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Vassileff N, Spiers JG, Bamford SE, Lowe RGT, Datta KK, Pigram PJ, Hill AF. Microglial activation induces nitric oxide signalling and alters protein S-nitrosylation patterns in extracellular vesicles. J Extracell Vesicles 2024; 13:e12455. [PMID: 38887871 PMCID: PMC11183937 DOI: 10.1002/jev2.12455] [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: 10/04/2023] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 06/20/2024] Open
Abstract
Neuroinflammation is an underlying feature of neurodegenerative conditions, often appearing early in the aetiology of a disease. Microglial activation, a prominent initiator of neuroinflammation, can be induced through lipopolysaccharide (LPS) treatment resulting in expression of the inducible form of nitric oxide synthase (iNOS), which produces nitric oxide (NO). NO post-translationally modifies cysteine thiols through S-nitrosylation, which can alter function of the target protein. Furthermore, packaging of these NO-modified proteins into extracellular vesicles (EVs) allows for the exertion of NO signalling in distant locations, resulting in further propagation of the neuroinflammatory phenotype. Despite this, the NO-modified proteome of activated microglial EVs has not been investigated. This study aimed to identify the protein post-translational modifications NO signalling induces in neuroinflammation. EVs isolated from LPS-treated microglia underwent mass spectral surface imaging using time of flight-secondary ion mass spectrometry (ToF-SIMS), in addition to iodolabelling and comparative proteomic analysis to identify post-translation S-nitrosylation modifications. ToF-SIMS imaging successfully identified cysteine thiol side chains modified through NO signalling in the LPS treated microglial-derived EV proteins. In addition, the iodolabelling proteomic analysis revealed that the EVs from LPS-treated microglia carried S-nitrosylated proteins indicative of neuroinflammation. These included known NO-modified proteins and those associated with LPS-induced microglial activation that may play an essential role in neuroinflammatory communication. Together, these results show activated microglia can exert broad NO signalling changes through the selective packaging of EVs during neuroinflammation.
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Affiliation(s)
- Natasha Vassileff
- The Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Jereme G. Spiers
- The Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
- Clear Vision Research, Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and MedicineThe Australian National UniversityActonAustralia
- School of Medicine and Psychology, College of Health and MedicineThe Australian National UniversityActonAustralia
| | - Sarah E. Bamford
- Centre for Materials and Surface Science and Department of Mathematical and Physical SciencesLa Trobe UniversityBundooraVictoriaAustralia
| | - Rohan G. T. Lowe
- La Trobe University Proteomics and Metabolomics PlatformLa Trobe UniversityBundooraVictoriaAustralia
| | - Keshava K. Datta
- La Trobe University Proteomics and Metabolomics PlatformLa Trobe UniversityBundooraVictoriaAustralia
| | - Paul J. Pigram
- Centre for Materials and Surface Science and Department of Mathematical and Physical SciencesLa Trobe UniversityBundooraVictoriaAustralia
| | - Andrew F. Hill
- The Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
- Institute for Health and SportVictoria UniversityMelbourneAustralia
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2
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Liang Z, Zhuang H, Cao X, Ma G, Shen L. Subcellular proteomics insights into Alzheimer's disease development. Proteomics Clin Appl 2024; 18:e2200112. [PMID: 37650321 DOI: 10.1002/prca.202200112] [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: 04/30/2023] [Revised: 07/27/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023]
Abstract
Alzheimer's disease (AD), one of the most common dementias, is a neurodegenerative disease characterized by cognitive impairment and decreased judgment function. The expected number of AD patient is increasing in the context of the world's advancing medical care and increasing human life expectancy. Since current molecular mechanism studies on AD pathogenesis are incomplete, there is no specific and effective therapeutic agent. Mass spectrometry (MS)-based unbiased proteomics studies provide an effective and comprehensive approach. Many advances have been made in the study of the mechanism, diagnostic markers, and drug targets of AD using proteomics. This paper focus on subcellular level studies, reviews studies using proteomics to study AD-associated mitochondrial dysfunction, synaptic, and myelin damage, the protein composition of amyloid plaques (APs) and neurofibrillary tangles (NFTs), changes in tissue extracellular vehicles (EVs) and exosome proteome, and the protein changes in ribosomes and lysosomes. The methods of sample separation and preparation and proteomic analysis as well as the main findings of these studies are involved. The results of these proteomics studies provide insights into the pathogenesis of AD and provide theoretical resource and direction for future research in AD, helping to identify new biomarkers and drugs targets for AD.
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Affiliation(s)
- Zhiyuan Liang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Hongbin Zhuang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Xueshan Cao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
- College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, P. R. China
| | - Guanwei Ma
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, P. R. China
| | - Liming Shen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, P. R. China
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Zhu L, Wang L, Yang Z, Xu P, Yang S. PPSNO: A Feature-Rich SNO Sites Predictor by Stacking Ensemble Strategy from Protein Sequence-Derived Information. Interdiscip Sci 2024; 16:192-217. [PMID: 38206557 DOI: 10.1007/s12539-023-00595-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
The protein S-nitrosylation (SNO) is a significant post-translational modification that affects the stability, activity, cellular localization, and function of proteins. Therefore, highly accurate prediction of SNO sites aids in grasping biological function mechanisms. In this document, we have constructed a predictor, named PPSNO, forecasting protein SNO sites using stacked integrated learning. PPSNO integrates multiple machine learning techniques into an ensemble model, enhancing its predictive accuracy. First, we established benchmark datasets by collecting SNO sites from various sources, including literature, databases, and other predictors. Second, various techniques for feature extraction are applied to derive characteristics from protein sequences, which are subsequently amalgamated into the PPSNO predictor for training. Five-fold cross-validation experiments show that PPSNO outperformed existing predictors, such as PSNO, PreSNO, pCysMod, DeepNitro, RecSNO, and Mul-SNO. The PPSNO predictor achieved an impressive accuracy of 92.8%, an area under the curve (AUC) of 96.1%, a Matthews correlation coefficient (MCC) of 81.3%, an F1-score of 85.6%, an SN of 79.3%, an SP of 97.7%, and an average precision (AP) of 92.2%. We also employed ROC curves, PR curves, and radar plots to show the superior performance of PPSNO. Our study shows that fused protein sequence features and two-layer stacked ensemble models can improve the accuracy of predicting SNO sites, which can aid in comprehending cellular processes and disease mechanisms. The codes and data are available at https://github.com/serendipity-wly/PPSNO .
