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Mubeen H, Masood A, Zafar A, Khan ZQ, Khan MQ, Nisa AU. Insights into AlphaFold's breakthrough in neurodegenerative diseases. Ir J Med Sci 2024:10.1007/s11845-024-03721-6. [PMID: 38833116 DOI: 10.1007/s11845-024-03721-6] [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: 04/16/2024] [Accepted: 05/19/2024] [Indexed: 06/06/2024]
Abstract
Neurodegenerative diseases (ND) are disorders of the central nervous system (CNS) characterized by impairment in neurons' functions, and complete loss, leading to memory loss, and difficulty in learning, language, and movement processes. The most common among these NDs are Alzheimer's disease (AD) and Parkinson's disease (PD), although several other disorders also exist. These are frontotemporal dementia (FTD), amyotrophic lateral syndrome (ALS), Huntington's disease (HD), and others; the major pathological hallmark of NDs is the proteinopathies, either of amyloid-β (Aβ), tauopathies, or synucleinopathies. Aggregation of proteins that do not undergo normal configuration, either due to mutations or through some disturbance in cellular pathway contributes to the diseases. Artificial Intelligence (AI) and deep learning (DL) have proven to be successful in the diagnosis and treatment of various congenital diseases. DL approaches like AlphaFold (AF) are a major leap towards success in CNS disorders. This 3D protein geometry modeling algorithm developed by DeepMind has the potential to revolutionize biology. AF has the potential to predict 3D-protein confirmation at an accuracy level comparable to experimentally predicted one, with the additional advantage of precisely estimating protein interactions. This breakthrough will be beneficial to identify diseases' advancement and the disturbance of signaling pathways stimulating impaired functions of proteins. Though AlphaFold has solved a major problem in structural biology, it cannot predict membrane proteins-a beneficial approach for drug designing.
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Affiliation(s)
- Hira Mubeen
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan.
| | - Ammara Masood
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Asma Zafar
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Zohaira Qayyum Khan
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Muneeza Qayyum Khan
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Alim Un Nisa
- Pakistan Council of Scientific and Industrial Research, Lahore, Pakistan
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2
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Bashir S, Aiman A, Shahid M, Chaudhary AA, Sami N, Basir SF, Hassan I, Islam A. Amyloid-induced neurodegeneration: A comprehensive review through aggregomics perception of proteins in health and pathology. Ageing Res Rev 2024; 96:102276. [PMID: 38499161 DOI: 10.1016/j.arr.2024.102276] [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: 11/03/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Amyloidosis of protein caused by fibrillation and aggregation are some of the most exciting new edges not only in protein sciences but also in molecular medicines. The present review discusses recent advancements in the field of neurodegenerative diseases and therapeutic applications with ongoing clinical trials, featuring new areas of protein misfolding resulting in aggregation. The endogenous accretion of protein fibrils having fibrillar morphology symbolizes the beginning of neuro-disorders. Prognostic amyloidosis is prominent in numerous degenerative infections such as Alzheimer's and Parkinson's disease, Amyotrophic lateral sclerosis (ALS), etc. However, the molecular basis determining the intracellular or extracellular evidence of aggregates, playing a significant role as a causative factor in neurodegeneration is still unclear. Structural conversions and protein self-assembly resulting in the formation of amyloid oligomers and fibrils are important events in the pathophysiology of the disease. This comprehensive review sheds light on the evolving landscape of potential treatment modalities, highlighting the ongoing clinical trials and the potential socio-economic impact of novel therapeutic interventions in the realm of neurodegenerative diseases. Furthermore, many drugs are undergoing different levels of clinical trials that would certainly help in treating these disorders and will surely improve the socio-impact of human life.
