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Momen YS, Mishra J, Kumar N. Brain-Gut and Microbiota-Gut-Brain Communication in Type-2 Diabetes Linked Alzheimer's Disease. Nutrients 2024; 16:2558. [PMID: 39125436 PMCID: PMC11313915 DOI: 10.3390/nu16152558] [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: 05/27/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 08/12/2024] Open
Abstract
The gastrointestinal (GI) tract, home to the largest microbial population in the human body, plays a crucial role in overall health through various mechanisms. Recent advancements in research have revealed the potential implications of gut-brain and vice-versa communication mediated by gut-microbiota and their microbial products in various diseases including type-2 diabetes and Alzheimer's disease (AD). AD is the most common type of dementia where most of cases are sporadic with no clearly identified cause. However, multiple factors are implicated in the progression of sporadic AD which can be classified as non-modifiable (e.g., genetic) and modifiable (e.g. Type-2 diabetes, diet etc.). Present review focusses on key players particularly the modifiable factors such as Type-2 diabetes (T2D) and diet and their implications in microbiota-gut-brain (MGB) and brain-gut (BG) communication and cognitive functions of healthy brain and their dysfunction in Alzheimer's Disease. Special emphasis has been given on elucidation of the mechanistic aspects of the impact of diet on gut-microbiota and the implications of some of the gut-microbial products in T2D and AD pathology. For example, mechanistically, HFD induces gut dysbiosis with driven metabolites that in turn cause loss of integrity of intestinal barrier with concomitant colonic and systemic chronic low-grade inflammation, associated with obesity and T2D. HFD-induced obesity and T2D parallel neuroinflammation, deposition of Amyloid β (Aβ), and ultimately cognitive impairment. The review also provides a new perspective of the impact of diet on brain-gut and microbiota-gut-brain communication in terms of transcription factors as a commonly spoken language that may facilitates the interaction between gut and brain of obese diabetic patients who are at a higher risk of developing cognitive impairment and AD. Other commonality such as tyrosine kinase expression and functions maintaining intestinal integrity on one hand and the phagocytic clarence by migratory microglial functions in brain are also discussed. Lastly, the characterization of the key players future research that might shed lights on novel potential pharmacological target to impede AD progression are also discussed.
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Affiliation(s)
| | | | - Narendra Kumar
- Department of Pharmaceutical Sciences, ILR College of Pharmacy, Texas A&M Health Science Center, Kingsville, TX 78363, USA
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2
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Nguyen HD, Kim WK, Huong Vu G. Molecular mechanisms implicated in protein changes in the Alzheimer's disease human hippocampus. Mech Ageing Dev 2024; 219:111930. [PMID: 38554950 DOI: 10.1016/j.mad.2024.111930] [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: 12/03/2023] [Revised: 01/18/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
This study aimed to elucidate the specific biochemical pathways linked to changes in proteins in the Alzheimer's disease (AD) human hippocampus. Our data demonstrate a constant rise in the expression of four proteins (VGF, GFAP, HSPB1, and APP) across all eleven studies. Notably, UBC was the most centrally involved and had increased expression in the hippocampus tissue of individuals with AD. Modified proteins in the hippocampal tissue were found to activate the innate immune system and disrupt communication across chemical synapses. Four hub proteins (CD44, APP, ITGB2, and APOE) are connected to amyloid plaques, whereas two hub proteins (RPL24 and RPS23) are related to neurofibrillary tangles (NFTs). The presence of modified proteins was discovered to trigger the activation of microglia and decrease the functioning of ribosomes and mitochondria in the hippocampus. Three significant microRNAs (hsa-miR-106b-5p, hsa-miR-17-5p, and hsa-miR-16-5p) and transcription factors (MYT1L, PIN1, and CSRNP3) have been discovered to improve our understanding of the alterations in proteins within the hippocampal tissues that lead to the progression of AD. These findings establish a path for possible treatments for AD to employ therapeutic strategies that specifically focus on the proteins or processes linked to the illness.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea; Division of Microbiology, Tulane National Primate Research Center, Tulane University, Louisiana, USA.
| | - Woong-Ki Kim
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Louisiana, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Giang Huong Vu
- Department of Public Health, Hong Bang Health Center, Hai Phong, Vietnam
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3
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Qi T, Zhou Y, Sheng Y, Li Z, Yang Y, Liu Q, Ge Q. Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning. J Chem Inf Model 2024; 64:4002-4008. [PMID: 38798191 DOI: 10.1021/acs.jcim.4c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Transcription factors (TFs) are important regulatory elements for vital cellular activities, and the identification of transcription factor binding sites (TFBS) can help to explore gene regulatory mechanisms. Research studies have proved that cfDNA (cell-free DNA) shows relatively higher coverage at TFBS due to the protection by TF from degradation by nucleases and short fragments of cfDNA are enriched in TFBS. However, there are still great difficulties in the noninvasive identification of TFBSs from experimental techniques. In this study, we propose a deep learning-based approach that can noninvasively predict TFBSs of cfDNA by learning sequence information from known TFBSs through convolutional neural networks. Under the addition of long short-term memory, our model achieved an area under the curve of 84%. Based on this model to predict cfDNA, we found consistent motifs in cfDNA fragments and lower coverage occurred upstream and downstream of these cfDNA fragments, which is consistent with a previous study. We also found that the binding sites of the same TF differ in different cell lines. TF-specific target genes were detected from cfDNA and were enriched in cancer-related pathways. In summary, our method of locating TFBSs from plasma has the potential to reflect the intrinsic regulatory mechanism from a noninvasive perspective and provide technical guidance for dynamic monitoring of disease in clinical practice.
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Affiliation(s)
- Ting Qi
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Ying Zhou
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Yuqi Sheng
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Zhihui Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Yuwei Yang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Quanjun Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
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4
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Llera-Oyola J, Carceller H, Andreu Z, Hidalgo MR, Soler-Sáez I, Gordillo F, Gómez-Cabañes B, Roson B, de la Iglesia-Vayá M, Mancuso R, Guerini FR, Mizokami A, García-García F. The role of microRNAs in understanding sex-based differences in Alzheimer's disease. Biol Sex Differ 2024; 15:13. [PMID: 38297404 PMCID: PMC10832236 DOI: 10.1186/s13293-024-00588-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND The incidence of Alzheimer's disease (AD)-the most frequent cause of dementia-is expected to increase as life expectancies rise across the globe. While sex-based differences in AD have previously been described, there remain uncertainties regarding any association between sex and disease-associated molecular mechanisms. Studying sex-specific expression profiles of regulatory factors such as microRNAs (miRNAs) could contribute to more accurate disease diagnosis and treatment. METHODS A systematic review identified six studies of microRNA expression in AD patients that incorporated information regarding the biological sex of samples in the Gene Expression Omnibus repository. A differential microRNA expression analysis was performed, considering disease status and patient sex. Subsequently, results were integrated within a meta-analysis methodology, with a functional enrichment of meta-analysis results establishing an association between altered miRNA expression and relevant Gene Ontology terms. RESULTS Meta-analyses of miRNA expression profiles in blood samples revealed the alteration of sixteen miRNAs in female and 22 miRNAs in male AD patients. We discovered nine miRNAs commonly overexpressed in both sexes, suggesting a shared miRNA dysregulation profile. Functional enrichment results based on miRNA profiles revealed sex-based differences in biological processes; most affected processes related to ubiquitination, regulation of different kinase activities, and apoptotic processes in males, but RNA splicing and translation in females. Meta-analyses of miRNA expression profiles in brain samples revealed the alteration of six miRNAs in female and four miRNAs in male AD patients. We observed a single underexpressed miRNA in female and male AD patients (hsa-miR-767-5p); however, the functional enrichment analysis for brain samples did not reveal any specifically affected biological process. CONCLUSIONS Sex-specific meta-analyses supported the detection of differentially expressed miRNAs in female and male AD patients, highlighting the relevance of sex-based information in biomedical data. Further studies on miRNA regulation in AD patients should meet the criteria for comparability and standardization of information.
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Affiliation(s)
- Jaime Llera-Oyola
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
- Carlos Simon Foundation-INCLIVA Instituto de Investigación Sanitaria, Valencia, Spain
| | - Héctor Carceller
- Neurobiology Unit, Program in Neurosciences and Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, Burjassot, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spanish National Network for Research in Mental Health, Madrid, Spain
- Joint Unit in Biomedical Imaging FISABIO-CIPF, Foundation for the Promotion of Health and Biomedical Research of Valencia Region, València, Spain
| | - Zoraida Andreu
- Foundation Valencian Institute of Oncology (FIVO), 46009, Valencia, Spain
| | - Marta R Hidalgo
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Irene Soler-Sáez
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Fernando Gordillo
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Borja Gómez-Cabañes
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Beatriz Roson
- Carlos Simon Foundation-INCLIVA Instituto de Investigación Sanitaria, Valencia, Spain
| | - Maria de la Iglesia-Vayá
- Joint Unit in Biomedical Imaging FISABIO-CIPF, Foundation for the Promotion of Health and Biomedical Research of Valencia Region, València, Spain
| | - Roberta Mancuso
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, 20148, Milan, Italy
| | | | - Akiko Mizokami
- Oral Health/Brain Health/Total Health (OBT) Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Francisco García-García
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
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Chandran S, Binninger D. Role of Oxidative Stress, Methionine Oxidation and Methionine Sulfoxide Reductases (MSR) in Alzheimer's Disease. Antioxidants (Basel) 2023; 13:21. [PMID: 38275641 PMCID: PMC10812627 DOI: 10.3390/antiox13010021] [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: 09/30/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
A major contributor to dementia seen in aging is Alzheimer's disease (AD). Amyloid beta (Aβ), a main component of senile plaques (SPs) in AD, induces neuronal death through damage to cellular organelles and structures, caused by oxidation of important molecules such as proteins by reactive oxygen species (ROS). Hyperphosphorylation and accumulation of the protein tau in the microtubules within the brain also promote ROS production. Methionine, a residue of proteins, is particularly sensitive to oxidation by ROS. One of the enzyme systems that reverses the oxidative damage in mammalian cells is the enzyme system known as Methionine Sulfoxide Reductases (MSRs). The components of the MSR system, namely MSRA and MSRB, reduce oxidized forms of methionine (Met-(o)) in proteins back to methionine (Met). Furthermore, the MSRs scavenge ROS by allowing methionine residues in proteins to utilize their antioxidant properties. This review aims to improve the understanding of the role of the MSR system of enzymes in reducing cellular oxidative damage and AD pathogenesis, which may contribute to effective therapeutic approaches for AD by targeting the MSR system.