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Affiliation(s)
- Lun Zhu
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou, 213164, China
| | - Liuyang Wang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou, 213164, China
| | - Zexi Yang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou, 213164, China
| | - Piao Xu
- College of Economics and Management, Nanjing Forestry University, Nanjing, 210037, China
| | - Sen Yang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou, 213164, China.
- The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, 213164, China.
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Gaudet ID, Xu H, Gordon E, Cannestro GA, Lu ML, Wei J. Elevated SLC7A2 expression is associated with an abnormal neuroinflammatory response and nitrosative stress in Huntington's disease. J Neuroinflammation 2024; 21:59. [PMID: 38419038 PMCID: PMC10900710 DOI: 10.1186/s12974-024-03038-2] [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: 09/06/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
We previously identified solute carrier family 7 member 2 (SLC7A2) as one of the top upregulated genes when normal Huntingtin was deleted. SLC7A2 has a high affinity for L-arginine. Arginine is implicated in inflammatory responses, and SLC7A2 is an important regulator of innate and adaptive immunity in macrophages. Although neuroinflammation is clearly demonstrated in animal models and patients with Huntington's disease (HD), the question of whether neuroinflammation actively participates in HD pathogenesis is a topic of ongoing research and debate. Here, we studied the role of SLC7A2 in mediating the neuroinflammatory stress response in HD cells. RNA sequencing (RNA-seq), quantitative RT-PCR and data mining of publicly available RNA-seq datasets of human patients were performed to assess the levels of SLC7A2 mRNA in different HD cellular models and patients. Biochemical studies were then conducted on cell lines and primary mouse astrocytes to investigate arginine metabolism and nitrosative stress in response to neuroinflammation. The CRISPR-Cas9 system was used to knock out SLC7A2 in STHdhQ7 and Q111 cells to investigate its role in mediating the neuroinflammatory response. Live-cell imaging was used to measure mitochondrial dynamics. Finally, exploratory studies were performed using the Enroll-HD periodic human patient dataset to analyze the effect of arginine supplements on HD progression. We found that SLC7A2 is selectively upregulated in HD cellular models and patients. HD cells exhibit an overactive response to neuroinflammatory challenges, as demonstrated by abnormally high iNOS induction and NO production, leading to increased protein nitrosylation. Depleting extracellular Arg or knocking out SLC7A2 blocked iNOS induction and NO production in STHdhQ111 cells. We further examined the functional impact of protein nitrosylation on a well-documented protein target, DRP-1, and found that more mitochondria were fragmented in challenged STHdhQ111 cells. Last, analysis of Enroll-HD datasets suggested that HD patients taking arginine supplements progressed more rapidly than others. Our data suggest a novel pathway that links arginine uptake to nitrosative stress via upregulation of SLC7A2 in the pathogenesis and progression of HD. This further implies that arginine supplements may potentially pose a greater risk to HD patients.
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Affiliation(s)
- Ian D Gaudet
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Hongyuan Xu
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Emily Gordon
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Gianna A Cannestro
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Michael L Lu
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Jianning Wei
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA.
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Jia J, Lv P, Wei X, Qiu W. SNO-DCA: A model for predicting S-nitrosylation sites based on densely connected convolutional networks and attention mechanism. Heliyon 2024; 10:e23187. [PMID: 38148797 PMCID: PMC10750070 DOI: 10.1016/j.heliyon.2023.e23187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Protein S-nitrosylation is a reversible oxidative reduction post-translational modification that is widely present in the biological community. S-nitrosylation can regulate protein function and is closely associated with a variety of diseases, thus identifying S-nitrosylation sites are crucial for revealing the function of proteins and related drug discovery. Traditional experimental methods are time-consuming and expensive; therefore, it is necessary to explore more efficient computational methods. Deep learning algorithms perform well in the field of bioinformatics sites prediction, and many studies show that they outperform existing machine learning algorithms. In this work, we proposed a deep learning algorithm-based predictor SNO-DCA for distinguishing between S-nitrosylated and non-S-nitrosylated sequences. First, one-hot encoding of protein sequences was performed. Second, the dense convolutional blocks were used to capture feature information, and an attention module was added to weigh different features to improve the prediction ability of the model. The 10-fold cross-validation and independent testing experimental results show that our SNO-DCA model outperforms existing S-nitrosylation sites prediction models under imbalanced data. In this paper, a web server prediction website: https://sno.cangmang.xyz/SNO-DCA/was established to provide an online prediction service for users. SNO-DCA can be available at https://github.com/peanono/SNO-DCA.