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Affiliation(s)
- Sania Bashir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Ayesha Aiman
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia.
| | - Neha Sami
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Seemi Farhat Basir
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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3
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Passero M, Zhai T, Huang Z. Investigation of Potential Drug Targets for Cholesterol Regulation to Treat Alzheimer's Disease. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6217. [PMID: 37444065 PMCID: PMC10341567 DOI: 10.3390/ijerph20136217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
Despite extensive research and seven approved drugs, the complex interplay of genes, proteins, and pathways in Alzheimer's disease remains a challenge. This implies the intricacies of the mechanism for Alzheimer's disease, which involves the interaction of hundreds of genes, proteins, and pathways. While the major hallmarks of Alzheimer's disease are the accumulation of amyloid plaques and tau protein tangles, excessive accumulation of cholesterol is reportedly correlated with Alzheimer's disease patients. In this work, protein-protein interaction analysis was conducted based upon the genes from a clinical database to identify the top protein targets with most data-indicated involvement in Alzheimer's disease, which include ABCA1, CYP46A1, BACE1, TREM2, GSK3B, and SREBP2. The reactions and pathways associated with these genes were thoroughly studied for their roles in regulating brain cholesterol biosynthesis, amyloid beta accumulation, and tau protein tangle formation. Existing clinical trials for each protein target were also investigated. The research indicated that the inhibition of SREBP2, BACE1, or GSK3B is beneficial to reduce cholesterol and amyloid beta accumulation, while the activation of ABCA1, CYP46A1, or TREM2 has similar effects. In this study, Sterol Regulatory Element-Binding Protein 2 (SREBP2) emerged as the primary protein target. SREBP2 serves a pivotal role in maintaining cholesterol balance, acting as a transcription factor that controls the expression of several enzymes pivotal for cholesterol biosynthesis. Novel studies suggest that SREBP2 performs a multifaceted role in Alzheimer's disease. The hyperactivity of SREBP2 may lead to heightened cholesterol biosynthesis, which suggested association with the pathogenesis of Alzheimer's disease. Lowering SREBP2 levels in an Alzheimer's disease mouse model results in reduced production of amyloid-beta, a major contributor to Alzheimer's disease progression. Moreover, its thoroughly analyzed crystal structure allows for computer-aided screening of potential inhibitors; SREBP2 is thus selected as a prospective drug target. While more protein targets can be added onto the list in the future, this work provides an overview of key proteins involved in the regulation of brain cholesterol biosynthesis that may be further investigated for Alzheimer's disease intervention.
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Affiliation(s)
| | | | - Zuyi Huang
- Department of Chemical Engineering, Villanova University, Villanova, PA 19085, USA
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Yang M, Matan-Lithwick S, Wang Y, De Jager PL, Bennett DA, Felsky D. Multi-omic integration via similarity network fusion to detect molecular subtypes of ageing. Brain Commun 2023; 5:fcad110. [PMID: 37082508 PMCID: PMC10110975 DOI: 10.1093/braincomms/fcad110] [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: 01/23/2023] [Revised: 02/17/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023] Open
Abstract
Molecular subtyping of brain tissue provides insights into the heterogeneity of common neurodegenerative conditions, such as Alzheimer's disease. However, existing subtyping studies have mostly focused on single data modalities and only those individuals with severe cognitive impairment. To address these gaps, we applied similarity network fusion, a method capable of integrating multiple high-dimensional multi-omic data modalities simultaneously, to an elderly sample spanning the full spectrum of cognitive ageing trajectories. We analyzed human frontal cortex brain samples characterized by five omic modalities: bulk RNA sequencing (18 629 genes), DNA methylation (53 932 CpG sites), histone acetylation (26 384 peaks), proteomics (7737 proteins) and metabolomics (654 metabolites). Similarity network fusion followed by spectral clustering was used for subtype detection, and subtype numbers were determined by Eigen-gap and rotation cost statistics. Normalized mutual information determined the relative contribution of each modality to the fused network. Subtypes were characterized by associations with 13 age-related neuropathologies and cognitive decline. Fusion of all five data modalities (n = 111) yielded two subtypes (n S1 = 53, n S2 = 58), which were nominally associated with diffuse amyloid plaques; however, this effect was not significant after correction for multiple testing. Histone acetylation (normalized mutual information = 0.38), DNA methylation (normalized mutual information = 0.18) and RNA abundance (normalized mutual information = 0.15) contributed most strongly to this network. Secondary analysis integrating only these three modalities in a larger subsample (n = 513) indicated support for both three- and five-subtype solutions, which had significant overlap, but showed varying degrees of internal stability and external validity. One subtype showed marked cognitive decline, which remained significant even after correcting for tests across both three- and five-subtype solutions (p Bonf = 5.9 × 10-3). Comparison to single-modality subtypes demonstrated that the three-modal subtypes were able to uniquely capture cognitive variability. Comprehensive sensitivity analyses explored influences of sample size and cluster number parameters. We identified highly integrative molecular subtypes of ageing derived from multiple high dimensional, multi-omic data modalities simultaneously. Fusing RNA abundance, DNA methylation, and histone acetylation measures generated subtypes that were associated with cognitive decline. This work highlights the potential value and challenges of multi-omic integration in unsupervised subtyping of post-mortem brain.