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Affiliation(s)
- Sanjana Chandran
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA;
| | - David Binninger
- Department of Biological Sciences, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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6
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Li H, Zhou C, Zhang M, Yuan N, Huang X, Xiang J, Wang L, Shi L. Transcriptomics yields valuable information regarding the response mechanisms of Chinese Min pigs infected with PEDV. Front Vet Sci 2023; 10:1295723. [PMID: 38192721 PMCID: PMC10773921 DOI: 10.3389/fvets.2023.1295723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/15/2023] [Indexed: 01/10/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) causes porcine epidemic diarrhea (PED), a highly infectious disease, which has resulted in huge economic losses for the pig industry. To date, the pathogenic and immune response mechanism was not particularly clear. The purpose of this study was to investigate the pathogenic and immune responses of pigs infected with PEDV.In this study, 12 Min pigs were randomly selected without taking colostrum. At 3 days old, eight piglets were infected with 1 mL of PEDV solution (10 TCID50/ml), and the remaining four piglets were handled by 1 mL of 0.9% normal saline. Within the age of 7 days old, four piglets died and were considered as the death group. Correspondingly, four alive individuals were classified into the resistance group. Tissues of the duodenum, jejunum, ileum, colon, cecum, and rectum of piglets in the three groups were collected to measure the PEDV content. Additionally, the jejunum was used for the measurements and analyses of Hematoxylin-eosinstaining (HE), immunohistochemical sections, and transcriptomics. The phenotypes of Min piglets infected with PEDV showed that the viral copy numbers and jejunal damage had significant differences between the death and resistance groups. We also observed the transcriptome of the jejunum, and the differentially expressed (DE) analysis observed 6,585 DE protein-coding genes (PCGs), 3,188 DE long non-coding RNAs (lncRNAs), and 350 DE microRNAs (miRNAs), which were mainly involved in immune response and metabolic pathways. Furthermore, the specific expressed molecules for each group were identified, and 97 PCGs,108 lncRNAs, and 51 miRNAs were included in the ceRNA-regulated networks. By weighted gene co-expression network analysis (WGCNA) and transcription factor (TF) prediction, 27 significant modules and 32 significant motifs (E-value < 0.05) annotated with 519 TFs were detected. Of these TFs, 53 were DE PCGs. In summary, the promising key PCGs, lncRNAs, and miRNAs related to the pathogenic and immunological response of pigs infected with PEDV were detected and provided new insights into the pathogenesis of PEDV.
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Affiliation(s)
- Huihui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunxiang Zhou
- Huanghe Science and Technology University, Zhengzhou, China
| | - Meimei Zhang
- Beijing Vica Biotechnology Co., LTD, Beijing, China
| | - Na Yuan
- Beijing Vica Biotechnology Co., LTD, Beijing, China
| | - Xiaoyu Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaojiao Xiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Jiang Y, MacNeil LT. Simple model systems reveal conserved mechanisms of Alzheimer's disease and related tauopathies. Mol Neurodegener 2023; 18:82. [PMID: 37950311 PMCID: PMC10638731 DOI: 10.1186/s13024-023-00664-x] [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: 04/02/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023] Open
Abstract
The lack of effective therapies that slow the progression of Alzheimer's disease (AD) and related tauopathies highlights the need for a more comprehensive understanding of the fundamental cellular mechanisms underlying these diseases. Model organisms, including yeast, worms, and flies, provide simple systems with which to investigate the mechanisms of disease. The evolutionary conservation of cellular pathways regulating proteostasis and stress response in these organisms facilitates the study of genetic factors that contribute to, or protect against, neurodegeneration. Here, we review genetic modifiers of neurodegeneration and related cellular pathways identified in the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the fruit fly Drosophila melanogaster, focusing on models of AD and related tauopathies. We further address the potential of simple model systems to better understand the fundamental mechanisms that lead to AD and other neurodegenerative disorders.
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Affiliation(s)
- Yuwei Jiang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
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Orobets KS, Karamyshev AL. Amyloid Precursor Protein and Alzheimer's Disease. Int J Mol Sci 2023; 24:14794. [PMID: 37834241 PMCID: PMC10573485 DOI: 10.3390/ijms241914794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative disorders associated with age or inherited mutations. It is characterized by severe dementia in the late stages that affect memory, cognitive functions, and daily life overall. AD progression is linked to the accumulation of cytotoxic amyloid beta (Aβ) and hyperphosphorylated tau protein combined with other pathological features such as synaptic loss, defective energy metabolism, imbalances in protein, and metal homeostasis. Several treatment options for AD are under investigation, including antibody-based therapy and stem cell transplantation. Amyloid precursor protein (APP) is a membrane protein considered to play a main role in AD pathology. It is known that APP in physiological conditions follows a non-amyloidogenic pathway; however, it can proceed to an amyloidogenic scenario, which leads to the generation of extracellular deleterious Aβ plaques. Not all steps of APP biogenesis are clear so far, and these questions should be addressed in future studies. AD is a complex chronic disease with many factors that contribute to disease progression.
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Affiliation(s)
| | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
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9
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Varesi A, Campagnoli LIM, Barbieri A, Rossi L, Ricevuti G, Esposito C, Chirumbolo S, Marchesi N, Pascale A. RNA binding proteins in senescence: A potential common linker for age-related diseases? Ageing Res Rev 2023; 88:101958. [PMID: 37211318 DOI: 10.1016/j.arr.2023.101958] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Aging represents the major risk factor for the onset and/or progression of various disorders including neurodegenerative diseases, metabolic disorders, and bone-related defects. As the average age of the population is predicted to exponentially increase in the coming years, understanding the molecular mechanisms underlying the development of aging-related diseases and the discovery of new therapeutic approaches remain pivotal. Well-reported hallmarks of aging are cellular senescence, genome instability, autophagy impairment, mitochondria dysfunction, dysbiosis, telomere attrition, metabolic dysregulation, epigenetic alterations, low-grade chronic inflammation, stem cell exhaustion, altered cell-to-cell communication and impaired proteostasis. With few exceptions, however, many of the molecular players implicated within these processes as well as their role in disease development remain largely unknown. RNA binding proteins (RBPs) are known to regulate gene expression by dictating at post-transcriptional level the fate of nascent transcripts. Their activity ranges from directing primary mRNA maturation and trafficking to modulation of transcript stability and/or translation. Accumulating evidence has shown that RBPs are emerging as key regulators of aging and aging-related diseases, with the potential to become new diagnostic and therapeutic tools to prevent or delay aging processes. In this review, we summarize the role of RBPs in promoting cellular senescence and we highlight their dysregulation in the pathogenesis and progression of the main aging-related diseases, with the aim of encouraging further investigations that will help to better disclose this novel and captivating molecular scenario.
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Affiliation(s)
- Angelica Varesi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
| | | | - Annalisa Barbieri
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Lorenzo Rossi
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | | | - Ciro Esposito
- Department of Internal Medicine and Therapeutics, University of Pavia, Italy; Nephrology and dialysis unit, ICS S. Maugeri SPA SB Hospital, Pavia, Italy; High School in Geriatrics, University of Pavia, Italy
| | | | - Nicoletta Marchesi
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy.
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Sebastian S, Roy S, Kalita J. A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer's disease network. Brief Bioinform 2023; 24:6868522. [PMID: 36534961 DOI: 10.1093/bib/bbac482] [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: 04/25/2022] [Revised: 09/14/2022] [Accepted: 10/11/2022] [Indexed: 12/23/2022] Open
Abstract
The inference of large-scale gene regulatory networks is essential for understanding comprehensive interactions among genes. Most existing methods are limited to reconstructing networks with a few hundred nodes. Therefore, parallel computing paradigms must be leveraged to construct large networks. We propose a generic parallel framework that enables any existing method, without re-engineering, to infer large networks in parallel, guaranteeing quality output. The framework is tested on 15 inference methods (not limited to) employing in silico benchmarks and real-world large expression matrices, followed by qualitative and speedup assessment. The framework does not compromise the quality of the base serial inference method. We rank the candidate methods and use the top-performing method to infer an Alzheimer's Disease (AD) affected network from large expression profiles of a triple transgenic mouse model consisting of 45,101 genes. The resultant network is further explored to obtain hub genes that emerge functionally related to the disease. We partition the network into 41 modules and conduct pathway enrichment analysis, revealing that a good number of participating genes are collectively responsible for several brain disorders, including AD. Finally, we extract the interactions of a few known AD genes and observe that they are periphery genes connected to the network's hub genes. Availability: The R implementation of the framework is downloadable from https://github.com/Netralab/GenericParallelFramework.
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Affiliation(s)
- Softya Sebastian
- Network Reconstruction and Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, 6th Mile, Gangtok, 737102, Sikkim, India
| | - Swarup Roy
- Network Reconstruction and Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, 6th Mile, Gangtok, 737102, Sikkim, India
| | - Jugal Kalita
- Department of Computer Science, University of Colorado at Colorado Springs, CO, 80918 USA
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Quantitative Sequencing Analysis of the Striatal Transcriptome in a Mouse Model of Alzheimer Disease. Int Neurourol J 2022; 26:S117-125. [PMID: 36503214 PMCID: PMC9767686 DOI: 10.5213/inj.2244256.128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/18/2022] [Indexed: 11/30/2022] Open
Abstract
PURPOSE The purpose of this study was to analyze the transcriptomic changes in the striatum of amyloid precursor protein/presenilin 1 (APP/PS1) transgenic mice and uncover its association with the methyl-CpG binding protein 2 (MeCP2) mediated-changes in striatal epigenetic signature during Alzheimer disease (AD) pathological progression. METHODS To observe transcriptomic alterations in the striatum before the onset of cognitive impairment in APP/PS1 mice, quantitative 3'mRNA sequencing was performed with RNA extracted from the striatum of 6-month-old and 12-month-old wildtype and APP/PS1 mice. In addition, chromatin immunoprecipitation sequencing was conducted with the DNA from wildtype and APP/PS1 mice of the same age as aforementioned. For transcriptomic analysis, comparison terms were constructed based on aging and transgene expression-normal-aging (12-month-old wildtype/6-month-old wildtype), early-AD (6-month-old APP/PS1/6-month-old wildtype), and late-AD (12-month-old APP/PS1/6-month-old wildtype). To compare the changes in biological pathways and networks, we analyzed gene lists from each comparison term via bioinformatics tools including DAVID (Database for Annotation, Visualization, and Integrated Discovery), STRING (Search Tool for the Retrieval of Interacting Genes/Proteins), and SynGO (Synaptic Gene Ontologies). Furthermore, to assume the effect MeCP2 in AD pathological conditions may have on the transcriptome regulation, analysis of the common genes from Quant-Seq and MeCP2-ChIP-Seq was performed. RESULTS Enriched pathways including immune system and inflammatory response were confirmed in normal- aging and lateAD, respectively. In particular, enriched pathways of gene expression regulation, transcriptional regulation, and protein catabolic pathways were found to be significantly altered in early-AD. MeCP2-bound genes that were significantly altered in the transcriptome were suggested to be target genes that have a role in the striatum of the early-stage AD model. CONCLUSION This study confirmed that the alteration of the striatal transcriptomic profile in APP/PS1 mice was involved with several biological pathways. Additionally, comparative analysis of the transcriptomic changes and the MeCP2 bound regions found that a group of differentially expressed genes may be regulated under the epigenetic control of MeCP2.
