment of energy provision.
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Kalyanasundaram A, Henry BJ, Henry C, Kendall RJ. Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus). Mol Biol Rep 2021; 48:1093-1101. [PMID: 33580461 DOI: 10.1007/s11033-021-06186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
Many recent studies have been focused on prevalence and impact of two helminth parasites, eyeworm Oxyspirura petrowi and caecal worm Aulonocephalus pennula, in the northern bobwhite quail (Colinus virginianus). However, few studies have attempted to examine the effect of these parasites on the bobwhite immune system. This is likely due to the lack of proper reference genes for relative gene expression studies. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that is often utilized as a reference gene, and in this preliminary study, we evaluated the similarity of bobwhite GAPDH to GAPDH in other avian species to evaluate its potential as a reference gene in bobwhite. GAPDH was identified in the bobwhite full genome sequence and multiple sets of PCR primers were designed to generate overlapping PCR products. These products were then sequenced and then aligned to generate the sequence for the full-length open reading frame (ORF) of bobwhite GAPDH. Utilizing this sequence, phylogenetic analyses and comparative analysis of the exon-intron pattern were conducted that revealed high similarity of GAPDH encoding sequences among bobwhite and other Galliformes. Additionally, This ORF sequence was also used to predict the encoded protein and its three-dimensional structure which like the phylogenetic analyses reveal that bobwhite GAPDH is similar to GAPDH in other Galliformes. Finally, GAPDH qPCR primers were designed, standardized, and tested with bobwhite both uninfected and infected with O. petrowi, and this preliminary test showed no statistical difference in expression of GAPDH between the two groups. These analyses are the first to investigate GAPDH in bobwhite. These efforts in phylogeny, sequence analysis, and protein structure suggest that there is > 97% conservation of GADPH among Galliformes. Furthermore, the results of these in silico tests and the preliminary qPCR indicate that GAPDH is a prospective candidate for use in gene expression analyses in bobwhite.
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Affiliation(s)
| | - Brett J Henry
- The Wildlife Toxicology Laboratory, Texas Tech University, Lubbock, TX, 79409-3290, USA
| | - Cassandra Henry
- The Wildlife Toxicology Laboratory, Texas Tech University, Lubbock, TX, 79409-3290, USA
| | - Ronald J Kendall
- The Wildlife Toxicology Laboratory, Texas Tech University, Lubbock, TX, 79409-3290, USA.
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Kosmachevskaya OV, Novikova NN, Topunov AF. Carbonyl Stress in Red Blood Cells and Hemoglobin. Antioxidants (Basel) 2021; 10:253. [PMID: 33562243 PMCID: PMC7914924 DOI: 10.3390/antiox10020253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The paper overviews the peculiarities of carbonyl stress in nucleus-free mammal red blood cells (RBCs). Some functional features of RBCs make them exceptionally susceptible to reactive carbonyl compounds (RCC) from both blood plasma and the intracellular environment. In the first case, these compounds arise from the increased concentrations of glucose or ketone bodies in blood plasma, and in the second-from a misbalance in the glycolysis regulation. RBCs are normally exposed to RCC-methylglyoxal (MG), triglycerides-in blood plasma of diabetes patients. MG modifies lipoproteins and membrane proteins of RBCs and endothelial cells both on its own and with reactive oxygen species (ROS). Together, these phenomena may lead to arterial hypertension, atherosclerosis, hemolytic anemia, vascular occlusion, local ischemia, and hypercoagulation phenotype formation. ROS, reactive nitrogen species (RNS), and RCC might also damage hemoglobin (Hb), the most common protein in the RBC cytoplasm. It was Hb with which non-enzymatic glycation was first shown in living systems under physiological conditions. Glycated HbA1c is used as a very reliable and useful diagnostic marker. Studying the impacts of MG, ROS, and RNS on the physiological state of RBCs and Hb is of undisputed importance for basic and applied science.