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Affiliation(s)
- Mu Yang
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
| | - Stuart Matan-Lithwick
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
| | - Yanling Wang
- Rush Alzheimer’s Disease Center, Rush University, Chicago, IL 60612, USA
| | - Philip L De Jager
- The Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY 10033, USA
| | - David A Bennett
- Rush Alzheimer’s Disease Center, Rush University, Chicago, IL 60612, USA
| | - Daniel Felsky
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
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Custodia A, Romaus-Sanjurjo D, Aramburu-Núñez M, Álvarez-Rafael D, Vázquez-Vázquez L, Camino-Castiñeiras J, Leira Y, Pías-Peleteiro JM, Aldrey JM, Sobrino T, Ouro A. Ceramide/Sphingosine 1-Phosphate Axis as a Key Target for Diagnosis and Treatment in Alzheimer’s Disease and Other Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23158082. [PMID: 35897658 PMCID: PMC9331765 DOI: 10.3390/ijms23158082] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 12/10/2022] Open
Abstract
Alzheimer’s disease (AD) is considered the most prevalent neurodegenerative disease and the leading cause of dementia worldwide. Sphingolipids, such as ceramide or sphingosine 1-phosphate, are bioactive molecules implicated in structural and signaling functions. Metabolic dysfunction in the highly conserved pathways to produce sphingolipids may lead to or be a consequence of an underlying disease. Recent studies on transcriptomics and sphingolipidomics have observed alterations in sphingolipid metabolism of both enzymes and metabolites involved in their synthesis in several neurodegenerative diseases, including AD. In this review, we highlight the most relevant findings related to ceramide and neurodegeneration, with a special focus on AD.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tomás Sobrino
- Correspondence: (T.S.); (A.O.); Tel.: +34-981951098 (T.S.); +34-664326589 (A.O.)
| | - Alberto Ouro
- Correspondence: (T.S.); (A.O.); Tel.: +34-981951098 (T.S.); +34-664326589 (A.O.)
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Abdul Aziz M, Md Ashraf G, Safiqul Islam M. Link of BIN1, CLU and IDE gene polymorphisms with the susceptibility of Alzheimer's disease: evidence from a meta-analysis. Curr Alzheimer Res 2022; 19:302-316. [PMID: 35546756 DOI: 10.2174/1567205019666220511140955] [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: 12/29/2021] [Revised: 02/15/2022] [Accepted: 03/06/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common form of neurodegenerative disorder. The association of BIN1, CLU and IDE genetic polymorphisms with AD risk have been evaluated overtimes that produced conflicting outcomes. OBJECTIVE We performed this meta-analysis to investigate the contribution of BIN1 (rs744373 and rs7561528), CLU (rs11136000 and rs9331888), and IDE (rs1887922) polymorphisms to AD risk. METHODS From a systemic literature search up to July 15, 2021, we included 25 studies with rs744373, 16 studies with rs7561528, 37 studies with rs11136000, 16 studies with rs9331888, and 4 studies with rs1887922. To analyze the correlation, we constructed seven genetic models that used odds ratio and 95% confidence intervals. We used RevMan 5.4 for meta-analysis. RESULTS Our study suggests that BIN1 rs744373 is associated with a significantly increased risk of AD in five genetic models (OR>1). Again, CLU rs11136000 showed reduced association in all genetic models (OR<1). CLU rs9331888 revealed an increased association in two models (OR>1). The IDE rs1887922 showed significantly increased risk in four models (OR>1). From subgroup analysis, a significantly increased risk of AD was observed in Caucasians and Asians for BIN1 rs744373. Again, BIN1 rs7561528 showed a significantly enhanced risk of AD only in Caucasians. CLU rs11136000 showed significantly reduced risk in Caucasians but rs9331888 showed increased risk in the same ethnicity. CONCLUSION Our meta-analysis confirms the association of BIN1 rs744373, CLU rs9331888 and IDE rs1887922 polymorphisms with an increased risk of AD, especially in Caucasians. Again, CLU rs11136000 is associated with reduced AD risk in the overall population and Caucasians.