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12
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Guo Z, Shafik AM, Jin P, Wu H. Differential RNA methylation analysis for MeRIP-seq data under general experimental design. Bioinformatics 2022; 38:4705-4712. [PMID: 36063045 PMCID: PMC9563684 DOI: 10.1093/bioinformatics/btac601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 08/03/2022] [Accepted: 09/02/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION RNA epigenetics is an emerging field to study the post-transcriptional gene regulation. The dynamics of RNA epigenetic modification have been reported to associate with many human diseases. Recently developed high-throughput technology named Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) enables the transcriptome-wide profiling of N6-methyladenosine (m6A) modification and comparison of RNA epigenetic modifications. There are a few computational methods for the comparison of mRNA modifications under different conditions but they all suffer from serious limitations. RESULTS In this work, we develop a novel statistical method to detect differentially methylated mRNA regions from MeRIP-seq data. We model the sequence count data by a hierarchical negative binomial model that accounts for various sources of variations and derive parameter estimation and statistical testing procedures for flexible statistical inferences under general experimental designs. Extensive benchmark evaluations in simulation and real data analyses demonstrate that our method is more accurate, robust and flexible compared to existing methods. AVAILABILITY AND IMPLEMENTATION Our method TRESS is implemented as an R/Bioconductor package and is available at https://bioconductor.org/packages/devel/TRESS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhenxing Guo
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Andrew M Shafik
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
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13
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Asadi MR, Talebi M, Gharesouran J, Sabaie H, Jalaiei A, Arsang-Jang S, Taheri M, Sayad A, Rezazadeh M. Analysis of ROQUIN, Tristetraprolin (TTP), and BDNF/miR-16/TTP regulatory axis in late onset Alzheimer’s disease. Front Aging Neurosci 2022; 14:933019. [PMID: 36016853 PMCID: PMC9397504 DOI: 10.3389/fnagi.2022.933019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/14/2022] [Indexed: 12/25/2022] Open
Abstract
Alzheimer’s disease (AD) is a heterogeneous degenerative disorder of the brain that is on the rise worldwide. One of the critical processes that might be disturbed in AD is gene expression regulation. Tristetraprolin (TTP) and RC3H1 gene (ROQUIN) are two RNA-binding proteins (RBPs) that target AU-rich elements (AREs) and constitutive decay elements (CDEs), respectively. TTP and ROQUIN, members of the CCCH zinc-finger protein family, have been demonstrated to fine-tune numerous inflammatory factors. In addition, miR-16 has distinct characteristics and may influence the target mRNA through the ARE site. Interestingly, BDNF mRNA has ARE sites in the 3’ untranslated region (UTR) and can be targeted by regulatory factors, such as TTP and miR-16 on MRE sequences, forming BDNF/miR-16/TTP regulatory axis. A number of two microarray datasets were downloaded, including information on mRNAs (GSE106241) and miRNAs (GSE157239) from individuals with AD and corresponding controls. R software was used to identify BDNF, TTP, ROQUIN, and miR-16 expression levels in temporal cortex (TC) tissue datasets. Q-PCR was also used to evaluate the expression of these regulatory factors and the expression of BDNF in the blood of 50 patients with AD and 50 controls. Bioinformatic evaluation showed that TTP and miR-16 overexpression might act as post-transcriptional regulatory factors to control BDNF expression in AD in TC samples. Instead, this expression pattern was not found in peripheral blood samples from patients with AD compared to normal controls. ROQUIN expression was increased in the peripheral blood of patients with AD. Hsa-miR-16-5p levels did not show significant differences in peripheral blood samples. Finally, it was shown that TTP and BDNF, based on evaluating the receiver operating characteristic (ROC), effectively identify patients with AD from healthy controls. This study could provide a new perspective on the molecular regulatory processes associated with AD pathogenic mechanisms linked to the BDNF growth factor, although further research is needed on the possible roles of these factors in AD.
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Affiliation(s)
- Mohammad Reza Asadi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahnaz Talebi
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Gharesouran
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Jalaiei
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahram Arsang-Jang
- Cancer Gene Therapy Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Arezou Sayad
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Arezou Sayad,
| | - Maryam Rezazadeh
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Maryam Rezazadeh,
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14
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Wang RR, Qiu X, Pan R, Fu H, Zhang Z, Wang Q, Chen H, Wu QQ, Pan X, Zhou Y, Shan P, Wang S, Guo G, Zheng M, Zhu L, Meng ZX. Dietary intervention preserves β cell function in mice through CTCF-mediated transcriptional reprogramming. J Exp Med 2022; 219:213256. [PMID: 35652891 DOI: 10.1084/jem.20211779] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 04/04/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
Pancreatic β cell plasticity is the primary determinant of disease progression and remission of type 2 diabetes (T2D). However, the dynamic nature of β cell adaptation remains elusive. Here, we establish a mouse model exhibiting the compensation-to-decompensation adaptation of β cell function in response to increasing duration of high-fat diet (HFD) feeding. Comprehensive islet functional and transcriptome analyses reveal a dynamic orchestration of transcriptional networks featuring temporal alteration of chromatin remodeling. Interestingly, prediabetic dietary intervention completely rescues β cell dysfunction, accompanied by a remarkable reversal of HFD-induced reprogramming of islet chromatin accessibility and transcriptome. Mechanistically, ATAC-based motif analysis identifies CTCF as the top candidate driving dietary intervention-induced preservation of β cell function. CTCF expression is markedly decreased in β cells from obese and diabetic mice and humans. Both dietary intervention and AAV-mediated restoration of CTCF expression ameliorate β cell dysfunction ex vivo and in vivo, through transducing the lipid toxicity and inflammatory signals to transcriptional reprogramming of genes critical for β cell glucose metabolism and stress response.
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Affiliation(s)
- Ruo-Ran Wang
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyuan Qiu
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan, China
| | - Ran Pan
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongxing Fu
- Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ziyin Zhang
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qintao Wang
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qing-Qian Wu
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaowen Pan
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanping Zhou
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pengfei Shan
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shusen Wang
- Organ Transplant Center, Tianjin First Central Hospital, Tianjin, China.,NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Min Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan, China
| | - Zhuo-Xian Meng
- Department of Pathology and Pathophysiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Chronic Disease Research Institute, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Geriatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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15
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Abstract
Apolipoprotein E (APOE) has three different isoforms, with APOE4 carriers representing a major risk factor for the development of Alzheimer’s disease (AD). AD is the most common form of dementia, and is a relentlessly progressive disorder that afflicts the aged, characterized by severe memory loss. Presently, AD does not have a cure, increasing the urgency for the development of novel therapeutics for the prevention/treatment of AD. The APOE4 isoform is associated with many pathological mechanisms, such as increased neuroinflammation and a reduction in β-amyloid (Aβ) clearance. The accumulation of Aβ plaques in the brain is a hallmark of AD. The presence of APOE4 can increase neuroinflammation via overactivation of the nuclear factor kappa B (NF-κB) pathway. The NF-κB pathway is a family of transcription factors involved with regulating over 400 genes involved with inflammation. AD is associated with sustained inflammation and an overactivation of the NF-κB pathway. Therefore, targeting the APOE4 isoform and suppressing the NF-κB pathway using anti-inflammatory compounds may result in the development of novel therapeutics for the prevention/treatment of AD.
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16
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Zhang W, Bai SS, Zhang Q, Shi RL, Wang HC, Liu YC, Ni TJ, Wu Y, Yao ZY, Sun Y, Wang MY. Physalin B reduces Aβ secretion through down-regulation of BACE1 expression by activating FoxO1 and inhibiting STAT3 phosphorylation. Chin J Nat Med 2021; 19:732-740. [PMID: 34688463 DOI: 10.1016/s1875-5364(21)60090-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Indexed: 11/18/2022]
Abstract
Physalin B (PB), one of the major active steroidal constituents of Solanaceae Physalis plants, has a wide variety of biological activities. We found that PB significantly down-regulated β-amyloid (Aβ) secretion in N2a/APPsw cells. However, the underlying mechanisms are not well understood. In the current study, we investigated the changes in key enzymes involved in β-amyloid precursor protein (APP) metabolism and other APP metabolites by treating N2a/APPsw cells with PB at different concentrations. The results indicated that PB reduced Aβ secretion, which was caused by down-regulation of β-secretase (BACE1) expression, as indicated at both the protein and mRNA levels. Further research revealed that PB regulated BACE1 expression by inducing the activation of forkhead box O1 (FoxO1) and inhibiting the phosphorylation of signal transducer and activator of transcription 3 (STAT3). In addition, the effect of PB on BACE1 expression and Aβ secretion was reversed by treatment with FoxO1 siRNA and STAT3 antagonist S3I-201. In conclusion, these data demonstrated that PB can effectively down-regulate the expression of BACE1 to reduce Aβsecretion by activating the expression of FoxO1 and inhibiting the phosphorylation of STAT3.
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Affiliation(s)
- Wei Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Shan-Shan Bai
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China; Central Laboratory, the First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471003, China
| | - Qi Zhang
- Grade 2019, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Ru-Ling Shi
- School of Public Health, Xinxiang Medical University, Xinxiang 453003, China
| | - He-Cheng Wang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin 124221, China
| | - You-Cai Liu
- School of Basic Medical Sciences, Sanquan College of Xinxiang Medical University, Xinxiang 453003, China
| | - Tian-Jun Ni
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Ying Wu
- School of Nursing Care, Xinxiang Medical University, Xinxiang 453003, China
| | - Zhao-Yang Yao
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Yi Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Ming-Yong Wang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China; Xinxiang Key Laboratory of Immunoregulation and Molecular Diagnostics, Xinxiang 453003, China.