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Affiliation(s)
- Olga V. Kosmachevskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | | | - Alexey F. Topunov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
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Martínez-Banaclocha M. N-acetyl-cysteine in Schizophrenia: Potential Role on the Sensitive Cysteine Proteome. Curr Med Chem 2021; 27:6424-6439. [PMID: 33115390 DOI: 10.2174/0929867326666191015091346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 09/11/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND N-acetyl-cysteine (NAC) has shown widespread utility in different psychiatric disorders, including a beneficial role in schizophrenic patients. Although the replenishment of glutathione and the antioxidant activity of NAC have been suggested as the mechanisms that improve such a wide range of disorders, none seems to be sufficiently specific to explain these intriguing effects. A sensitive cysteine proteome is emerging as a functional and structural network of interconnected Sensitive Cysteine-containing Proteins (SCCPs) that together with reactive species and the cysteine/ glutathione cycles can regulate the bioenergetic metabolism, the redox homeostasis and the cellular growth, differentiation and survival, acting through different pathways that are regulated by the same thiol radical in cysteine residues. OBJECTIVE Since this sensitive cysteine network has been implicated in the pathogenesis of Parkinson's and Alzheimer's diseases, I have reviewed if the proteins that play a role in schizophrenia can be classified as SCCPs. RESULTS The results show that the principal proteins playing a role in schizophrenia can be classified as SCCPs, suggesting that the sensitive cysteine proteome (cysteinet) is defective in this type of psychosis. CONCLUSION The present review proposes that there is a deregulation of the sensitive cysteine proteome in schizophrenia as the consequence of a functional imbalance among different SCCPs, which play different functions in neurons and glial cells. In this context, the role of NAC to restore and prevent schizophrenic disorders is discussed.
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Xue Y, Bai H, Peng B, Fang B, Baell J, Li L, Huang W, Voelcker NH. Stimulus-cleavable chemistry in the field of controlled drug delivery. Chem Soc Rev 2021; 50:4872-4931. [DOI: 10.1039/d0cs01061h] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review comprehensively summarises stimulus-cleavable linkers from various research areas and their cleavage mechanisms, thus provides an insightful guideline to extend their potential applications to controlled drug release from nanomaterials.
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Affiliation(s)
- Yufei Xue
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Bin Fang
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Jonathan Baell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton
- Victoria 3168
- Australia
| | - Lin Li
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Nicolas Hans Voelcker
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
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47
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Glycation of glyceraldehyde-3-phosphate dehydrogenase inhibits the binding with α-synuclein and RNA. Arch Biochem Biophys 2020; 698:108744. [PMID: 33385367 DOI: 10.1016/j.abb.2020.108744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/18/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) shows great diversity of functions, interaction partners and post-translational modifications. GAPDH undergoes glycation of positively charged residues in diabetic patient's tissues and therefore may change interaction with partners. The influence of GAPDH glycation on interaction with two important partners, α-synuclein and RNA, has been investigated in silico using molecular dynamics simulations and in vitro using surface plasmon resonance measurements. Since positively charged groove including substrate- and NAD+-binding sites is proposed as potential binding site for α-synuclein and RNA, GAPDH was glycated on residues in grooves and randomly distributed over the whole surface. Lysine residues were replaced with negatively charged carboxymethyl lysine as a widespread advanced glycation end product. As results, GAPDH glycation suppressed the interaction with α-synuclein and RNA. Although the modified GAPDH residues participated in binding with α-synuclein, no stable binding site with both glycated forms was observed. Glycation along the whole GAPDH surface completely suppressed interaction with RNA, whereas the alternative possible RNA binding site was identified in case of groove glycation. The findings were supported by direct measurement of the binding affinity. The obtained results clarify effect of glycation on GAPDH interaction with α-synuclein and RNA and elucidate a possible mechanism of interplay between glycation occurred in diabetes and neurodegenerative diseases, which GAPDH and α-synuclein are involved in.
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Xu H, Zhou W, Zhan L, Sui H, Zhang L, Zhao C, Lu X. The ZiBuPiYin recipe regulates proteomic alterations in brain mitochondria-associated ER membranes caused by chronic psychological stress exposure: Implications for cognitive decline in Zucker diabetic fatty rats. Aging (Albany NY) 2020; 12:23698-23726. [PMID: 33221746 PMCID: PMC7762487 DOI: 10.18632/aging.103894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/23/2020] [Indexed: 01/10/2023]
Abstract
Chronic psychological stress (PS) cumulatively affects memory performance through the deleterious effects on hypothalamic-pituitary-adrenal axis regulation. Several functions damaged in cognitive impairment-related diseases are regulated by mitochondria-associated ER membranes (MAMs). To elucidate the role of ZiBuPiYin recipe (ZBPYR) in regulating the MAM proteome to improve PS-induced diabetes-associated cognitive decline (PSD), differentially expressed MAM proteins were identified among Zucker diabetic fatty rats, PSD rats, and PS combined with ZBPYR administration rats via iTRAQ with LC-MS/MS. Proteomic analysis revealed that the expressions of 85 and 33 proteins were altered by PS and ZBPYR treatment, respectively. Among these, 21 proteins were differentially expressed under both PS and ZBPYR treatments, whose functional categories included energy metabolism, lipid and protein metabolism, and synaptic dysfunction. Furthermore, calcium signaling and autophagy-related proteins may play roles in the pathogenesis of PSD and the mechanism of ZBPYR, respectively. Notably, KEGG pathway analysis suggested that ‘Alzheimer's disease’ and ‘oxidative phosphorylation’ pathways may be impaired in PSD pathogenesis, while ZBPYR could play a neuroprotective role through regulating the above pathways. Overall, exposure to chronic PS contributes to the evolution of diabetes-associated cognitive decline and ZBPYR might prevent and treat PSD by regulating the MAM proteome.