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Affiliation(s)
- Md Abdul Aziz
- Department of Pharmacy, Faculty of Pharmacy and Health Sciences, State University of Bangladesh, Dhaka-1205, Bangladesh
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Safiqul Islam
- Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh
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7
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Alzheimer's Disease Seen through the Eye: Ocular Alterations and Neurodegeneration. Int J Mol Sci 2022; 23:ijms23052486. [PMID: 35269629 PMCID: PMC8910735 DOI: 10.3390/ijms23052486] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/18/2022] Open
Abstract
Alzheimer’s Disease (AD) is one of the main neurodegenerative diseases worldwide. Unfortunately, AD shares many similarities with other dementias at early stages, which impedes an accurate premortem diagnosis. Therefore, it is urgent to find biomarkers to allow for early diagnosis of the disease. There is increasing scientific evidence highlighting the similarities between the eye and other structures of the CNS, suggesting that knowledge acquired in eye research could be useful for research and diagnosis of AD. For example, the retina and optic nerve are considered part of the central nervous system, and their damage can result in retrograde and anterograde axon degeneration, as well as abnormal protein aggregation. In the anterior eye segment, the aqueous humor and tear film may be comparable to the cerebrospinal fluid. Both fluids are enriched with molecules that can be potential neurodegenerative biomarkers. Indeed, the pathophysiology of AD, characterized by cerebral deposits of amyloid-beta (Aβ) and tau protein, is also present in the eyes of AD patients, besides numerous structural and functional changes observed in the structure of the eyes. Therefore, all this evidence suggests that ocular changes have the potential to be used as either predictive values for AD assessment or as diagnostic tools.
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8
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Custodia A, Ouro A, Romaus-Sanjurjo D, Pías-Peleteiro JM, de Vries HE, Castillo J, Sobrino T. Endothelial Progenitor Cells and Vascular Alterations in Alzheimer’s Disease. Front Aging Neurosci 2022; 13:811210. [PMID: 35153724 PMCID: PMC8825416 DOI: 10.3389/fnagi.2021.811210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease representing the most common type of dementia worldwide. The early diagnosis of AD is very difficult to achieve due to its complexity and the practically unknown etiology. Therefore, this is one of the greatest challenges in the field in order to develop an accurate therapy. Within the different etiological hypotheses proposed for AD, we will focus on the two-hit vascular hypothesis and vascular alterations occurring in the disease. According to this hypothesis, the accumulation of β-amyloid protein in the brain starts as a consequence of damage in the cerebral vasculature. Given that there are several vascular and angiogenic alterations in AD, and that endothelial progenitor cells (EPCs) play a key role in endothelial repair processes, the study of EPCs in AD may be relevant to the disease etiology and perhaps a biomarker and/or therapeutic target. This review focuses on the involvement of endothelial dysfunction in the onset and progression of AD with special emphasis on EPCs as a biomarker and potential therapeutic target.
