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Sahu MR, Ahmad MH, Mondal AC. MST1 selective inhibitor Xmu-mp-1 ameliorates neuropathological changes in a rat model of sporadic Alzheimer's Disease by modulating Hippo-Wnt signaling crosstalk. Apoptosis 2024; 29:1824-1851. [PMID: 38760516 DOI: 10.1007/s10495-024-01975-0] [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] [Accepted: 05/01/2024] [Indexed: 05/19/2024]
Abstract
Alzheimer's disease (AD), the most prevalent form of dementia, is characterized by progressive cognitive impairment accompanied by aberrant neuronal apoptosis. Reports suggest that the pro-apoptotic mammalian set20-like kinase 1/2 (MST1/2) instigates neuronal apoptosis via activating the Hippo signaling pathway under various stress conditions, including AD. However, whether inhibiting MST1/2 has any therapeutic benefits in AD remains unknown. Thus, we tested the therapeutic effects of intervening MST1/2 activation via the pharmacological inhibitor Xmu-mp-1 in a sporadic AD rat model. Sporadic AD was established in adult rats by intracerebroventricular streptozotocin (ICV-STZ) injection (3 mg/kg body weight). Xmu-mp-1 (0.5 mg/kg/body weight) was administered once every 48 h for two weeks, and Donepezil (5 mg/kg body weight) was used as a reference standard drug. The therapeutic effects of Xmu-mp-1 on ICV-STZ rats were determined through various behavioral, biochemical, histopathological, and molecular tests. At the behavioral level, Xmu-mp-1 improved cognitive deficits in sporadic AD rats. Further, Xmu-mp-1 treatment reduced STZ-associated tau phosphorylation, amyloid-beta deposition, oxidative stress, neurotoxicity, neuroinflammation, synaptic dysfunction, neuronal apoptosis, and neurodegeneration. Mechanistically, Xmu-mp-1 exerted these neuroprotective actions by inactivating the Hippo signaling while potentiating the Wnt/β-Catenin signaling in the AD rats. Together, the results of the present study provide compelling support that Xmu-mp-1 negated the neuronal dysregulation in the rat model of sporadic AD. Therefore, inhibiting MST/Hippo signaling and modulating its crosstalk with the Wnt/β-Catenin pathway can be a promising alternative treatment strategy against AD pathology. This is the first study providing novel mechanistic insights into the therapeutic use of Xmu-mp-1 in sporadic AD.
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Affiliation(s)
- Manas Ranjan Sahu
- Laboratory of Cellular and Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mir Hilal Ahmad
- Laboratory of Cellular and Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Amal Chandra Mondal
- Laboratory of Cellular and Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Schuller A, Oakes J, LaRocca T, Matz J, Eden M, Bellini C, Montrose L. Robust differential gene expression patterns in the prefrontal cortex of male mice exposed to an occupationally relevant dose of laboratory-generated wildfire smoke. Toxicol Sci 2024; 201:300-310. [PMID: 39107885 PMCID: PMC11424885 DOI: 10.1093/toxsci/kfae097] [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] [Indexed: 09/27/2024] Open
Abstract
Wildfires have become common global phenomena concurrent with warmer and drier climates and are now major contributors to ambient air pollution worldwide. Exposure to wildfire smoke has been classically associated with adverse cardiopulmonary health outcomes, especially in vulnerable populations. Recent work has expanded our understanding of wildfire smoke toxicology to include effects on the central nervous system and reproductive function; however, the neurotoxic profile of this toxicant remains ill-explored in an occupational context. Here, we sought to address this by using RNA sequencing to examine transcriptomic signatures in the prefrontal cortex of male mice modeling career wildland firefighter smoke exposure. We report robust changes in gene expression profiles between smoke-exposed samples and filtered air controls, evidenced by 2,862 differentially expressed genes (51.2% increased). We further characterized the functional relevance of these genes highlighting enriched pathways related to synaptic transmission, neuroplasticity, blood-brain barrier integrity, and neurotransmitter metabolism. Additionally, we identified possible contributors to these alterations through protein-protein interaction network mapping, which revealed a central node at ß-catenin and secondary hubs centered around mitochondrial oxidases, the Wnt signaling pathway, and gene expression machinery. The data reported here will serve as the foundation for future experiments aiming to characterize the phenotypic effects and mechanistic underpinnings of occupational wildfire smoke neurotoxicology.