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Affiliation(s)
- Jianhua Jia
- Computer Department, Jingdezhen Ceramic University, Jingdezhen, 330403, China
| | - Peinuo Lv
- Computer Department, Jingdezhen Ceramic University, Jingdezhen, 330403, China
| | - Xin Wei
- Business School, Jiangxi Institute of Fashion Technology, Nanchang, 330201, China
| | - Wangren Qiu
- Computer Department, Jingdezhen Ceramic University, Jingdezhen, 330403, China
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6
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Vasanthi SS, Rao NS, Samidurai M, Massey N, Meyer C, Gage M, Kharate M, Almanza A, Wachter L, Mafuta C, Trevino L, Carlo AM, Bryant E, Corson BE, Wohlgemuth M, Ostrander M, Wang C, Thippeswamy T. Disease-Modifying Effects of a Glial-targeted Inducible Nitric Oxide Synthase Inhibitor (1400W) in Mixed-sex Cohorts of a Rat Soman (GD) Model of Epilepsy. RESEARCH SQUARE 2023:rs.3.rs-2883247. [PMID: 37214912 PMCID: PMC10197763 DOI: 10.21203/rs.3.rs-2883247/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Acute exposure to seizurogenic organophosphate (OP) nerve agents (OPNA) such as diisopropylfluorophosphate (DFP) or soman (GD), at high concentrations, induce immediate status epilepticus (SE), reactive gliosis, neurodegeneration, and epileptogenesis as a consequence. Medical countermeasures (MCMs- atropine, oximes, benzodiazepines), if administered in < 20 minutes of OPNA exposure, can control acute symptoms and mortality. However, MCMs alone are inadequate to prevent OPNA-induced brain injury and behavioral dysfunction in survivors. We have previously shown that OPNA exposure-induced SE increases the production of inducible nitric oxide synthase (iNOS) in glial cells in both short- and long- terms. Treating with a water soluble and highly selective iNOS inhibitor, 1400W, for three days significantly reduced OPNA-induced brain changes in those animals that had mild-moderate SE in the rat DFP model. However, such mitigating effects and the mechanisms of 1400W are unknown in a highly volatile nerve agent GD exposure. Methods Mixed-sex cohort of adult Sprague Dawley rats were exposed to GD (132µg/kg, s.c.) and immediately treated with atropine (2mg/kg, i.m) and HI-6 (125mg/kg, i.m.). Severity of seizures were quantified for an hour and treated with midazolam (3mg/kg, i.m.). An hour post-midazolam, 1400W (20mg/kg, i.m.) or vehicle was administered daily for two weeks. After behavioral testing and EEG acquisition, animals were euthanized at 3.5 months post-GD. Brains were processed for neuroinflammatory and neurodegeneration markers. Serum and CSF were used for nitrooxidative and proinflammatory cytokines assays. Results We demonstrate a significant long-term (3.5 months post-soman) disease-modifying effect of 1400W in animals that had severe SE for > 20min of continuous convulsive seizures. 1400W significantly reduced GD-induced motor and cognitive dysfunction; nitrooxidative stress (nitrite, ROS; increased GSH: GSSG); proinflammatory cytokines in the serum and some in the cerebrospinal fluid (CSF); epileptiform spikes and spontaneously recurring seizures (SRS) in males; reactive gliosis (GFAP + C3 and IBA1 + CD68 positive glia) as a measure of neuroinflammation, and neurodegeneration (including parvalbumin positive neurons) in some brain regions. Conclusion These findings demonstrate the long-term disease-modifying effects of a glial-targeted iNOS inhibitor, 1400W, in a rat GD model by modulating reactive gliosis, neurodegeneration, and neuronal hyperexcitability.
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Zhou M, Sun J, Yu Z, Wu Z, Li W, Liu G, Ma L, Wang R, Tang Y. Investigation of Anti-Alzheimer's Mechanisms of Sarsasapogenin Derivatives by Network-Based Combining Structure-Based Methods. J Chem Inf Model 2023; 63:2881-2894. [PMID: 37104820 DOI: 10.1021/acs.jcim.3c00018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Alzheimer's disease (AD), a neurodegenerative disease with no cure, affects millions of people worldwide and has become one of the biggest healthcare challenges. Some investigated compounds play anti-AD roles at the cellular or the animal level, but their molecular mechanisms remain unclear. In this study, we designed a strategy combining network-based and structure-based methods together to identify targets for anti-AD sarsasapogenin derivatives (AAs). First, we collected drug-target interactions (DTIs) data from public databases, constructed a global DTI network, and generated drug-substructure associations. After network construction, network-based models were built for DTI prediction. The best bSDTNBI-FCFP_4 model was further used to predict DTIs for AAs. Second, a structure-based molecular docking method was employed for rescreening the prediction results to obtain more credible target proteins. Finally, in vitro experiments were conducted for validation of the predicted targets, and Nrf2 showed significant evidence as the target of anti-AD compound AA13. Moreover, we analyzed the potential mechanisms of AA13 for the treatment of AD. Generally, our combined strategy could be applied to other novel drugs or compounds and become a useful tool in identification of new targets and elucidation of disease mechanisms. Our model was deployed on our NetInfer web server (http://lmmd.ecust.edu.cn/netinfer/).
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Affiliation(s)
- Moran Zhou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jiamin Sun
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhuohang Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lei Ma
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Rui Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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Hindley N, Sanchez Avila A, Henstridge C. Bringing synapses into focus: Recent advances in synaptic imaging and mass-spectrometry for studying synaptopathy. Front Synaptic Neurosci 2023; 15:1130198. [PMID: 37008679 PMCID: PMC10050382 DOI: 10.3389/fnsyn.2023.1130198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Synapses are integral for healthy brain function and are becoming increasingly recognized as key structures in the early stages of brain disease. Understanding the pathological processes driving synaptic dysfunction will unlock new therapeutic opportunities for some of the most devastating diseases of our time. To achieve this we need a solid repertoire of imaging and molecular tools to interrogate synaptic biology at greater resolution. Synapses have historically been examined in small numbers, using highly technical imaging modalities, or in bulk, using crude molecular approaches. However, recent advances in imaging techniques are allowing us to analyze large numbers of synapses, at single-synapse resolution. Furthermore, multiplexing is now achievable with some of these approaches, meaning we can examine multiple proteins at individual synapses in intact tissue. New molecular techniques now allow accurate quantification of proteins from isolated synapses. The development of increasingly sensitive mass-spectrometry equipment means we can now scan the synaptic molecular landscape almost in totality and see how this changes in disease. As we embrace these new technical developments, synapses will be viewed with clearer focus, and the field of synaptopathy will become richer with insightful and high-quality data. Here, we will discuss some of the ways in which synaptic interrogation is being facilitated by methodological advances, focusing on imaging, and mass spectrometry.