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Affiliation(s)
- Antía Custodia
- NeuroAging Group (NEURAL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Alberto Ouro
- NeuroAging Group (NEURAL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- *Correspondence: Alberto Ouro,
| | - Daniel Romaus-Sanjurjo
- NeuroAging Group (NEURAL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Juan Manuel Pías-Peleteiro
- NeuroAging Group (NEURAL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Helga E. de Vries
- Neuroimmunology Research Group, Department of Molecular Cell Biology and Immunology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - José Castillo
- Neuroimaging and Biotechnology Laboratory (NOBEL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Tomás Sobrino
- NeuroAging Group (NEURAL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Tomás Sobrino,
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9
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Network medicine for disease module identification and drug repurposing with the NeDRex platform. Nat Commun 2021; 12:6848. [PMID: 34824199 PMCID: PMC8617287 DOI: 10.1038/s41467-021-27138-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/04/2021] [Indexed: 12/17/2022] Open
Abstract
Traditional drug discovery faces a severe efficacy crisis. Repurposing of registered drugs provides an alternative with lower costs and faster drug development timelines. However, the data necessary for the identification of disease modules, i.e. pathways and sub-networks describing the mechanisms of complex diseases which contain potential drug targets, are scattered across independent databases. Moreover, existing studies are limited to predictions for specific diseases or non-translational algorithmic approaches. There is an unmet need for adaptable tools allowing biomedical researchers to employ network-based drug repurposing approaches for their individual use cases. We close this gap with NeDRex, an integrative and interactive platform for network-based drug repurposing and disease module discovery. NeDRex integrates ten different data sources covering genes, drugs, drug targets, disease annotations, and their relationships. NeDRex allows for constructing heterogeneous biological networks, mining them for disease modules, prioritizing drugs targeting disease mechanisms, and statistical validation. We demonstrate the utility of NeDRex in five specific use-cases.
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10
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Sultan SE, Moczek AP, Walsh D. Bridging the explanatory gaps: What can we learn from a biological agency perspective? Bioessays 2021; 44:e2100185. [PMID: 34747061 DOI: 10.1002/bies.202100185] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022]
Abstract
We begin this article by delineating the explanatory gaps left by prevailing gene-focused approaches in our understanding of phenotype determination, inheritance, and the origin of novel traits. We aim not to diminish the value of these approaches but to highlight where their implementation, despite best efforts, has encountered persistent limitations. We then discuss how each of these explanatory gaps can be addressed by expanding research foci to take into account biological agency-the capacity of living systems at various levels to participate in their own development, maintenance, and function by regulating their structures and activities in response to conditions they encounter. Here we aim to define formally what agency and agents are and-just as importantly-what they are not, emphasizing that agency is an empirical property connoting neither intention nor consciousness. Lastly, we discuss how incorporating agency helps to bridge explanatory gaps left by conventional approaches, highlight scientific fields in which implicit agency approaches are already proving valuable, and assess the opportunities and challenges of more systematically incorporating biological agency into research programs.
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Affiliation(s)
- Sonia E Sultan
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Denis Walsh
- Department of Philosophy, Institute for the History and Philosophy of Science and Technology, Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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11
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Multi-modal Single-Cell Analysis Reveals Brain Immune Landscape Plasticity during Aging and Gut Microbiota Dysbiosis. Cell Rep 2020; 33:108438. [PMID: 33264626 DOI: 10.1016/j.celrep.2020.108438] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/15/2020] [Accepted: 11/05/2020] [Indexed: 12/21/2022] Open
Abstract
Phenotypic and functional plasticity of brain immune cells contribute to brain tissue homeostasis and disease. Immune cell plasticity is profoundly influenced by tissue microenvironment cues and systemic factors. Aging and gut microbiota dysbiosis that reshape brain immune cell plasticity and homeostasis has not been fully delineated. Using Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq), we analyze compositional and transcriptional changes of the brain immune landscape in response to aging and gut dysbiosis. Discordance between canonical surface-marker-defined immune cell types and their transcriptomes suggest transcriptional plasticity among immune cells. Ly6C+ monocytes predominate a pro-inflammatory signature in the aged brain, while innate lymphoid cells (ILCs) shift toward an ILC2-like profile. Aging increases ILC-like cells expressing a T memory stemness (Tscm) signature, which is reduced through antibiotics-induced gut dysbiosis. Systemic changes due to aging and gut dysbiosis increase propensity for neuroinflammation, providing insights into gut dysbiosis in age-related neurological diseases.