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17
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A nexus of miR-1271, PAX4 and ALK/RYK influences the cytoskeletal architectures in Alzheimer's Disease and Type 2 Diabetes. Biochem J 2021; 478:3297-3317. [PMID: 34409981 PMCID: PMC8454712 DOI: 10.1042/bcj20210175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023]
Abstract
Alzheimer's Disease (AD) and Type 2 Diabetes (T2D) share a common hallmark of insulin resistance. Reportedly, two non-canonical Receptor Tyrosine Kinases (RTKs), ALK and RYK, both targets of the same micro RNA miR-1271, exhibit significant and consistent functional down-regulation in post-mortem AD and T2D tissues. Incidentally, both have Grb2 as a common downstream adapter and NOX4 as a common ROS producing factor. Here we show that Grb2 and NOX4 play critical roles in reducing the severity of both the diseases. The study demonstrates that the abundance of Grb2 in degenerative conditions, in conjunction with NOX4, reverse cytoskeletal degradation by counterbalancing the network of small GTPases. PAX4, a transcription factor for both Grb2 and NOX4, emerges as the key link between the common pathways of AD and T2D. Down-regulation of both ALK and RYK through miR-1271, elevates the PAX4 level by reducing its suppressor ARX via Wnt/β-Catenin signaling. For the first time, this study brings together RTKs beyond Insulin Receptor (IR) family, transcription factor PAX4 and both AD and T2D pathologies on a common regulatory platform.
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18
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Chung CH, Lin DW, Eames A, Chandrasekaran S. Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms. Metabolites 2021; 11:606. [PMID: 34564422 PMCID: PMC8470976 DOI: 10.3390/metabo11090606] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
Genome-scale metabolic models (GEMs) are powerful tools for understanding metabolism from a systems-level perspective. However, GEMs in their most basic form fail to account for cellular regulation. A diverse set of mechanisms regulate cellular metabolism, enabling organisms to respond to a wide range of conditions. This limitation of GEMs has prompted the development of new methods to integrate regulatory mechanisms, thereby enhancing the predictive capabilities and broadening the scope of GEMs. Here, we cover integrative models encompassing six types of regulatory mechanisms: transcriptional regulatory networks (TRNs), post-translational modifications (PTMs), epigenetics, protein-protein interactions and protein stability (PPIs/PS), allostery, and signaling networks. We discuss 22 integrative GEM modeling methods and how these have been used to simulate metabolic regulation during normal and pathological conditions. While these advances have been remarkable, there remains a need for comprehensive and widespread integration of regulatory constraints into GEMs. We conclude by discussing challenges in constructing GEMs with regulation and highlight areas that need to be addressed for the successful modeling of metabolic regulation. Next-generation integrative GEMs that incorporate multiple regulatory mechanisms and their crosstalk will be invaluable for discovering cell-type and disease-specific metabolic control mechanisms.
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Affiliation(s)
- Carolina H. Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (C.H.C.); (A.E.)
| | - Da-Wei Lin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Alec Eames
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (C.H.C.); (A.E.)
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (C.H.C.); (A.E.)
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Bioinformatics and Computational Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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19
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Uddin MS, Kabir MT, Jalouli M, Rahman MA, Jeandet P, Behl T, Alexiou A, Albadrani GM, Abdel-Daim MM, Perveen A, Ashraf GM. Neuroinflammatory Signaling in the Pathogenesis of Alzheimer's Disease. Curr Neuropharmacol 2021; 20:126-146. [PMID: 34525932 PMCID: PMC9199559 DOI: 10.2174/1570159x19666210826130210] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/16/2021] [Accepted: 05/10/2021] [Indexed: 11/22/2022] Open
Abstract
Alzheimer’s disease (AD) is a chronic neurodegenerative disease characterized by the formation of intracellular neurofibrillary tangles (NFTs) and extracellular amyloid plaques. Growing evidence has suggested that AD pathogenesis is not only limited to the neuronal compartment but also strongly interacts with immunological processes in the brain. On the other hand, aggregated and misfolded proteins can bind with pattern recognition receptors located on astroglia and microglia and can, in turn, induce an innate immune response, characterized by the release of inflammatory mediators, ultimately playing a role in both the severity and the progression of the disease. It has been reported by genome-wide analysis that several genes which elevate the risk for sporadic AD encode for factors controlling the inflammatory response and glial clearance of misfolded proteins. Obesity and systemic inflammation are examples of external factors which may interfere with the immunological mechanisms of the brain and can induce disease progression. In this review, we discussed the mechanisms and essential role of inflammatory signaling pathways in AD pathogenesis. Indeed, interfering with immune processes and modulation of risk factors may lead to future therapeutic or preventive AD approaches.
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Affiliation(s)
- Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka. Bangladesh
| | | | - Maroua Jalouli
- College of Science, King Saud University, P.O. Box 2455, Riyadh 11451. Saudi Arabia
| | - Md Ataur Rahman
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul. Korea
| | - Philippe Jeandet
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2. France
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab. India
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, 2770 Hebersham. Australia
| | - Ghadeer M Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11474. Saudi Arabia
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522. Egypt
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Saharanpur. India
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah. Saudi Arabia
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20
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D’Andrea L, Stringhi R, Di Luca M, Marcello E. Looking at Alzheimer's Disease Pathogenesis from the Nuclear Side. Biomolecules 2021; 11:biom11091261. [PMID: 34572474 PMCID: PMC8467578 DOI: 10.3390/biom11091261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 01/22/2023] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder representing the most common form of dementia. It is biologically characterized by the deposition of extracellular amyloid-β (Aβ) senile plaques and intracellular neurofibrillary tangles, constituted by hyperphosphorylated tau protein. The key protein in AD pathogenesis is the amyloid precursor protein (APP), which is cleaved by secretases to produce several metabolites, including Aβ and APP intracellular domain (AICD). The greatest genetic risk factor associated with AD is represented by the Apolipoprotein E ε4 (APOE ε4) allele. Importantly, all of the above-mentioned molecules that are strictly related to AD pathogenesis have also been described as playing roles in the cell nucleus. Accordingly, evidence suggests that nuclear functions are compromised in AD. Furthermore, modulation of transcription maintains cellular homeostasis, and alterations in transcriptomic profiles have been found in neurodegenerative diseases. This report reviews recent advancements in the AD players-mediated gene expression. Aβ, tau, AICD, and APOE ε4 localize in the nucleus and regulate the transcription of several genes, part of which is involved in AD pathogenesis, thus suggesting that targeting nuclear functions might provide new therapeutic tools for the disease.
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21
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Olajide OJ, Suvanto ME, Chapman CA. Molecular mechanisms of neurodegeneration in the entorhinal cortex that underlie its selective vulnerability during the pathogenesis of Alzheimer's disease. Biol Open 2021; 10:bio056796. [PMID: 33495355 PMCID: PMC7860115 DOI: 10.1242/bio.056796] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The entorhinal cortex (EC) is a vital component of the medial temporal lobe, and its contributions to cognitive processes and memory formation are supported through its extensive interconnections with the hippocampal formation. During the pathogenesis of Alzheimer's disease (AD), many of the earliest degenerative changes are seen within the EC. Neurodegeneration in the EC and hippocampus during AD has been clearly linked to impairments in memory and cognitive function, and a growing body of evidence indicates that molecular and functional neurodegeneration within the EC may play a primary role in cognitive decline in the early phases of AD. Defining the mechanisms underlying molecular neurodegeneration in the EC is crucial to determining its contributions to the pathogenesis of AD. Surprisingly few studies have focused on understanding the mechanisms of molecular neurodegeneration and selective vulnerability within the EC. However, there have been advancements indicating that early dysregulation of cellular and molecular signaling pathways in the EC involve neurodegenerative cascades including oxidative stress, neuroinflammation, glia activation, stress kinases activation, and neuronal loss. Dysfunction within the EC can impact the function of the hippocampus, which relies on entorhinal inputs, and further degeneration within the hippocampus can compound this effect, leading to severe cognitive disruption. This review assesses the molecular and cellular mechanisms underlying early degeneration in the EC during AD. These mechanisms may underlie the selective vulnerability of neuronal subpopulations in this brain region to the disease development and contribute both directly and indirectly to cognitive loss.This paper has an associated Future Leader to Watch interview with the first author of the article.
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Affiliation(s)
- Olayemi Joseph Olajide
- Division of Neurobiology, Department of Anatomy, University of Ilorin, Ilorin, Nigeria, PMB 1515
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, Montréal, Québec, Canada H4B 1R6
| | - Marcus E Suvanto
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, Montréal, Québec, Canada H4B 1R6
| | - Clifton Andrew Chapman
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, Montréal, Québec, Canada H4B 1R6
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22
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Syeda T, Cannon JR. Environmental exposures and the etiopathogenesis of Alzheimer's disease: The potential role of BACE1 as a critical neurotoxic target. J Biochem Mol Toxicol 2021; 35:e22694. [PMID: 33393683 DOI: 10.1002/jbt.22694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is a major public health crisis due to devastating cognitive symptoms, a lack of curative treatments, and increasing prevalence. Most cases are sporadic (>95% of cases) after the age of 65 years, implicating an important role of environmental factors in disease pathogenesis. Environmental neurotoxicants have been implicated in neurodegenerative disorders including Parkinson's Disease and AD. Animal models of AD and in vitro studies have shed light on potential neuropathological mechanisms, yet the biochemical and molecular underpinnings of AD-relevant environmental neurotoxicity remain poorly understood. Beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) is a potentially critical pathogenic target of environmentally induced neurotoxicity. BACE1 clearly has a critical role in AD pathophysiology: It is required for amyloid beta production and expression and activity of BACE1 are increased in the AD brain. Though the literature on BACE1 in response to environmental insults is limited, current studies, along with extensive AD neurobiology literature suggest that BACE1 deserves attention as an important neurotoxic target. Here, we critically review research on environmental neurotoxicants such as metals, pesticides, herbicides, fungicides, polyfluoroalkyl substances, heterocyclic aromatic amines, advanced glycation end products, and acrolein that modulate BACE1 and potential mechanisms of action. Though more research is needed to clearly understand whether BACE1 is a critical mediator of AD-relevant neurotoxicity, available reports provide convincing evidence that BACE1 is altered by environmental risk factors associated with AD pathology, implying that BACE1 inhibition and its use as a biomarker should be considered in AD management and research.