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Affiliation(s)
- Nicole Hindley
- Division of Cellular and Systems Medicine, University of Dundee, Dundee, United Kingdom
- *Correspondence: Nicole Hindley,
| | - Anna Sanchez Avila
- Division of Cellular and Systems Medicine, University of Dundee, Dundee, United Kingdom
- Euan Macdonald Centre for Motor Neuron Disease, University of Edinburgh, Edinburgh, United Kingdom
| | - Christopher Henstridge
- Division of Cellular and Systems Medicine, University of Dundee, Dundee, United Kingdom
- Euan Macdonald Centre for Motor Neuron Disease, University of Edinburgh, Edinburgh, United Kingdom
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Yang H, Oh CK, Amal H, Wishnok JS, Lewis S, Schahrer E, Trudler D, Nakamura T, Tannenbaum SR, Lipton SA. Mechanistic insight into female predominance in Alzheimer's disease based on aberrant protein S-nitrosylation of C3. SCIENCE ADVANCES 2022; 8:eade0764. [PMID: 36516243 PMCID: PMC9750152 DOI: 10.1126/sciadv.ade0764] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein S-nitros(yl)ation (SNO) is a posttranslational modification involved in diverse processes in health and disease and can contribute to synaptic damage in Alzheimer's disease (AD). To identify SNO proteins in AD brains, we used triaryl phosphine (SNOTRAP) combined with mass spectrometry (MS). We detected 1449 SNO proteins with 2809 SNO sites, representing a wide range of S-nitrosylated proteins in 40 postmortem AD and non-AD human brains from patients of both sexes. Integrative protein ranking revealed the top 10 increased SNO proteins, including complement component 3 (C3), p62 (SQSTM1), and phospholipase D3. Increased levels of S-nitrosylated C3 were present in female over male AD brains. Mechanistically, we show that formation of SNO-C3 is dependent on falling β-estradiol levels, leading to increased synaptic phagocytosis and thus synapse loss and consequent cognitive decline. Collectively, we demonstrate robust alterations in the S-nitrosoproteome that contribute to AD pathogenesis in a sex-dependent manner.
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Affiliation(s)
- Hongmei Yang
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130021, China
| | - Chang-ki Oh
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Haitham Amal
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - John S. Wishnok
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah Lewis
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Emily Schahrer
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dorit Trudler
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tomohiro Nakamura
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven R. Tannenbaum
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Corresponding author. (S.R.T.); (S.A.L.)
| | - Stuart A. Lipton
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla CA 92093, USA
- Corresponding author. (S.R.T.); (S.A.L.)
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10
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Vrettou S, Wirth B. S-Glutathionylation and S-Nitrosylation in Mitochondria: Focus on Homeostasis and Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms232415849. [PMID: 36555492 PMCID: PMC9779533 DOI: 10.3390/ijms232415849] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Redox post-translational modifications are derived from fluctuations in the redox potential and modulate protein function, localization, activity and structure. Amongst the oxidative reversible modifications, the S-glutathionylation of proteins was the first to be characterized as a post-translational modification, which primarily protects proteins from irreversible oxidation. However, a growing body of evidence suggests that S-glutathionylation plays a key role in core cell processes, particularly in mitochondria, which are the main source of reactive oxygen species. S-nitrosylation, another post-translational modification, was identified >150 years ago, but it was re-introduced as a prototype cell-signaling mechanism only recently, one that tightly regulates core processes within the cell’s sub-compartments, especially in mitochondria. S-glutathionylation and S-nitrosylation are modulated by fluctuations in reactive oxygen and nitrogen species and, in turn, orchestrate mitochondrial bioenergetics machinery, morphology, nutrients metabolism and apoptosis. In many neurodegenerative disorders, mitochondria dysfunction and oxidative/nitrosative stresses trigger or exacerbate their pathologies. Despite the substantial amount of research for most of these disorders, there are no successful treatments, while antioxidant supplementation failed in the majority of clinical trials. Herein, we discuss how S-glutathionylation and S-nitrosylation interfere in mitochondrial homeostasis and how the deregulation of these modifications is associated with Alzheimer’s, Parkinson’s, amyotrophic lateral sclerosis and Friedreich’s ataxia.
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Affiliation(s)
- Sofia Vrettou
- Institute of Human Genetics, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence: (S.V.); (B.W.)
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence: (S.V.); (B.W.)
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Lipton SA. Hidden networks of aberrant protein transnitrosylation contribute to synapse loss in Alzheimer's disease. Free Radic Biol Med 2022; 193:171-176. [PMID: 36243209 PMCID: PMC9875813 DOI: 10.1016/j.freeradbiomed.2022.10.272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 01/27/2023]
Abstract
Emerging evidence indicates the importance of S-nitrosation in regulating protein function and activity. This chemical reaction has been termed protein S-nitrosylation to emphasize its biological importance as a posttranslational modification, in some ways reminiscent of phosphorylation. The reaction at cysteine thiols is distinct from other chemical reactions of nitric oxide (NO) that activate soluble guanylate cyclase via nitrosylation of heme or formation of peroxynitrite via reaction with superoxide anion to produce tyrosine nitration. Here, we review the importance of pathological, aberrant transnitrosylation reactions, i.e., transfer of the NO group from one protein to another, and its consequent effect on the pathogenesis of neurological disorders, to date on Alzheimer's disease (AD), but also expected to affect Parkinson's disease (PD)/Lewy body dementia (LBD), HIV-associated neurocognitive disorder (HAND), and other neurodegenerative and neurodevelopmental disorders.
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Affiliation(s)
- Stuart A Lipton
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA; Department of Neurology, Yale School of Medicine, New Haven, CT, 6510, USA.