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12
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Transcriptome Profile of Nicotinic Receptor-Linked Sensitization of Beta Amyloid Neurotoxicity. Sci Rep 2020; 10:5696. [PMID: 32231242 PMCID: PMC7105468 DOI: 10.1038/s41598-020-62726-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 03/18/2020] [Indexed: 11/29/2022] Open
Abstract
Understanding the specific gene changes underlying the prodromic stages of Alzheimer’s disease pathogenesis will aid the development of new, targeted therapeutic strategies for this neurodegenerative disorder. Here, we employed RNA-sequencing to analyze global differential gene expression in a defined model nerve cell line expressing α4β2 nicotinic receptors (nAChRs), high-affinity targets for beta amyloid (Aβ). The nAChR-expressing neuronal cells were treated with nanomolar Aβ1–42 to gain insights into the molecular mechanisms underlying Aβ-induced neurotoxicity in the presence of this sensitizing target receptor. We identified 15 genes (out of 15,336) that were differentially expressed upon receptor-linked Aβ treatment. Genes up-regulated with Aβ treatment were associated with calcium signaling and axonal vesicle transport (including the α4 nAChR subunit, the calcineurin regulator RCAN3, and KIF1C of the kinesin family). Downregulated genes were associated with metabolic, apoptotic or DNA repair pathways (including APBA3, PARP1 and RAB11). Validation of the differential expression was performed via qRT-PCR and immunoblot analysis in the defined model nerve cell line and primary mouse neurons. Further verification was performed using immunocytochemistry. In conclusion, we identified apparent changes in gene expression on Aβ treatment in the presence of the sensitizing nAChRs, linked to early-stage Aβ-induced neurotoxicity, which may represent novel therapeutic targets.
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13
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Bajic VP, Essack M, Zivkovic L, Stewart A, Zafirovic S, Bajic VB, Gojobori T, Isenovic E, Spremo-Potparevic B. The X Files: "The Mystery of X Chromosome Instability in Alzheimer's Disease". Front Genet 2020; 10:1368. [PMID: 32047510 PMCID: PMC6997486 DOI: 10.3389/fgene.2019.01368] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD). In recent years, despite the hypothesis that many additional unidentified genes are likely to play a role in AD development, it is surprising that additional gene polymorphisms associated with LOAD have failed to come to light. In this review, we examine the role of X chromosome epigenetics and, based upon GWAS studies, the PCDHX11 gene. Furthermore, we explore other genetic risk factors of AD that involve X-chromosome epigenetics.
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Affiliation(s)
- Vladan P Bajic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lada Zivkovic
- Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Alan Stewart
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Sonja Zafirovic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Esma Isenovic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
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14
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He B, Chen W, Zeng J, Tong W, Zheng P. MicroRNA-326 decreases tau phosphorylation and neuron apoptosis through inhibition of the JNK signaling pathway by targeting VAV1 in Alzheimer's disease. J Cell Physiol 2019; 235:480-493. [PMID: 31385301 DOI: 10.1002/jcp.28988] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is a progressive and age-related neurological dysfunction. Abundant data have profiled microRNA (miR) patterns in healthy, aging brain, and in the moderate and late-stages of AD. Herein, this study aimed to explore whether miR-326 could influence neuron apoptosis in AD mice and how miR-326 functions in this process. The candidate differentially expressed gene VAV1 was obtained by microarray analysis, and miRNAs that could regulate VAV1 candidate gene were predicted. Luciferase activity determination confirmed VAV1 as a target gene of miR-326. AD mice models were established for investigating the effect of miR-326 on AD mice. The overexpression of miR-326 contributed to decreased time of the mice to find the platform and the escape latency and increased residence time on the target area. Besides, elevation of miR-326 decreased Aβ deposition and contents of Aβ1-40 and Aβ1-42 . Moreover, miR-326 overexpression increased neuron cell ability, mediated cell entry, and inhibited neuron apoptosis via JNK signaling pathway. Of crucial importance, miR-326 negatively regulated the expression of VAV1, inhibited tau phosphorylation, and blocked the activation of the JNK signaling pathway. Taken together these observations, we demonstrate that miR-326 improves cognitive function of AD mice and inhibits neuron apoptosis in AD mice through inactivation of the JNK signaling pathway by targeting VAV1. Based on those findings, miR-326 might exert promise as target for the treatment of AD.