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Affiliation(s)
- Tauqeerunnisa Syeda
- School of Health Sciences, Purdue University, West Lafayette, Indiana, USA.,Purdue Institute for Integrative Neurosciences, Purdue University, West Lafayette, Indiana, USA
| | - Jason R Cannon
- School of Health Sciences, Purdue University, West Lafayette, Indiana, USA.,Purdue Institute for Integrative Neurosciences, Purdue University, West Lafayette, Indiana, USA
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Goswami S, Kareem O, Goyal RK, Mumtaz SM, Tonk RK, Gupta R, Pottoo FH. Role of Forkhead Transcription Factors of the O Class (FoxO) in Development and Progression of Alzheimer's Disease. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2020; 19:709-721. [PMID: 33001019 DOI: 10.2174/1871527319666201001105553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 07/20/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
In the Central Nervous System (CNS), a specific loss of focal neurons leads to mental and neurological disorders like dementia, Alzheimer's Disease (AD), Huntington's disease, Parkinson's disease, etc. AD is a neurological degenerative disorder, which is progressive and irreversible in nature and is the widely recognized reason for dementia in the geriatric populace. It affects 10% of people above the age of 65 and is the fourth driving reason for death in the United States. Numerous evidence suggests that the neuronal compartment is not the only genesis of AD, but transcription factors also hold significant importance in the occurrence and advancement of the disease. It is the need of the time to find the novel molecular targets and new techniques for treating or slowing down the progression of neurological disorders, especially AD. In this article, we summarised a conceivable association between transcriptional factors and their defensive measures against neurodegeneration and AD. The mammalian forkhead transcription factors of the class O (FoxO) illustrate one of the potential objectives for the development of new methodologies against AD and other neurocognitive disorders. The presence of FoxO is easily noticeable in the "cognitive centers" of the brain, specifically in the amygdala, hippocampus, and the nucleus accumbens. FoxO proteins are the prominent and necessary factors in memory formation and cognitive functions. FoxO also assumes a pertinent role in the protection of multiple cells in the brain by controlling the involving mechanism of autophagy and apoptosis and also modulates the process of phosphorylation of the targeted protein, thus FoxO must be a putative target in the mitigation of AD. This review features the role of FoxO as an important biomarker and potential new targets for the treatment of AD.
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Affiliation(s)
- Shikha Goswami
- Delhi Pharmaceutical Sciences and Research University, Mehrauli- Badarpur Rd, Sector 3, PushpVihar, New Delhi, India
| | - Ozaifa Kareem
- Department of Pharmaceutical Sciences, Faculty of Applied Sciences and Technology, University of Kashmir, Srinagar, JK, India
| | - Ramesh K Goyal
- Delhi Pharmaceutical Sciences and Research University, Mehrauli- Badarpur Rd, Sector 3, PushpVihar, New Delhi, India
| | - Sayed M Mumtaz
- Delhi Pharmaceutical Sciences and Research University, Mehrauli- Badarpur Rd, Sector 3, PushpVihar, New Delhi, India
| | - Rajiv K Tonk
- Delhi Pharmaceutical Sciences and Research University, Mehrauli- Badarpur Rd, Sector 3, PushpVihar, New Delhi, India
| | - Rahul Gupta
- Delhi Pharmaceutical Sciences and Research University, Mehrauli- Badarpur Rd, Sector 3, PushpVihar, New Delhi, India
| | - Faheem H Pottoo
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University P.O.BOX 1982, Dammam 31441, Saudi Arabia
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Pandey RS, Graham L, Uyar A, Preuss C, Howell GR, Carter GW. Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer's disease. Mol Neurodegener 2019; 14:50. [PMID: 31878951 PMCID: PMC6933917 DOI: 10.1186/s13024-019-0351-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/11/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND New genetic and genomic resources have identified multiple genetic risk factors for late-onset Alzheimer's disease (LOAD) and characterized this common dementia at the molecular level. Experimental studies in model organisms can validate these associations and elucidate the links between specific genetic factors and transcriptomic signatures. Animal models based on LOAD-associated genes can potentially connect common genetic variation with LOAD transcriptomes, thereby providing novel insights into basic biological mechanisms underlying the disease. METHODS We performed RNA-Seq on whole brain samples from a panel of six-month-old female mice, each carrying one of the following mutations: homozygous deletions of Apoe and Clu; hemizygous deletions of Bin1 and Cd2ap; and a transgenic APOEε4. Similar data from a transgenic APP/PS1 model was included for comparison to early-onset variant effects. Weighted gene co-expression network analysis (WGCNA) was used to identify modules of correlated genes and each module was tested for differential expression by strain. We then compared mouse modules with human postmortem brain modules from the Accelerating Medicine's Partnership for AD (AMP-AD) to determine the LOAD-related processes affected by each genetic risk factor. RESULTS Mouse modules were significantly enriched in multiple AD-related processes, including immune response, inflammation, lipid processing, endocytosis, and synaptic cell function. WGCNA modules were significantly associated with Apoe-/-, APOEε4, Clu-/-, and APP/PS1 mouse models. Apoe-/-, GFAP-driven APOEε4, and APP/PS1 driven modules overlapped with AMP-AD inflammation and microglial modules; Clu-/- driven modules overlapped with synaptic modules; and APP/PS1 modules separately overlapped with lipid-processing and metabolism modules. CONCLUSIONS This study of genetic mouse models provides a basis to dissect the role of AD risk genes in relevant AD pathologies. We determined that different genetic perturbations affect different molecular mechanisms comprising AD, and mapped specific effects to each risk gene. Our approach provides a platform for further exploration into the causes and progression of AD by assessing animal models at different ages and/or with different combinations of LOAD risk variants.
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Affiliation(s)
- Ravi S. Pandey
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Leah Graham
- The Jackson Laboratory, Bar Harbor, ME USA
- Sackler School of graduate Biomedical Sciences, Tufts University, Boston, MA USA
| | - Asli Uyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | | | - Gareth R. Howell
- The Jackson Laboratory, Bar Harbor, ME USA
- Sackler School of graduate Biomedical Sciences, Tufts University, Boston, MA USA
| | - Gregory W. Carter
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
- The Jackson Laboratory, Bar Harbor, ME USA
- Sackler School of graduate Biomedical Sciences, Tufts University, Boston, MA USA
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25
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Balu D, Karstens AJ, Loukenas E, Maldonado Weng J, York JM, Valencia-Olvera AC, LaDu MJ. The role of APOE in transgenic mouse models of AD. Neurosci Lett 2019; 707:134285. [PMID: 31150730 PMCID: PMC6717006 DOI: 10.1016/j.neulet.2019.134285] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 12/17/2022]
Abstract
Identified in 1993, APOE4 is the greatest genetic risk factor for Alzheimer's disease (AD), increasing risk up to 15-fold compared to the common variant APOE3. Since the mid 1990's, transgenic (Tg) mice have been developed to model AD pathology and progression, primarily via expression of the familial AD (FAD) mutations in the presence of mouse-APOE (m-APOE). APOE4, associated with enhanced amyloid-β (Aβ) accumulation, has rarely been the focus in designing FAD-Tg mouse models. Initially, FAD-Tg mice were crossed with human (h)-APOE driven by heterologous promoters to identify an APOE genotype-specific AD phenotype. These models were later supplemented with FAD-Tg mice crossed with APOE-knockouts (APOE-/- or APOE-KO) and h-APOE-targeted replacement (h-APOE-TR) mice, originally generated to study the role of APOE genotype in peripheral lipid metabolism and atherosclerotic lesion development. Herein, we compare the m- and h-APOE multi-gene clusters, and then critically review the relevant history and approaches to developing a Tg mouse model to characterize APOE-dependent AD pathology, in combination with genetic (sex, age) and modifiable (e.g., inflammation, obesity) risk factors. Finally, we present recent data from the EFAD mice, which express 5xFAD mutations with the expression of the human apoE isoforms (E2FAD, E3FAD and E4FAD). This includes a study of 6- and 18-month-old male and female E3FAD and E4FAD, a comparison that enables examination of the interaction among the main AD risk factors: age, APOE genotype and sex. While no single transgenic mouse can capture the effects of all modifiable and genetic risk factors, going forward, a conscious effort needs to be made to include the factors that most significantly modulate AD pathology.
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Affiliation(s)
- Deebika Balu
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Aimee James Karstens
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Psychology, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Efstathia Loukenas
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Juan Maldonado Weng
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Jason M York
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | | | - Mary Jo LaDu
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA.
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26
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Lutz MW, Sprague D, Chiba-Falek O. Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation. Alzheimers Dement 2019; 15:1048-1058. [PMID: 31262699 PMCID: PMC6699885 DOI: 10.1016/j.jalz.2019.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/20/2019] [Accepted: 04/17/2019] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Genome-wide association studies (GWAS) discovered multiple late-onset Alzheimer's disease (LOAD)-associated SNPs and inferred the genes based on proximity; however, the actual causal genes are yet to be identified. METHODS We defined LOAD-GWAS regions by the most significantly associated SNP ±0.5 Mb and developed a bioinformatics pipeline that uses and integrates chromatin state segmentation track to map active enhancers and virtual 4C software to visualize interactions between active enhancers and gene promoters. We augmented our pipeline with biomedical and functional information. RESULTS We applied the bioinformatics pipeline using three ∼1 Mb LOAD-GWAS loci: BIN1, PICALM, CELF1. These loci contain 10-24 genes, an average of 106 active enhancers and 80 CTCF sites. Our strategy identified all genes corresponding to the promoters that interact with the active enhancer that is closest to the LOAD-GWAS-SNP and generated a shorter list of prioritized candidate LOAD genes (5-14/loci), feasible for post-GWAS investigations of causality. DISCUSSION Interpretation of LOAD-GWAS discoveries requires the integration of brain-specific functional genomic data sets and information related to regulatory activity.
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Affiliation(s)
- Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Daniel Sprague
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA.
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27
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Godini R, Pocock R, Fallahi H. Caenorhabditis elegans hub genes that respond to amyloid beta are homologs of genes involved in human Alzheimer's disease. PLoS One 2019; 14:e0219486. [PMID: 31291334 PMCID: PMC6619800 DOI: 10.1371/journal.pone.0219486] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/25/2019] [Indexed: 12/31/2022] Open
Abstract
The prominent characteristic of Alzheimer’s disease (AD) is the accumulation of amyloid beta (Abeta) proteins in the form of plaques that cause molecular and cellular alterations in the brain. Due to the paucity of brain samples of early-stage Abeta aggregation, animal models have been developed to study early events in AD. Caenorhabditis elegans is a genetically tractable animal model for AD. Here, we used transcriptomic data, network-based protein-protein interactions and weighted gene co-expression network analysis (WGCNA), to detect modules and their gene ontology in response to Abeta aggregation in C. elegans. Additionally, hub genes and their orthologues in human and mouse were identified to study their relation to AD. We also found several transcription factors (TFs) responding to Abeta accumulation. Our results show that Abeta expression in C. elegans relates to general processes such as molting cycle, locomotion, and larval development plus AD-associated processes, including protein phosphorylation, and G-protein coupled receptor-regulated pathways. We reveal that many hub genes and TFs including ttbk-2, daf-16, and unc-49 have human and mouse orthologues that are directly or potentially associated with AD and neural development. In conclusion, using systems biology we identified important genes and biological processes in C. elegans that respond to Abeta aggregation, which could be used as potential diagnostic or therapeutic targets. In addition, because of evolutionary relationship to AD in human, we suggest that C. elegans is a useful model for studying early molecular events in AD.