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12
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Impact of Reactive Species on Amino Acids-Biological Relevance in Proteins and Induced Pathologies. Int J Mol Sci 2022; 23:ijms232214049. [PMID: 36430532 PMCID: PMC9692786 DOI: 10.3390/ijms232214049] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
This review examines the impact of reactive species RS (of oxygen ROS, nitrogen RNS and halogens RHS) on various amino acids, analyzed from a reactive point of view of how during these reactions, the molecules are hydroxylated, nitrated, or halogenated such that they can lose their capacity to form part of the proteins or peptides, and can lose their function. The reactions of the RS with several amino acids are described, and an attempt was made to review and explain the chemical mechanisms of the formation of the hydroxylated, nitrated, and halogenated derivatives. One aim of this work is to provide a theoretical analysis of the amino acids and derivatives compounds in the possible positions. Tyrosine, methionine, cysteine, and tryptophan can react with the harmful peroxynitrite or •OH and •NO2 radicals and glycine, serine, alanine, valine, arginine, lysine, tyrosine, histidine, cysteine, methionine, cystine, tryptophan, glutamine and asparagine can react with hypochlorous acid HOCl. These theoretical results may help to explain the loss of function of proteins subjected to these three types of reactive stresses. We hope that this work can help to assess the potential damage that reactive species can cause to free amino acids or the corresponding residues when they are part of peptides and proteins.
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13
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An Shen Ding Zhi Ling Ameliorates the Symptoms of Attention Deficit Hyperactivity Disorder via Modulating Brain-Derived Neurotrophic Factor-Related Signaling Pathways. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5471586. [PMID: 35911131 PMCID: PMC9334057 DOI: 10.1155/2022/5471586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 06/16/2022] [Indexed: 11/18/2022]
Abstract
Attention deficit hyperactivity disorder (ADHD) is a common childhood neurodevelopmental disorder. It may impact the cognitive and social functions throughout childhood and determine adult outcomes. Dopamine (DA) deficiency theory is the pathogenesis of ADHD that is recognized by most international literature. Existing studies have shown that DA deficiency is caused by the abnormal function of the DA transporter and an imbalance in the DA receptor functionality. Recent clinical and experimental studies have found that the brain-derived neurotrophic factor (BDNF)/tropomyosin receptor kinase B (TrkB) signaling pathway acts a pivotal part in DA vesicle circulation and ADHD pathogenesis. An Shen Ding Zhi Ling (ASDZL) is a traditional Chinese medicine (TCM) prescription, which was widely prescribed to treat ADHD in Jiangsu, China, but its therapeutic mechanism is unclear. Therefore, we constructed a spontaneously hypertensive rat (SHR) model to explain its mechanism. SHRs were randomly assigned to four groups: SHR model group (vehicle), methylphenidate hydrochloride group (MPH), ASDZL group, and 7,8-dihydroxyflavone group (7,8-DHF). At the same time, the above groups were given continuous medication for four weeks. The results show that ASDZL, MPH, and 7,8-DHF group could significantly improve the spatial memory of SHRs in the Morris water maze tests. ASDZL increased the levels of BDNF, TrkB, p75 neurotrophin receptor (p75), C-Jun N-terminal kinases 1 (JNK1), and nuclear factor kappa B (NF-κB) in the prefrontal cortex (PFC) and hippocampus synaptosome of SHRs. The results of this study suggest that ASDZL can relieve the symptoms of ADHD in SHRs by regulating the balance between the BDNF/TrkB signaling pathway (promoting vesicle circulation) and the BDNF/P75/JNK1/NF-κB signaling pathway (inhibiting vesicle circulation) within the PFC and hippocampus synaptosome to increase the DA concentration in the synaptic cleft. The BDNF/TrkB signal pathway within the PFC and hippocampus synaptosome was activated by 7,8-DHF to increase DA concentration in the synaptic cleft. Whether 7,8-DHF can activate or inhibit the BDNF/P75 signaling pathway remains unclear.
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14
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Mat Zian NFA, Swain P, Mohd Faudzi SM, Zakaria N, Wan Ibrahim WN, Abu Bakar N, Shaari K, Stanslas J, Choi TI, Kim CH. Mapping Molecular Networks within Clitoria ternatea Linn. against LPS-Induced Neuroinflammation in Microglial Cells, with Molecular Docking and In Vivo Toxicity Assessment in Zebrafish. Pharmaceuticals (Basel) 2022; 15:ph15040467. [PMID: 35455463 PMCID: PMC9032563 DOI: 10.3390/ph15040467] [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: 04/09/2022] [Indexed: 02/04/2023] Open
Abstract
Clitoria ternatea Linn. (CT), or butterfly pea, is an Ayurvedic plant traditionally used as a brain tonic. Recently, it was reported to be of use in treating central nervous system (CNS) disorders, i.e., as an antistress treatment and antidepressant. In the present study, we report a detailed phytochemical profile of the ethyl acetate fraction of the flower of CT (CTF_EA) with significant neuroprotective and anti-neuroinflammatory properties in both LPS-activated BV-2 and SK-N-SH cells. Concurrently, the molecular network (MN) derived from the CTF_EA metabolome allows putative identification of flavonol 3-O-glycosides, hydrocinnamic acids, and primary metabolites. Molecular docking studies suggest that CTF_EA preferentially targets iNOS, resulting in a decrease in nitric oxide (NO). Furthermore, no toxic effects on normal embryonic development, blood vessel formation, and apoptosis are observed when CTF_EA is tested for in vivo toxicity in zebrafish models. The overall preliminary results suggest the anti-neuroinflammatory and neuroprotective effects of CT and provide scientific support for the efficacy of this medicinal plant at local and traditional levels. However, studies on the targeted isolation of bioactive metabolites, in-depth pharmacological efficacy, and safety in mammalian models are urgently needed to expand our understanding of this plant before it is developed into a promising therapeutic agent for brain-related diseases.