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Affiliation(s)
- Bin He
- Department of Neurosurgery, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Wei Chen
- Department of Neurosurgery, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Jingsong Zeng
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Wusong Tong
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, Shanghai, China
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15
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The Interplay between miRNA-Related Variants and Age-Related Macular Degeneration: EVIDENCE of Association of MIR146A and MIR27A. Int J Mol Sci 2019; 20:ijms20071578. [PMID: 30934838 PMCID: PMC6480223 DOI: 10.3390/ijms20071578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
The complex interplay among genetic, epigenetic, and environmental variables is the basis for the multifactorial origin of age-related macular degeneration (AMD). Previous results highlighted that single nucleotide polymorphisms (SNPs) of CFH, ARMS2, IL-8, TIMP3, SLC16A8, RAD51B, VEGFA, and COL8A1 were significantly associated with the risk of AMD in the Italian population. Given these data, this study aimed to investigate the impact of SNPs in genes coding for MIR146A, MIR31, MIR23A, MIR27A, MIR20A, and MIR150 on their susceptibility to AMD. Nine-hundred and seventy-six patients with exudative AMD and 1000 controls were subjected to an epigenotyping analysis through real-time PCR and direct sequencing. Biostatistical and bioinformatic analysis was performed to evaluate the association with susceptibility to AMD. These analyses reported that the SNPs rs11671784 (MIR27A, G/A) and rs2910164 (MIR146A, C/G) were significantly associated with AMD risk. Interestingly, the bioinformatic analysis showed that MIR27A and MIR146A take part in the angiogenic and inflammatory pathways underlying AMD etiopathogenesis. Thus, polymorphisms within the pre-miRNA sequences are likely to affect their functional activity, especially the interaction with specific targets. Therefore, our study represents a step forward in the comprehension of the mechanisms leading to AMD onset and progression, which certainly include the involvement of epigenetic modifications.
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16
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Anitha A, Thanseem I, Vasu MM, Viswambharan V, Poovathinal SA. Telomeres in neurological disorders. Adv Clin Chem 2019; 90:81-132. [PMID: 31122612 DOI: 10.1016/bs.acc.2019.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ever since their discovery, the telomeres and the telomerase have been topics of intensive research, first as a mechanism of cellular aging and later as an indicator of health and diseases in humans. By protecting the chromosome ends, the telomeres play a vital role in preserving the information in our genome. Telomeres shorten with age and the rate of telomere erosion provides insight into the proliferation history of cells. The pace of telomere attrition is known to increase at the onset of several pathological conditions. Telomere shortening has been emerging as a potential contributor in the pathogenesis of several neurological disorders including autism spectrum disorders (ASD), schizophrenia, Alzheimer's disease (AD), Parkinson's disease (PD) and depression. The rate of telomere attrition in the brain is slower than that of other tissues owing to the low rate of cell proliferation in brain. Telomere maintenance is crucial for the functioning of stem cells in brain. Taking together the studies on telomere attrition in various neurological disorders, an association between telomere shortening and disease status has been demonstrated in schizophrenia, AD and depression, in spite of a few negative reports. But, studies in ASD and PD have failed to produce conclusive results. The cause-effect relationship between TL and neurological disorders is yet to be elucidated. The factors responsible for telomere erosion, which have also been implicated in the pathogenesis of neurological disorders, need to be explored in detail. Telomerase activation is now being considered as a potential therapeutic strategy for neurological disorders.
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Affiliation(s)
- Ayyappan Anitha
- Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India.