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Affiliation(s)
- Rasoul Godini
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
- * E-mail:
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28
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Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I. Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nat Struct Mol Biol 2019; 26:397-406. [PMID: 31110295 PMCID: PMC6642811 DOI: 10.1038/s41594-019-0220-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/29/2019] [Indexed: 12/11/2022]
Abstract
Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly's global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE-p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.
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Affiliation(s)
- Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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29
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Gu MY, Chun YS, Yong RS, Yang HO. Licoflavonol Reduces Aβ Secretion by Increasing BACE1 Phosphorylation to Facilitate BACE1 Degradation. Mol Nutr Food Res 2019; 63:e1800474. [PMID: 30365228 DOI: 10.1002/mnfr.201800474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/18/2018] [Indexed: 12/16/2022]
Abstract
SCOPE In the previous study, Glycyrrhiza uralensis Fisch extract (GUE) inhibited Aβ secretion by inhibiting β-site APP-cleaving enzyme 1 (BACE1) transcription, and the active compounds semilicoisoflavone B (SB) and licoflavonol (LF) inhibited Aβ secretion. SB corresponds to the same mechanism as GUE, but LF has a different mechanism. In this study, the mechanism underlying inhibition of Aβ by LF is investigated. METHODS AND RESULTS The effects of LF on Aβ, sAPPα, and sAPPβ secretion are evaluated by ELISA, and the effect of LF on BACE1 expression is detected by western blotting. It is found that the effect of LF on Aβ secretion is due to promotion of BACE1 protein degradation, and that the effect of LF on Aβ and BACE1 expression is attenuated after cotreatment with the lysosome inhibitor chloroquine. In a subsequent mechanistic study, it is found that LF increases BACE1 phosphorylation to increase its interactions with ADP ribosylation factor-binding proteins 1 and 3 (GGA1 and GGA3, respectively) and eventually facilitate BACE1 delivery to lysosomes for degradation. CONCLUSION This study is the first to demonstrate that the BACE1 phosphorylation inducer LF can modulate BACE1 trafficking and lead to facilitating degradation of BACE1, eventually decreasing Aβ secretion.
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Affiliation(s)
- Ming-Yao Gu
- Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, 25457, Gangwon-do, Republic of Korea.,Division of Bio-Medical Science &Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Yoon Sun Chun
- Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, 25457, Gangwon-do, Republic of Korea
| | - Ryu Shi Yong
- Research Center for Medicinal Chemistry, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon, 34113, Republic of Korea
| | - Hyun Ok Yang
- Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, 25457, Gangwon-do, Republic of Korea.,Division of Bio-Medical Science &Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea
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30
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Paiva I, Jain G, Lázaro DF, Jerčić KG, Hentrich T, Kerimoglu C, Pinho R, Szegő ÈM, Burkhardt S, Capece V, Halder R, Islam R, Xylaki M, Caldi Gomes LA, Roser AE, Lingor P, Schulze-Hentrich JM, Borovečki F, Fischer A, Outeiro TF. Alpha-synuclein deregulates the expression of COL4A2 and impairs ER-Golgi function. Neurobiol Dis 2018; 119:121-135. [PMID: 30092270 DOI: 10.1016/j.nbd.2018.08.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/12/2018] [Accepted: 08/03/2018] [Indexed: 12/21/2022] Open
Abstract
Alpha-synuclein (aSyn) is the major protein component of Lewy bodies and Lewy neurites, the typical pathological hallmarks in Parkinson's disease (PD) and Dementia with Lewy bodies. aSyn is capable of inducing transcriptional deregulation, but the precise effect of specific aSyn mutants associated with familial forms of PD, remains unclear. Here, we used transgenic mice overexpressing human wild-type (WT) or A30P aSyn to compare the transcriptional profiles of the two animal models. We found that A30P aSyn promotes strong transcriptional deregulation and increases DNA binding. Interestingly, COL4A2, a major component of basement membranes, was found to be upregulated in both A30P aSyn transgenic mice and in dopaminergic neurons expressing A30P aSyn, suggesting a crucial role for collagen related genes in aSyn-induced toxicity. Finally, we observed that A30P aSyn alters Golgi morphology and increases the susceptibility to endoplasmic reticulum (ER) stress in dopaminergic cells. In total, our findings provide novel insight into the putative role of aSyn on transcription and on the molecular mechanisms involved, thereby opening novel avenues for future therapeutic interventions in PD and other synucleinopathies.
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Affiliation(s)
- Isabel Paiva
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen 37073, Germany
| | - Gaurav Jain
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Diana F Lázaro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen 37073, Germany
| | - Kristina Gotovac Jerčić
- Department for Functional Genomics, Center for Translational and Clinical Research, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, Faculty of Medicine, University of Tübingen, Tübingen 72076, Germany
| | - Cemil Kerimoglu
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany; Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Raquel Pinho
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen 37073, Germany
| | - Èva M Szegő
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen 37073, Germany
| | - Susanne Burkhardt
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Vincenzo Capece
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Rashi Halder
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Rezaul Islam
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Mary Xylaki
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen 37073, Germany
| | - Lucas A Caldi Gomes
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Anna-Elisa Roser
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Paul Lingor
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Julia M Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, Faculty of Medicine, University of Tübingen, Tübingen 72076, Germany
| | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical Research, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - André Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany; Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen 37073, Germany; CEDOC - Chronic Diseases Research Center, Faculdade de Ciencias Medicas, Universidade Nova de Lisboa, Lisboa, Portugal; Max Planck Institute for Experimental Medicine, Göttingen 37075, Germany; Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle NE2 4HH, UK.
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31
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Hoffman A, Taleski G, Qian H, Wasek B, Arning E, Bottiglieri T, Sontag JM, Sontag E. Methylenetetrahydrofolate Reductase Deficiency Deregulates Regional Brain Amyloid-β Protein Precursor Expression and Phosphorylation Levels. J Alzheimers Dis 2018; 64:223-237. [DOI: 10.3233/jad-180032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Alexander Hoffman
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Goce Taleski
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Helena Qian
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Brandi Wasek
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott and White Research Institute, Dallas, TX, USA
| | - Erland Arning
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott and White Research Institute, Dallas, TX, USA
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott and White Research Institute, Dallas, TX, USA
| | - Jean-Marie Sontag
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Estelle Sontag
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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32
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Berggren K, Agrawal S, Fox JA, Hildenbrand J, Nelson R, Bush AI, Fox JH. Amyloid Precursor Protein Haploinsufficiency Preferentially Mediates Brain Iron Accumulation in Mice Transgenic for The Huntington's Disease Mutation. J Huntingtons Dis 2018; 6:115-125. [PMID: 28550267 DOI: 10.3233/jhd-170242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Huntington's disease (HD) is an autosomal dominant disorder caused by a CAG expansion in the huntingtin gene that results in expression of mutant huntingtin protein. Iron accumulates in HD brain neurons. Amyloid precursor protein (APP) promotes neuronal iron export. However, the role of APP in brain iron accumulation in HD is unclear. OBJECTIVE To determine the effects of APP insufficiency on HD in YAC128 mice. METHODS We crossed APP hemizygous mice (APP+/-) with YAC128 mice that are transgenic (Tg) for human mutant huntingtin (hmHTT) to generate APP+/+ hmHTT-/-, APP+/- hmHTT-/-, APP+/+ hmHTT+/- and APP+/- hmHTT+/- progeny. Mice were evaluated for behavioral, biochemical and neuropathology HD outcomes at 2-12 months of age. RESULTS APP heterozygosity decreased cortical APP 25% and 60% in non-Tg and Tg mice, respectively. Cerebral and striatal iron levels were increased by APP knockdown in Tg mice only. Nest-building behavior was decreased in Tg mice; APP knockdown decreased nest building in non-Tg but not Tg mice. Rota-rod endurance was decreased in Tg mice. APP+/- hHTT+/- mice demonstrated additional decreases in rota-rod endurance from 4-10 months of age. Tg mice had smaller striatal volumes and fewer striatal neurons but were not affected by APP knockdown. CONCLUSIONS APP heterozygosity results in greater decreases of cortical APP in Tg versus non-Tg mice. Mutant huntingtin transgenic mice develop brain iron accumulation as a result of greater suppression of APP levels. Elevated brain iron in Tg mice was associated with a decline in motor endurance consistent with a disease promoting effect of iron in the YAC128 model of human HD.
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Affiliation(s)
- Kiersten Berggren
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Sonal Agrawal
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Julia A Fox
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Justin Hildenbrand
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Ryan Nelson
- Department of Zoology-Physiology, University of Wyoming, Laramie, WY, USA
| | - Ashley I Bush
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Australia
| | - Jonathan H Fox
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
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33
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Sadhukhan P, Saha S, Dutta S, Mahalanobish S, Sil PC. Nutraceuticals: An emerging therapeutic approach against the pathogenesis of Alzheimer’s disease. Pharmacol Res 2018; 129:100-114. [PMID: 29183770 DOI: 10.1016/j.phrs.2017.11.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/22/2017] [Accepted: 11/22/2017] [Indexed: 01/01/2023]
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34
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Chanana N, Pati U. ORP150-CHIP chaperone antagonism control BACE1-mediated amyloid processing. J Cell Biochem 2018; 119:4615-4626. [PMID: 29266373 DOI: 10.1002/jcb.26630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/19/2017] [Indexed: 12/18/2022]
Abstract
BACE1, a key protein involved in Alzheimer's progression, initiates Aβ42 generation that induce senile plaques in brain. However, the role of chaperone synergy or antagonism on BACE1-mediated amyloid processing is unknown. We have discovered that BACE1 as well as Aβ42 are antagonistically controlled by ER chaperone ORP150 and cellular chaperone CHIP. We have shown ORP150 as a chaperone interacts with and stabilizes BACE1 at post-translational level. Furthermore, ORP150 enhances BACE1-mediated amyloid processing thus masking CHIP-mediated BACE1 degradation. Conversely, siORP150 reversed the chaperone function of ORP150 resulting in BACE1 degradation. ORP150 and CHIP demonstrate antagonism under normal and stress conditions wherein they inversely regulate each other thus affecting BACE1 level. In conclusion, we have uncovered for the first time a phenomenon of chaperone antagonism on BACE1-mediated Aβ42 generation. Future strategy would require both suppression of ORP150 as well as activation of E3-ligase activity of CHIP that might prevent Aβ42 in Alzheimer's disease.