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Affiliation(s)
- Nurul Farah Adni Mat Zian
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.F.A.M.Z.); (W.N.W.I.); (K.S.)
| | - Puspanjali Swain
- Department of Biology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (P.S.); (T.-I.C.)
| | - Siti Munirah Mohd Faudzi
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.F.A.M.Z.); (W.N.W.I.); (K.S.)
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
- Correspondence: (S.M.M.F.); (C.-H.K.)
| | - Norzalina Zakaria
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Wan Norhamidah Wan Ibrahim
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.F.A.M.Z.); (W.N.W.I.); (K.S.)
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Noraini Abu Bakar
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Khozirah Shaari
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.F.A.M.Z.); (W.N.W.I.); (K.S.)
| | - Johnson Stanslas
- Department of Medicine, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (P.S.); (T.-I.C.)
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (P.S.); (T.-I.C.)
- Correspondence: (S.M.M.F.); (C.-H.K.)
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15
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Mass spectrometry analysis of S-nitrosylation of proteins and its role in cancer, cardiovascular and neurodegenerative diseases. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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16
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Phongpreecha T, Gajera CR, Liu CC, Vijayaragavan K, Chang AL, Becker M, Fallahzadeh R, Fernandez R, Postupna N, Sherfield E, Tebaykin D, Latimer C, Shively CA, Register TC, Craft S, Montine KS, Fox EJ, Poston KL, Keene CD, Angelo M, Bendall SC, Aghaeepour N, Montine TJ. Single-synapse analyses of Alzheimer's disease implicate pathologic tau, DJ1, CD47, and ApoE. SCIENCE ADVANCES 2021; 7:eabk0473. [PMID: 34910503 PMCID: PMC8673771 DOI: 10.1126/sciadv.abk0473] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Synaptic molecular characterization is limited for Alzheimer’s disease (AD). Our newly invented mass cytometry–based method, synaptometry by time of flight (SynTOF), was used to measure 38 antibody probes in approximately 17 million single-synapse events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), nonhuman primates (NHPs), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice single-synapse events. Clustering and pattern identification of human synapses showed expected disease-specific differences, like increased hippocampal pathologic tau in AD and reduced caudate dopamine transporter in LBD, and revealed previously unidentified findings including increased hippocampal CD47 and lowered DJ1 in AD and higher ApoE in AD with dementia. Our results were independently supported by multiplex ion beam imaging of intact tissue. This highlights the higher depth and breadth of insight on neurodegenerative diseases obtainable through SynTOF.
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Affiliation(s)
- Thanaphong Phongpreecha
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | - Candace C. Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Alan L. Chang
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Nadia Postupna
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Emily Sherfield
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Dmitry Tebaykin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Carol A. Shively
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Thomas C. Register
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Suzanne Craft
- Department of Internal Medicine–Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Edward J. Fox
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kathleen L. Poston
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Thomas J. Montine
- Department of Pathology, Stanford University, Stanford, CA, USA
- Corresponding author.
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17
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Ito H, Matsui T, Konno R, Itakura M, Kodera Y. LC-MS peak assignment based on unanimous selection by six machine learning algorithms. Sci Rep 2021; 11:23411. [PMID: 34862414 PMCID: PMC8642397 DOI: 10.1038/s41598-021-02899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Recent mass spectrometry (MS)-based techniques enable deep proteome coverage with relative quantitative analysis, resulting in increased identification of very weak signals accompanied by increased data size of liquid chromatography (LC)–MS/MS spectra. However, the identification of weak signals using an assignment strategy with poorer performance results in imperfect quantification with misidentification of peaks and ratio distortions. Manually annotating a large number of signals within a very large dataset is not a realistic approach. In this study, therefore, we utilized machine learning algorithms to successfully extract a higher number of peptide peaks with high accuracy and precision. Our strategy evaluated each peak identified using six different algorithms; peptide peaks identified by all six algorithms (i.e., unanimously selected) were subsequently assigned as true peaks, which resulted in a reduction in the false-positive rate. Hence, exact and highly quantitative peptide peaks were obtained, providing better performance than obtained applying the conventional criteria or using a single machine learning algorithm.
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Affiliation(s)
- Hiroaki Ito
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takashi Matsui
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.,Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan
| | - Ryo Konno
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Makoto Itakura
- Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan.,Department of Biochemistry, School of Medicine, Kitasato University, 1-15-1 Kitasato, Minami-ku , Sagamihara, 252-0373, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan. .,Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan.
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18
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Chatterji A, Banerjee D, Billiar TR, Sengupta R. Understanding the role of S-nitrosylation/nitrosative stress in inflammation and the role of cellular denitrosylases in inflammation modulation: Implications in health and diseases. Free Radic Biol Med 2021; 172:604-621. [PMID: 34245859 DOI: 10.1016/j.freeradbiomed.2021.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/22/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022]
Abstract
S-nitrosylation is a very fundamental post-translational modification of protein and non-protein thiols due the involvement of it in a variety of cellular processes including activation/inhibition of several ion channels such as ryanodine receptor in the cardiovascular system; blood vessel dilation; cGMP signaling and neurotransmission. S-nitrosothiol homeostasis in the cell is tightly regulated and perturbations in homeostasis result in an altered redox state leading to a plethora of disease conditions. However, the exact role of S-nitrosylated proteins and nitrosative stress metabolites in inflammation and in inflammation modulation is not well-reviewed. The cell utilizes its intricate defense mechanisms i.e. cellular denitrosylases such as Thioredoxin (Trx) and S-nitrosoglutathione reductase (GSNOR) systems to combat nitric oxide (NO) pathology which has also gained current attraction as novel anti-inflammatory molecules. This review attempts to provide state-of-the-art knowledge from past and present research on the mechanistic role of nitrosative stress intermediates (RNS, OONO-, PSNO) in pulmonary and autoimmune diseases and how cellular denitrosylases particularly GSNOR and Trx via imparting opposing effects can modulate and reduce inflammation in several health and disease conditions. This review would also bring into notice the existing gaps in current research where denitrosylases can be utilized for ameliorating inflammation that would leave avenues for future therapeutic interventions.