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Affiliation(s)
- Huiying Xu
- Modern Research Laboratory of Spleen Visceral Manifestations Theory, School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wen Zhou
- Modern Research Laboratory of Spleen Visceral Manifestations Theory, School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Libin Zhan
- Modern Research Laboratory of Spleen Visceral Manifestations Theory, School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hua Sui
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116044, China
| | - Lijing Zhang
- Modern Research Laboratory of Spleen Visceral Manifestations Theory, School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Chunyan Zhao
- Modern Research Laboratory of Spleen Visceral Manifestations Theory, School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaoguang Lu
- Department of Emergency Medicine, Zhongshan Hospital, Dalian University, Dalian 116001, China
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Abstract
The single gene, single protein, single function hypothesis is increasingly becoming obsolete. Numerous studies have demonstrated that individual proteins can moonlight, meaning they can have multiple functions based on their cellular or developmental context. In this review, we discuss moonlighting proteins, highlighting the biological pathways where this phenomenon may be particularly relevant. In addition, we combine genetic, cell biological, and evolutionary perspectives so that we can better understand how, when, and why moonlighting proteins may take on multiple roles.
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Affiliation(s)
- Nadia Singh
- Department of Biology, University of Oregon, Eugene, Oregon 97403, USA;
| | - Needhi Bhalla
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA;
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Davoudi M, Moradi-Sardareh H, Emamgholipour S, Nabatchian F, Paknejad M. The possible effect of silver nanoparticles on glyceraldehyde-3-phosphate dehydrogenase activity and formation of amyloid-like aggregates in MCF-7 cell line. IUBMB Life 2020; 72:2214-2224. [PMID: 32819028 DOI: 10.1002/iub.2362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 11/06/2022]
Abstract
Silver nanoparticles (AgNPs) are widely used in medicine, however, the underlying mechanisms of their action on cellular signaling have not been completely determined, and fundamental studies are required to clarify them. We aimed to investigate AgNPs effects on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as both the internal control gene and the redox-sensitive enzyme involved in apoptosis-related pathways and the formation of amyloid aggregates. To achieve this purpose, MCF-7 cells were treated with different concentrations (0, 3, 22, and 200 μg/ml) of AgNPs and then cell viability, generation of reactive oxygen species (ROS), induction of apoptosis, expression of GAPDH gene, the formation of amyloid aggregates, and GAPDH activity were assessed. The results indicated that treatment with AgNPs significantly reduced cell viability and increased apoptosis in a dose-dependent manner. The ROS levels increased at lower concentrations of AgNPs (up to 22 μg/ml) and during short-term exposure (30 min). The level of GAPDH gene expression was significantly upregulated by 1.22, 1.47, and 1.56 fold, in the concentrations of 3, 22, and 200 μg/ml, respectively. The amount of amyloid aggregates was significantly increased in a dose-dependent manner. The results of enzyme activity showed that AgNPs were affected on the activity of GAPDH protein, however, it has fluctuated that could not be interpreted by our limited data. In conclusion, our results suggested that AgNPs could affect the GAPDH gene expression and enzyme activity, therefore the selection of GAPDH as a gene and protein internal control in the (AgNPs)-related studies requires careful consideration. Additionally, AgNPs may cause apoptosis due to the increase in the production of amyloid aggregates.
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Affiliation(s)
- Maryam Davoudi
- Department of Medical Laboratory, School of Allied Health Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hemen Moradi-Sardareh
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Solaleh Emamgholipour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Nabatchian
- Department of Medical Laboratory, School of Allied Health Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maliheh Paknejad
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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