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Affiliation(s)
- Neha Chanana
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Uttam Pati
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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35
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Gu MY, Chun YS, Zhao D, Ryu SY, Yang HO. Glycyrrhiza uralensis and Semilicoisoflavone B Reduce Aβ Secretion by Increasing PPARγ Expression and Inhibiting STAT3 Phosphorylation to Inhibit BACE1 Expression. Mol Nutr Food Res 2018; 62:e1700633. [PMID: 29143445 DOI: 10.1002/mnfr.201700633] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 11/07/2017] [Indexed: 12/19/2022]
Abstract
SCOPE Glycyrrhiza uralensis extract (GUE) has been reported to improve amyloid beta (Aβ)-induced cognitive deficits in mice. However, the mechanisms underlying this effect and the components involved have not been previously explored. Extracellular Aβ plaques are one of the major pathological hallmarks of Alzheimer's disease (AD). Therefore, decreasing Aβ levels is one strategy for preventing the etiology of AD. This study aims to test the effect of GUE and semilicoisoflavone B (SB) on Aβ secretion and investigates the mechanism underlying this effect. METHODS AND RESULTS GUE and its bio-activated compound SB reduce Aβ secretion. We find that this effect contribute to the downregulation of the β-secretase-1 (BACE1) protein and mRNA. In a subsequent mechanism study, we find that GUE and SB regulate BACE1 transcription factors by inducing the expression of peroxisome proliferator activated receptor γ (PPARγ) and inhibiting the phosphorylation of signal transducer and activator of transcription 3. In addition, the effect of GUE and SB on BACE1 expression and Aβ secretion are attenuated by treatment with PPARγ-siRNA or its antagonist, GW9662. CONCLUSION These findings indicate that GUE and SB may function as PPARγ agonists, thereby inhibiting BACE1 expression and ultimately reducing the secretion of Aβ.
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Affiliation(s)
- Ming-Yao Gu
- Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, Gangwon-do, Republic of Korea.,Division of Bio-Medical Science &Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Yoon Sun Chun
- Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, Gangwon-do, Republic of Korea
| | - Dong Zhao
- Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, Gangwon-do, Republic of Korea.,Division of Bio-Medical Science &Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Shi Yong Ryu
- Research Center for Medicinal Chemistry, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Hyun Ok Yang
- Natural Products Research Center, Korea Institute of Science and Technology, Gangneung, Gangwon-do, Republic of Korea.,Division of Bio-Medical Science &Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
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36
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Omics Approaches for Identifying Physiological Adaptations to Genome Instability in Aging. Int J Mol Sci 2017; 18:ijms18112329. [PMID: 29113067 PMCID: PMC5713298 DOI: 10.3390/ijms18112329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/25/2017] [Accepted: 10/29/2017] [Indexed: 12/25/2022] Open
Abstract
DNA damage causally contributes to aging and age-related diseases. The declining functioning of tissues and organs during aging can lead to the increased risk of succumbing to aging-associated diseases. Congenital syndromes that are caused by heritable mutations in DNA repair pathways lead to cancer susceptibility and accelerated aging, thus underlining the importance of genome maintenance for withstanding aging. High-throughput mass-spectrometry-based approaches have recently contributed to identifying signalling response networks and gaining a more comprehensive understanding of the physiological adaptations occurring upon unrepaired DNA damage. The insulin-like signalling pathway has been implicated in a DNA damage response (DDR) network that includes epidermal growth factor (EGF)-, AMP-activated protein kinases (AMPK)- and the target of rapamycin (TOR)-like signalling pathways, which are known regulators of growth, metabolism, and stress responses. The same pathways, together with the autophagy-mediated proteostatic response and the decline in energy metabolism have also been found to be similarly regulated during natural aging, suggesting striking parallels in the physiological adaptation upon persistent DNA damage due to DNA repair defects and long-term low-level DNA damage accumulation occurring during natural aging. These insights will be an important starting point to study the interplay between signalling networks involved in progeroid syndromes that are caused by DNA repair deficiencies and to gain new understanding of the consequences of DNA damage in the aging process.
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37
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Hsu YL, Hung JY, Lee YL, Chen FW, Chang KF, Chang WA, Tsai YM, Chong IW, Kuo PL. Identification of novel gene expression signature in lung adenocarcinoma by using next-generation sequencing data and bioinformatics analysis. Oncotarget 2017; 8:104831-104854. [PMID: 29285217 PMCID: PMC5739604 DOI: 10.18632/oncotarget.21022] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/28/2017] [Indexed: 12/22/2022] Open
Abstract
Lung adenocarcinoma is one of the leading causes of cancer-related death worldwide. We showed transcriptomic profiles in three pairs of tumors and adjacent non-tumor lung tissues using next-generation sequencing (NGS) to screen protein-coding RNAs and microRNAs. Combined with meta-analysis from the Oncomine and Gene Expression Omnibus (GEO) databases, we identified a representative genetic expression signature in lung adenocarcinoma. There were 9 upregulated genes, and 8 downregulated genes in lung adenocarcinoma. The analysis of the effects from each gene expression on survival outcome indicated that 6 genes (AGR2, SPDEF, CDKN2A, CLDN3, SFN, and PHLDA2) play oncogenic roles, and 7 genes (PDK4, FMO2, CPED1, GNG11, IL33, BTNL9, and FABP4) act as tumor suppressors in lung adenocarcinoma. In addition, we also identified putative genetic interactions, in which there were 5 upregulated microRNAs with specific targets - hsa-miR-183-5p-BTNL9, hsa-miR-33b-5p-CPED1, hsa-miR-429-CPED1, hsa-miR-182-5p-FMO2, and hsa-miR-130b-5p-IL33. These 5 microRNAs have been shown to be associated with tumorigenesis in lung cancer. Our findings suggest that these genetic interactions play important roles in the progression of lung adenocarcinoma. We propose that this molecular change of genetic expression may represent a novel signature in lung adenocarcinoma, which may be developed for diagnostic and therapeutic strategies in the future.
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Affiliation(s)
- Ya-Ling Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jen-Yu Hung
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yen-Lung Lee
- Division of Thoracic surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Feng-Wei Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | | | - Wei-An Chang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ying-Ming Tsai
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Inn-Wen Chong
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan
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Marwarha G, Rostad S, Lilek J, Kleinjan M, Schommer J, Ghribi O. Palmitate Increases β-site AβPP-Cleavage Enzyme 1 Activity and Amyloid-β Genesis by Evoking Endoplasmic Reticulum Stress and Subsequent C/EBP Homologous Protein Activation. J Alzheimers Dis 2017; 57:907-925. [PMID: 28304295 PMCID: PMC5389045 DOI: 10.3233/jad-161130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Epidemiological studies implicate diets rich in saturated free fatty acids (sFFA) as a potential risk factor for developing Alzheimer's disease (AD). In particular, high plasma levels of the sFFA palmitic acid (palmitate) were shown to inversely correlate with cognitive function. However, the cellular mechanisms by which sFFA may increase the risk for AD are not well known. Endoplasmic reticulum (ER) stress has emerged as one of the signaling pathways initiating and fostering the neurodegenerative changes in AD by increasing the aspartyl protease β-site AβPP cleaving enzyme 1 (BACE1) and amyloid-β (Aβ) genesis. In this study, we determined the extent to which palmitate increases BACE1 and Aβ levels in vitro and in vivo as well as the potential role of ER stress as cellular mechanism underlying palmitate effects. We demonstrate, in palmitate-treated SH-SY5Y neuroblastoma cells and in the hippocampi of palmitate-enriched diet-fed mice, that palmitate evokes the activation of the C/EBP Homologous Protein (CHOP), a transcription factor that is specifically responsive to ER stress. Induction of CHOP expression is associated with increased BACE1 mRNA, protein and activity levels, and subsequent enhanced amyloidogenic processing of amyloid-β protein precursor (AβPP) that culminates in a substantial increase in Aβ genesis. We further show that CHOP is an indispensable molecular mediator of palmitate-induced upregulation in BACE1 activity and Aβ genesis. Indeed, we show that Chop-/- mice and CHOP knocked-down SH-SY5Y neuroblastoma cells do not exhibit the same commensurate degree of palmitate-induced increase in BACE1 expression levels and Aβ genesis.
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Affiliation(s)
| | | | | | | | | | - Othman Ghribi
- Correspondence to: Dr. Othman Ghribi, Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, North Dakota 58202, USA. Tel.: +1 701 777 2522; Fax: +1 701 777 4490; E-mail:
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Kim C, Kang D, Lee EK, Lee JS. Long Noncoding RNAs and RNA-Binding Proteins in Oxidative Stress, Cellular Senescence, and Age-Related Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2062384. [PMID: 28811863 PMCID: PMC5547732 DOI: 10.1155/2017/2062384] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/27/2017] [Accepted: 06/06/2017] [Indexed: 12/12/2022]
Abstract
Cellular senescence is a complex biological process that leads to irreversible cell-cycle arrest. Various extrinsic and intrinsic insults are associated with the onset of cellular senescence and frequently accompany genomic or epigenomic alterations. Cellular senescence is believed to contribute to tumor suppression, immune response, and tissue repair as well as aging and age-related diseases. Long noncoding RNAs (lncRNAs) are >200 nucleotides long, poorly conserved, and transcribed in a manner similar to that of mRNAs. They are tightly regulated during various cellular and physiological processes. Although many lncRNAs and their functional roles are still undescribed, the importance of lncRNAs in a variety of biological processes is widely recognized. RNA-binding proteins (RBPs) have a pivotal role in posttranscriptional regulation as well as in mRNA transport, storage, turnover, and translation. RBPs interact with mRNAs, other RBPs, and noncoding RNAs (ncRNAs) including lncRNAs, and they are involved in the regulation of a broad spectrum of cellular processes. Like other cell fate regulators, lncRNAs and RBPs, separately or cooperatively, are implicated in initiation and maintenance of cellular senescence, aging, and age-related diseases. Here, we review the current understanding of both lncRNAs and RBPs and their association with oxidative stress, senescence, and age-related diseases.