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Affiliation(s)
- Ajanta Chatterji
- Amity Institute of Biotechnology Kolkata, Amity University Kolkata, Action Area II, Rajarhat, Newtown, Kolkata, West Bengal, 700135, India
| | - Debasmita Banerjee
- Department of Molecular Biology and Biotechnology, University of Kalyani, Block C, Nadia, Kalyani, West Bengal, 741235, India
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 5213, USA
| | - Rajib Sengupta
- Amity Institute of Biotechnology Kolkata, Amity University Kolkata, Action Area II, Rajarhat, Newtown, Kolkata, West Bengal, 700135, India.
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19
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Inhibition of neuroinflammatory nitric oxide signaling suppresses glycation and prevents neuronal dysfunction in mouse prion disease. Proc Natl Acad Sci U S A 2021; 118:2009579118. [PMID: 33653950 PMCID: PMC7958397 DOI: 10.1073/pnas.2009579118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Several neurodegenerative diseases associated with protein misfolding (Alzheimer's and Parkinson's disease) exhibit oxidative and nitrergic stress following initiation of neuroinflammatory pathways. Associated nitric oxide (NO)-mediated posttranslational modifications impact upon protein functions that can exacerbate pathology. Nonenzymatic and irreversible glycation signaling has been implicated as an underlying pathway that promotes protein misfolding, but the direct interactions between both pathways are poorly understood. Here we investigated the therapeutic potential of pharmacologically suppressing neuroinflammatory NO signaling during early disease progression of prion-infected mice. Mice were injected daily with an NO synthase (NOS) inhibitor at early disease stages, hippocampal gene and protein expression levels of oxidative and nitrergic stress markers were analyzed, and electrophysiological characterization of pyramidal CA1 neurons was performed. Increased neuroinflammatory signaling was observed in mice between 6 and 10 wk postinoculation (w.p.i.) with scrapie prion protein. Their hippocampi were characterized by enhanced nitrergic stress associated with a decline in neuronal function by 9 w.p.i. Daily in vivo administration of the NOS inhibitor L-NAME between 6 and 9 w.p.i. at 20 mg/kg prevented the functional degeneration of hippocampal neurons in prion-diseased mice. We further found that this intervention in diseased mice reduced 3-nitrotyrosination of triose-phosphate isomerase, an enzyme involved in the formation of disease-associated glycation. Furthermore, L-NAME application led to a reduced expression of the receptor for advanced glycation end-products and the diminished accumulation of hippocampal prion misfolding. Our data suggest that suppressing neuroinflammatory NO signaling slows functional neurodegeneration and reduces nitrergic and glycation-associated cellular stress.
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20
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Manabe T, Rácz I, Schwartz S, Oberle L, Santarelli F, Emmrich JV, Neher JJ, Heneka MT. Systemic inflammation induced the delayed reduction of excitatory synapses in the CA3 during ageing. J Neurochem 2021; 159:525-542. [PMID: 34379806 DOI: 10.1111/jnc.15491] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Sepsis-associated encephalopathy (SAE) represents diverse cerebral dysfunctions in response to pathogen-induced systemic inflammation. Peripheral exposure to lipopolysaccharide (LPS), a component of the gram-negative bacterial cell wall, has been extensively used to model systemic inflammation. Our previous studies suggested that LPS led to hippocampal neuron death and synaptic destruction in vivo. However, the underlying roles of activated microglia in these neuronal changes remained unclear. Here, LPS from two different bacterial strains (Salmonella enterica or E. coli) were compared and injected in 14- to 16-month-old mice and evaluated for neuroinflammation and neuronal integrity in the hippocampus at 7 or 63 days post-injection (dpi). LPS injection resulted in persistent neuroinflammation lasting for seven days and a subsequent normalisation by 63 dpi. Of note, increases in proinflammatory cytokines, microglial morphology and microglial mean lysosome volume were more pronounced after E. coli LPS injection than Salmonella LPS at 7 dpi. While inhibitory synaptic puncta density remained normal, excitatory synaptic puncta were locally reduced in the CA3 region of the hippocampus at 63 dpi. Finally, we provide evidence that excitatory synapses coated with complement factor 3 (C3) decreased between 7 dpi and 63 dpi. Although we did not find an increase of synaptic pruning by microglia, it is plausible that microglia recognised and eliminated these C3-tagged synapses between the two time-points of investigation. Since a region-specific decline of CA3 synapses has previously been reported during normal ageing, we postulate that systemic inflammation may have accelerated or worsened the CA3 synaptic changes in the ageing brain.
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Affiliation(s)
- Tatsuya Manabe
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Center, Venusberg-Campus 1, 53127, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Ildikó Rácz
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Center, Venusberg-Campus 1, 53127, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Stephanie Schwartz
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Center, Venusberg-Campus 1, 53127, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Linda Oberle
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076, Tübingen, Germany
| | | | - Julius V Emmrich
- Department of Neurology and Department of Experimental Neurology, Freie Universität Berlin, Humboldt Universität zu Berlin, Berlin Institute of Health, Berlin, 10117, Germany
| | - Jonas J Neher
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
| | - Michael T Heneka
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Center, Venusberg-Campus 1, 53127, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany.,Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts, 01655, USA
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21
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Melatonin, Its Metabolites and Their Interference with Reactive Nitrogen Compounds. Molecules 2021; 26:molecules26134105. [PMID: 34279445 PMCID: PMC8271479 DOI: 10.3390/molecules26134105] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/14/2022] Open
Abstract
Melatonin and several of its metabolites are interfering with reactive nitrogen. With the notion of prevailing melatonin formation in tissues that exceeds by far the quantities in blood, metabolites come into focus that are poorly found in the circulation. Apart from their antioxidant actions, both melatonin and N1-acetyl-5-methoxykynuramine (AMK) downregulate inducible and inhibit neuronal NO synthases, and additionally scavenge NO. However, the NO adduct of melatonin redonates NO, whereas AMK forms with NO a stable product. Many other melatonin metabolites formed in oxidative processes also contain nitrosylatable sites. Moreover, AMK readily scavenges products of the CO2-adduct of peroxynitrite such as carbonate radicals and NO2. Protein AMKylation seems to be involved in protective actions.