| | - Ismail Thanseem
- Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India
| | - Mahesh Mundalil Vasu
- Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India
| | - Vijitha Viswambharan
- Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India
| | - Suresh A Poovathinal
- Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India
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17
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Mutation screening in Chinese patients with familial Alzheimer's disease by whole-exome sequencing. Neurobiol Aging 2018; 76:215.e15-215.e21. [PMID: 30598257 DOI: 10.1016/j.neurobiolaging.2018.11.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 11/02/2018] [Accepted: 11/29/2018] [Indexed: 01/26/2023]
Abstract
Familial Alzheimer's disease (FAD) is characterized by a positive family history of dementia and typically occurs at an early age with an autosomal dominant pattern of inheritance. Amyloid precursor protein (APP), presenilin1 (PSEN1), and presenilin2 (PSEN2) are the major causative genes of FAD. The spectrum of mutations in patients with FAD has been investigated extensively in the Caucasian population but rarely in the Chinese population. Here, we performed whole-exome sequencing in a total of 15 unrelated Chinese patients with FAD. Among them, 12 were found to carry missense variants in APP, PSEN1, and PSEN2. Two novel variants (APP: p.D244G, p.K687Q), 3 variants not previously associated with FAD (APP: p.T297M, p.D332G; PSEN1: p.R157S), and 7 previously reported pathogenic variants (APP: p.V717I; PSEN1: p.M139I, p.T147I, p.L173W, p.F177S, p.R269H; PSEN2: p.V139M) were identified. The novel variant APP p.K687Q was classified as likely pathogenic, and the other 4 variants (APP: p.D244G, p.T297M, p.D332G; PSEN1: p.R157S) were classified as uncertain significance. Therefore, APP, PSEN1, and PSEN2 mutations account for 2 (25.0%), 5 (62.5%), and 1 (12.5%) of the genotyped cases positive for mutations, respectively. Furthermore, the genotype-phenotype correlations were described. Our findings broaden the genetic spectrum of FAD with APP, PSEN1, and PSEN2 variants.
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18
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DeLeo AM, Ikezu T. Extracellular Vesicle Biology in Alzheimer's Disease and Related Tauopathy. J Neuroimmune Pharmacol 2018; 13:292-308. [PMID: 29185187 PMCID: PMC5972041 DOI: 10.1007/s11481-017-9768-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 12/14/2022]
Abstract
Extracellular vesicles (EVs) are physiological vesicles secreted from most eukaryotes and contain cargos of their cell of origin. EVs, and particularly a subset of EV known as exosomes, are emerging as key mediators of cell to cell communication and waste management for cells both during normal organismal function and in disease. In this review, we investigate the rapidly growing field of exosome biology, their biogenesis, cargo loading, and uptake by other cells. We particularly consider the role of exosomes in Alzheimer's disease, both as a pathogenic agent and as a disease biomarker. We also explore the emerging role of exosomes in chronic traumatic encephalopathy. Finally, we highlight open questions in these fields and the possible use of exosomes as therapeutic targets and agents.
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Affiliation(s)
- Annina M DeLeo
- Laboratory of Molecular NeuroTherapeutics, Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 72 East Concord St, L-606, Boston, MA, 02118, USA.
| | - Tsuneya Ikezu
- Laboratory of Molecular NeuroTherapeutics, Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 72 East Concord St, L-606, Boston, MA, 02118, USA.
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA.
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19
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Wu D, Wen X, Wang Y, Han X, Wang S, Shen M, Fan S, Zhuang J, Zhang Z, Shan Q, Li M, Hu B, Sun C, Lu J, Chen G, Zheng Y. Retracted
: Effect of microRNA‐186 on oxidative stress injury of neuron by targeting interleukin 2 through the janus kinase‐signal transducer and activator of transcription pathway in a rat model of Alzheimer’s disease. J Cell Physiol 2018; 233:9488-9502. [DOI: 10.1002/jcp.26843] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 05/10/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Dong‐Mei Wu
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Xin Wen
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Yong‐Jian Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Xin‐Rui Han
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Shan Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Min Shen
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Shao‐Hua Fan
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Juan Zhuang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- School of Environment Science and Spatial Informatics China University of Mining and Technology Xuzhou China
- Jiangsu Key Laboratory for Eco‐Agricultural Biotechnology Around Hongze Lake, School of Life Sciences Huaiyin Normal University Huaian China
| | - Zi‐Feng Zhang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Qun Shan
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Meng‐Qiu Li
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Bin Hu
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Chun‐Hui Sun
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Jun Lu
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
| | - Gui‐Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center Nanjing University Nanjing China
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center Nanjing University Nanjing China
| | - Yuan‐Lin Zheng
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science Jiangsu Normal University Xuzhou China
- College of Health Sciences Jiangsu Normal University Xuzhou Jiangsu China
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20
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Mendoza-Ruvalcaba NM, Arias-Merino ED, Flores-Villavicencio ME, Rodríguez-Díaz M, Díaz-García IF. Cognitive Aging. Gerontology 2018. [DOI: 10.5772/intechopen.71551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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