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Affiliation(s)
- Chongtae Kim
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, Republic of Korea
| | - Donghee Kang
- Department of Molecular Medicine and Hypoxia-Related Disease Research Center, Inha University College of Medicine, Incheon 22212, Republic of Korea
| | - Eun Kyung Lee
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, Republic of Korea
| | - Jae-Seon Lee
- Department of Molecular Medicine and Hypoxia-Related Disease Research Center, Inha University College of Medicine, Incheon 22212, Republic of Korea
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40
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Paiva I, Pinho R, Pavlou MA, Hennion M, Wales P, Schütz AL, Rajput A, Szegő ÉM, Kerimoglu C, Gerhardt E, Rego AC, Fischer A, Bonn S, Outeiro TF. Sodium butyrate rescues dopaminergic cells from alpha-synuclein-induced transcriptional deregulation and DNA damage. Hum Mol Genet 2017; 26:2231-2246. [DOI: 10.1093/hmg/ddx114] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/19/2017] [Indexed: 02/07/2023] Open
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41
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Ganguly G, Chakrabarti S, Chatterjee U, Saso L. Proteinopathy, oxidative stress and mitochondrial dysfunction: cross talk in Alzheimer's disease and Parkinson's disease. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:797-810. [PMID: 28352155 PMCID: PMC5358994 DOI: 10.2147/dddt.s130514] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alzheimer’s disease and Parkinson’s disease are two common neurodegenerative diseases of the elderly people that have devastating effects in terms of morbidity and mortality. The predominant form of the disease in either case is sporadic with uncertain etiology. The clinical features of Parkinson’s disease are primarily motor deficits, while the patients of Alzheimer’s disease present with dementia and cognitive impairment. Though neuronal death is a common element in both the disorders, the postmortem histopathology of the brain is very characteristic in each case and different from each other. In terms of molecular pathogenesis, however, both the diseases have a significant commonality, and proteinopathy (abnormal accumulation of misfolded proteins), mitochondrial dysfunction and oxidative stress are the cardinal features in either case. These three damage mechanisms work in concert, reinforcing each other to drive the pathology in the aging brain for both the diseases; very interestingly, the nature of interactions among these three damage mechanisms is very similar in both the diseases, and this review attempts to highlight these aspects. In the case of Alzheimer’s disease, the peptide amyloid beta (Aβ) is responsible for the proteinopathy, while α-synuclein plays a similar role in Parkinson’s disease. The expression levels of these two proteins and their aggregation processes are modulated by reactive oxygen radicals and transition metal ions in a similar manner. In turn, these proteins – as oligomers or in aggregated forms – cause mitochondrial impairment by apparently following similar mechanisms. Understanding the common nature of these interactions may, therefore, help us to identify putative neuroprotective strategies that would be beneficial in both the clinical conditions.
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Affiliation(s)
- Gargi Ganguly
- Department of Pathology, Institute of Post Graduate Medical Education and Research, Kolkata
| | - Sasanka Chakrabarti
- Department of Biochemistry, ICARE Institute of Medical Sciences and Research, Haldia, West Bengal, India
| | - Uttara Chatterjee
- Department of Pathology, Institute of Post Graduate Medical Education and Research, Kolkata
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Rome, Italy
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42
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Chiarini A, Armato U, Liu D, Dal Prà I. Calcium-Sensing Receptors of Human Neural Cells Play Crucial Roles in Alzheimer's Disease. Front Physiol 2016; 7:134. [PMID: 27199760 PMCID: PMC4844916 DOI: 10.3389/fphys.2016.00134] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/28/2016] [Indexed: 12/21/2022] Open
Abstract
In aged subjects, late-onset Alzheimer's disease (LOAD) starts in the lateral entorhinal allocortex where a failure of clearance mechanisms triggers an accumulation of neurotoxic amyloid-β42 oligomers (Aβ42-os). In neurons and astrocytes, Aβ42-os enhance the transcription of Aβ precursor protein (APP) and β-secretase/BACE1 genes. Thus, by acting together with γ-secretase, the surpluses of APP and BACE1 amplify the endogenous production of Aβ42-os which pile up, damage mitochondria, and are oversecreted. At the plasmalemma, exogenous Aβ42-os bind neurons' and astrocytes' calcium-sensing receptors (CaSRs) activating a set of intracellular signaling pathways which upkeep Aβ42-os intracellular accumulation and oversecretion by hindering Aβ42-os proteolysis. In addition, Aβ42-os accumulating in the extracellular milieu spread and reach mounting numbers of adjacent and remoter teams of neurons and astrocytes which in turn are recruited, again via Aβ42-os•CaSR-governed mechanisms, to produce and release additional Aβ42-os amounts. This relentless self-sustaining mechanism drives AD progression toward upper cortical areas. Later on accumulating Aβ42-os elicit the advent of hyperphosphorylated (p)-Tau oligomers which acting together with Aβ42-os and other glial neurotoxins cooperatively destroy wider and wider cognition-related cortical areas. In parallel, Aβ42-os•CaSR signals also elicit an excess production and secretion of nitric oxide and vascular endothelial growth factor-A from astrocytes, of Aβ42-os and myelin basic protein from oligodendrocytes, and of proinflammatory cytokines, nitric oxide and (likely) Aβ42-os from microglia. Activated astrocytes and microglia survive the toxic onslaught, whereas neurons and oligodendrocytes increasingly die. However, we have shown that highly selective allosteric CaSR antagonists (calcilytics), like NPS 2143 and NPS 89626, efficiently suppress all the neurotoxic effects Aβ42-os•CaSR signaling drives in cultured cortical untransformed human neurons and astrocytes. In fact, calcilytics increase Aβ42 proteolysis and discontinue the oversecretion of Aβ42-os, nitric oxide, and vascular endothelial growth factor-A from both astrocytes and neurons. Seemingly, calcilytics would also benefit the other types of glial cells and cerebrovascular cells otherwise damaged by the effects of Aβ42-os•CaSR signaling. Thus, given at amnestic minor cognitive impairment (aMCI) or initial symptomatic stages, calcilytics could prevent or terminate the propagation of LOAD neuropathology and preserve human neurons' viability and hence patients' cognitive abilities.
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Affiliation(s)
- Anna Chiarini
- Human Histology and Embryology Unit, University of Verona Medical SchoolVerona, Italy
| | - Ubaldo Armato
- Human Histology and Embryology Unit, University of Verona Medical SchoolVerona, Italy
| | - Daisong Liu
- Human Histology and Embryology Unit, University of Verona Medical SchoolVerona, Italy
- Proteomics Laboratory, Institute for Burn Research, Third Military Medical UniversityChongqing, China
| | - Ilaria Dal Prà
- Human Histology and Embryology Unit, University of Verona Medical SchoolVerona, Italy
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Ordemann JM, Austin RN. Lead neurotoxicity: exploring the potential impact of lead substitution in zinc-finger proteins on mental health. Metallomics 2016; 8:579-88. [DOI: 10.1039/c5mt00300h] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This critical review focuses on one possible link between the cellular biology of lead and its neurotoxic effects: the link between Pb2+substitution for Zn2+in zinc-finger proteins and mental illness in adulthood.
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44
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Daneshmand P, Saliminejad K, Dehghan Shasaltaneh M, Kamali K, Riazi GH, Nazari R, Azimzadeh P, Khorram Khorshid HR. Neuroprotective Effects of Herbal Extract (Rosa canina, Tanacetum vulgare and Urtica dioica) on Rat Model of Sporadic Alzheimer's Disease. Avicenna J Med Biotechnol 2016; 8:120-5. [PMID: 27563424 PMCID: PMC4967545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Sporadic Alzheimer's Disease (SAD) is caused by genetic risk factors, aging and oxidative stresses. The herbal extract of Rosa canina (R. canina), Tanacetum vulgare (T. vulgare) and Urtica dioica (U. dioica) has a beneficial role in aging, as an anti-inflammatory and anti-oxidative agent. In this study, the neuroprotective effects of this herbal extract in the rat model of SAD was investigated. METHODS The rats were divided into control, sham, model, herbal extract -treated and ethanol-treated groups. Drug interventions were started on the 21(st) day after modeling and each treatment group was given the drugs by intraperitoneal (I.P.) route for 21 days. The expression levels of the five important genes for pathogenesis of SAD including Syp, Psen1, Mapk3, Map2 and Tnf-α were measured by qPCR between the hippocampi of SAD model which were treated by this herbal extract and control groups. The Morris Water Maze was adapted to test spatial learning and memory ability of the rats. RESULTS Treatment of the rat model of SAD with herbal extract induced a significant change in expression of Syp (p=0.001) and Psen1 (p=0.029). In Morris Water Maze, significant changes in spatial learning seen in the rat model group were improved in herbal-treated group. CONCLUSION This herbal extract could have anti-dementia properties and improve spatial learning and memory in SAD rat model.
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Affiliation(s)
- Parvaneh Daneshmand
- Genetic Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kioomars Saliminejad
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Marzieh Dehghan Shasaltaneh
- Laboratory of Neuro-organic Chemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Koorosh Kamali
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Gholam Hossein Riazi
- Laboratory of Neuro-organic Chemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Reza Nazari
- Laboratory of Neuro-organic Chemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Pedram Azimzadeh
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Khorram Khorshid
- Genetic Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran,Corresponding author: Hamid Reza Khorram Khorshid MD., Ph.D., Genetic Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran, Tel/Fax: +98 21 22180138, E-mail:
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45
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Ren RJ, Zhang YF, Dammer EB, Zhou Y, Wang LL, Liu XH, Feng BL, Jiang GX, Chen SD, Wang G, Cheng Q. Peripheral Blood MicroRNA Expression Profiles in Alzheimer’s Disease: Screening, Validation, Association with Clinical Phenotype and Implications for Molecular Mechanism. Mol Neurobiol 2015; 53:5772-81. [DOI: 10.1007/s12035-015-9484-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
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46
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Kim S, Yu NK, Kaang BK. CTCF as a multifunctional protein in genome regulation and gene expression. Exp Mol Med 2015; 47:e166. [PMID: 26045254 PMCID: PMC4491725 DOI: 10.1038/emm.2015.33] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/08/2015] [Accepted: 02/27/2015] [Indexed: 12/18/2022] Open
Abstract
CCCTC-binding factor (CTCF) is a highly conserved zinc finger protein and is best known as a transcription factor. It can function as a transcriptional activator, a repressor or an insulator protein, blocking the communication between enhancers and promoters. CTCF can also recruit other transcription factors while bound to chromatin domain boundaries. The three-dimensional organization of the eukaryotic genome dictates its function, and CTCF serves as one of the core architectural proteins that help establish this organization. The mapping of CTCF-binding sites in diverse species has revealed that the genome is covered with CTCF-binding sites. Here we briefly describe the diverse roles of CTCF that contribute to genome organization and gene expression.
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Affiliation(s)
- Somi Kim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Nam-Kyung Yu
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Korea
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