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22
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Pham TK, Buczek WA, Mead RJ, Shaw PJ, Collins MO. Proteomic Approaches to Study Cysteine Oxidation: Applications in Neurodegenerative Diseases. Front Mol Neurosci 2021; 14:678837. [PMID: 34177463 PMCID: PMC8219902 DOI: 10.3389/fnmol.2021.678837] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/03/2021] [Indexed: 11/15/2022] Open
Abstract
Oxidative stress appears to be a key feature of many neurodegenerative diseases either as a cause or consequence of disease. A range of molecules are subject to oxidation, but in particular, proteins are an important target and measure of oxidative stress. Proteins are subject to a range of oxidative modifications at reactive cysteine residues, and depending on the level of oxidative stress, these modifications may be reversible or irreversible. A range of experimental approaches has been developed to characterize cysteine oxidation of proteins. In particular, mass spectrometry-based proteomic methods have emerged as a powerful means to identify and quantify cysteine oxidation sites on a proteome scale; however, their application to study neurodegenerative diseases is limited to date. Here we provide a guide to these approaches and highlight the under-exploited utility of these methods to measure oxidative stress in neurodegenerative diseases for biomarker discovery, target engagement and to understand disease mechanisms.
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Affiliation(s)
- Trong Khoa Pham
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Weronika A. Buczek
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Richard J. Mead
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Mark O. Collins
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
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Recent Advances in Predicting Protein S-Nitrosylation Sites. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5542224. [PMID: 33628788 PMCID: PMC7892234 DOI: 10.1155/2021/5542224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/09/2023]
Abstract
Protein S-nitrosylation (SNO) is a process of covalent modification of nitric oxide (NO) and its derivatives and cysteine residues. SNO plays an essential role in reversible posttranslational modifications of proteins. The accurate prediction of SNO sites is crucial in revealing a certain biological mechanism of NO regulation and related drug development. Identification of the sites of SNO in proteins is currently a very hot topic. In this review, we briefly summarize recent advances in computationally identifying SNO sites. The challenges and future perspectives for identifying SNO sites are also discussed. We anticipate that this review will provide insights into research on SNO site prediction.
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Nakamura T, Oh CK, Liao L, Zhang X, Lopez KM, Gibbs D, Deal AK, Scott HR, Spencer B, Masliah E, Rissman RA, Yates JR, Lipton SA. Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer's disease. Science 2020; 371:science.aaw0843. [PMID: 33273062 DOI: 10.1126/science.aaw0843] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 11/18/2020] [Indexed: 12/21/2022]
Abstract
Here we describe mechanistically distinct enzymes (a kinase, a guanosine triphosphatase, and a ubiquitin protein hydrolase) that function in disparate biochemical pathways and can also act in concert to mediate a series of redox reactions. Each enzyme manifests a second, noncanonical function-transnitrosylation-that triggers a pathological biochemical cascade in mouse models and in humans with Alzheimer's disease (AD). The resulting series of transnitrosylation reactions contributes to synapse loss, the major pathological correlate to cognitive decline in AD. We conclude that enzymes with distinct primary reaction mechanisms can form a completely separate network for aberrant transnitrosylation. This network operates in the postreproductive period, so natural selection against such abnormal activity may be decreased.
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Affiliation(s)
- Tomohiro Nakamura
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA. .,Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA
| | - Chang-Ki Oh
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA
| | - Lujian Liao
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xu Zhang
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA
| | - Kevin M Lopez
- Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA
| | - Daniel Gibbs
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Amanda K Deal
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry R Scott
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Brian Spencer
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Robert A Rissman
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA.,VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - John R Yates
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stuart A Lipton
- Departments of Molecular Medicine and Neuroscience, and Neuroscience Translational Center, The Scripps Research Institute, La Jolla, CA 92037, USA. .,Neurodegenerative Disease Center, Scintillon Institute, San Diego, CA 92121, USA.,Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
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25
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Butterfield DA, Boyd-Kimball D. Mitochondrial Oxidative and Nitrosative Stress and Alzheimer Disease. Antioxidants (Basel) 2020; 9:E818. [PMID: 32887505 PMCID: PMC7554713 DOI: 10.3390/antiox9090818] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/29/2020] [Indexed: 12/29/2022] Open
Abstract
Oxidative and nitrosative stress are widely recognized as critical factors in the pathogenesis and progression of Alzheimer disease (AD) and its earlier stage, amnestic mild cognitive impairment (MCI). A major source of free radicals that lead to oxidative and nitrosative damage is mitochondria. This review paper discusses oxidative and nitrosative stress and markers thereof in the brain, along with redox proteomics, which are techniques that have been pioneered in the Butterfield laboratory. Selected biological alterations in-and oxidative and nitrosative modifications of-mitochondria in AD and MCI and systems of relevance thereof also are presented. The review article concludes with a section on the implications of mitochondrial oxidative and nitrosative stress in MCI and AD with respect to imaging studies in and targeted therapies toward these disorders. Taken together, this review provides support for the notion that brain mitochondrial alterations in AD and MCI are key components of oxidative and nitrosative stress observed in these two disorders, and as such, they provide potentially promising therapeutic targets to slow-and hopefully one day stop-the progression of AD, which is a devastating dementing disorder.
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Affiliation(s)
- D. Allan Butterfield
- Department of Chemistry and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - Debra Boyd-Kimball
- Department of Chemistry and Biochemistry, University of Mount Union, Alliance, OH 44601, USA;
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