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Affiliation(s)
- Adam Schuller
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Jessica Oakes
- Department of Bioengineering, Northeastern University, Boston, MA 02120, United States
| | - Tom LaRocca
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Jacqueline Matz
- Department of Bioengineering, Northeastern University, Boston, MA 02120, United States
| | - Matthew Eden
- Department of Bioengineering, Northeastern University, Boston, MA 02120, United States
| | - Chiara Bellini
- Department of Bioengineering, Northeastern University, Boston, MA 02120, United States
| | - Luke Montrose
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States
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Pan J, Yao Q, Wang Y, Chang S, Li C, Wu Y, Shen J, Yang R. The role of PI3K signaling pathway in Alzheimer's disease. Front Aging Neurosci 2024; 16:1459025. [PMID: 39399315 PMCID: PMC11466886 DOI: 10.3389/fnagi.2024.1459025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/10/2024] [Indexed: 10/15/2024] Open
Abstract
Alzheimer's disease (AD) is a debilitating progressively neurodegenerative disease. The best-characterized hallmark of AD, which is marked by behavioral alterations and cognitive deficits, is the aggregation of deposition of amyloid-beta (Aβ) and hyper-phosphorylated microtubule-associated protein Tau. Despite decades of experimental progress, the control rate of AD remains poor, and more precise deciphering is needed for potential therapeutic targets and signaling pathways involved. In recent years, phosphoinositide 3-kinase (PI3K) and Akt have been recognized for their role in the neuroprotective effect of various agents, and glycogen synthase kinase 3 (GSK3), a downstream enzyme, is also crucial in the tau phosphorylation and Aβ deposition. An overview of the function of PI3K/Akt pathway in the pathophysiology of AD is provided in this review, along with a discussion of recent developments in the pharmaceuticals and herbal remedies that target the PI3K/Akt signaling pathway. In conclusion, despite the challenges and hurdles, cumulative findings of novel targets and agents in the PI3K/Akt signaling axis are expected to hold promise for advancing AD prevention and treatment.
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Affiliation(s)
- Jingying Pan
- Department of Histology and Embryology, Medical School of Nantong University, Nantong, China
| | - Qi Yao
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Yankai Wang
- Department of Histology and Embryology, Medical School of Nantong University, Nantong, China
| | - Suyan Chang
- Department of Histology and Embryology, Medical School of Nantong University, Nantong, China
| | - Chenlong Li
- Department of Histology and Embryology, Medical School of Nantong University, Nantong, China
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Yongjiang Wu
- Department of Histology and Embryology, Medical School of Nantong University, Nantong, China
| | - Jianhong Shen
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Riyun Yang
- Department of Histology and Embryology, Medical School of Nantong University, Nantong, China
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4
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Sanajou S, Yirün A, Demirel G, Erkekoğlu P, Şahin G, Baydar T. The ameliorative potential of metformin against aluminum-induced neurotoxicity: Insights from in vitro studies. J Appl Toxicol 2024. [PMID: 39275926 DOI: 10.1002/jat.4695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/16/2024]
Abstract
Alzheimer's disease (AD) is increasingly recognized as a metabolic disorder, often referred to as type 3 diabetes, due to its strong association with insulin resistance. Chronic exposure to aluminum, a known neurotoxin, has been identified as a significant risk factor in the development and progression of AD. This study explores the potential of metformin, a common anti-diabetic drug, to mitigate aluminum-induced neurotoxicity in an in vitro model of AD. Our findings reveal that metformin significantly reduces oxidative stress markers such as malonaldehyde, carbonyl groups, and reactive oxygen species while enhancing antioxidant defenses. Metformin modulates critical signaling pathways, including glycogen synthase kinase 3 beta (GSK3-β)/RAC-alpha serine/threonine protein kinase (RAC-alpha serine/threonine protein kinase (Akt1)/protein phosphatase 2A (PP2A) and Wnt/β-catenin, decreasing Tau protein levels and promoting neurogenesis. These results suggest that metformin may offer a novel therapeutic approach for AD, particularly in cases where aluminum exposure is a contributing factor.
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Affiliation(s)
- Sonia Sanajou
- Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Hacettepe University, Ankara, Turkey
- Faculty of Pharmacy, Department of Toxicology, Istanbul Aydin University, Istanbul, Turkey
| | - Anil Yirün
- Faculty of Pharmacy, Department of Toxicology, Cukurova University, Adana, Turkey
| | - Göksun Demirel
- Faculty of Pharmacy, Department of Toxicology, Cukurova University, Adana, Turkey
| | - Pinar Erkekoğlu
- Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Hacettepe University, Ankara, Turkey
| | - Gönül Şahin
- Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Hacettepe University, Ankara, Turkey
| | - Terken Baydar
- Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Hacettepe University, Ankara, Turkey
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Sato K, Takayama KI, Saito Y, Inoue S. ERRα and ERRγ coordinate expression of genes associated with Alzheimer's disease, inhibiting DKK1 to suppress tau phosphorylation. Proc Natl Acad Sci U S A 2024; 121:e2406854121. [PMID: 39231208 PMCID: PMC11406303 DOI: 10.1073/pnas.2406854121] [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: 04/04/2024] [Accepted: 08/01/2024] [Indexed: 09/06/2024] Open
Abstract
Alzheimer's disease (AD) is a prevalent neurodegenerative disease characterized by cognitive decline and learning/memory impairment associated with neuronal cell loss. Estrogen-related receptor α (ERRα) and ERRγ, which are highly expressed in the brain, have emerged as potential AD regulators, with unelucidated underlying mechanisms. Here, we identified genome-wide binding sites for ERRα and ERRγ in human neuronal cells. They commonly target a subset of genes associated with neurodegenerative diseases, including AD. Notably, Dickkopf-1 (DKK1), a Wnt signaling pathway antagonist, was transcriptionally repressed by both ERRα and ERRγ in human neuronal cells and brain. ERRα and ERRγ repress RNA polymerase II (RNAP II) accessibility at the DKK1 promoter by modulating a specific active histone modification, histone H3 lysine acetylation (H3K9ac), with the potential contribution of their corepressor. This transcriptional repression maintains Wnt signaling activity, preventing tau phosphorylation and promoting a healthy neuronal state in the context of AD.
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Affiliation(s)
- Kaoru Sato
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
- Integrated Research Initiative for Living Well with Dementia, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
| | - Yuko Saito
- Department of Neuropathology (Brain Bank for Aging Research), Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
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Hussein Z, Michel HE, El-Naga RN, El-Demerdash E, Mantawy EM. Coenzyme Q10 ameliorates cyclophosphamide-induced chemobrain by repressing neuronal apoptosis and preserving hippocampal neurogenesis: Mechanistic roles of Wnt/ β-catenin signaling pathway. Neurotoxicology 2024; 105:21-33. [PMID: 39209270 DOI: 10.1016/j.neuro.2024.08.003] [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: 05/24/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Deterioration in the neurocognitive function of cancer patients referred to as "Chemobrain" is a devastating obstacle associated with cyclophosphamide (CYP). CYP is an alkylating agent, clinically utilized as an efficient anticancer and immunosuppressant. Coenzyme Q10 (CoQ10) is a worthwhile micronutrient with diverse biological activities embracing antioxidant, anti-apoptotic, and neuroprotective effects. The current experiment was designed for investigating the neuroprotective capability of CoQ10 versus CYP-elicited chemobrain in rats besides elucidating the causal molecular mechanisms. Male Sprague Dawley rats received CoQ10 (10 mg/kg, orally, once daily, for 10 days) and/or a single dose of CYP (200 mg/kg i.p. on day 7). CoQ10 counteracted CYP-induced cognitive and motor dysfunction as demonstrated by the findings of neurobehavioral tests (passive avoidance, Y maze, locomotion, and rotarod tests). Histopathological analysis further affirmed the neuroprotective abilities of CoQ10. CoQ10 effectually diminished CYP-provoked oxidative injury by restoring the antioxidant activity of catalase (CAT) enzyme while reducing malondialdehyde (MDA) levels. Besides, CoQ10 efficiently repressed CYP-induced neuronal apoptosis by downregulating the expression of Bax and caspase-3 while upregulating the Bcl-2 expression. Moreover, CoQ10 hampered CYP-provoked upregulation in acetylcholinesterase (AChE) activity. Furthermore, CoQ10 considerably augmented hippocampal neurogenesis by elevating the expressions of brain-derived neurotrophic factor (BDNF) and Ki-67. These promising neuroprotective effects can be credited to upregulating Wnt/β-catenin pathway as evidenced by the elevated expressions of Wnt-3a, β-catenin, and Phoshpo-glycogen synthase kinase-3 β (p-GSK-3β). Collectively, these findings proved the neuroprotective capabilities of CoQ10 against CYP-induced chemobrain through combating oxidative injury, repressing intrinsic apoptosis, boosting neurogenesis, and eventually upregulating the Wnt/β-catenin pathway.
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Affiliation(s)
- Zeina Hussein
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Haidy E Michel
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
| | - Reem N El-Naga
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Ebtehal El-Demerdash
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt; Preclinical and Translational Research Center, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Eman M Mantawy
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt; Preclinical and Translational Research Center, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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Melas K, Talevi V, Imtiaz MA, Etteldorf R, Estrada S, Krüger DM, Pena-Centeno T, Aziz NA, Fischer A, Breteler MMB. Blood-derived microRNAs are related to cognitive domains in the general population. Alzheimers Dement 2024. [PMID: 39210637 DOI: 10.1002/alz.14197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/02/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Blood-derived microRNAs (miRNAs) are potential candidates for detecting and preventing subclinical cognitive dysfunction. However, replication of previous findings and identification of novel miRNAs associated with cognitive domains, including their relation to brain structure and the pathways they regulate, are still lacking. METHODS We examined blood-derived miRNAs and miRNA co-expression clusters in relation to cognitive domains, structural magnetic resonance imaging measures, target gene expression, and genetic variants in 2869 participants of a population-based cohort. RESULTS Five previously identified and 14 novel miRNAs were associated with cognitive domains. Eleven of these were also associated with cortical thickness and two with hippocampal volume. Multi-omics analysis showed that certain identified miRNAs were genetically influenced and regulated genes in pathways like neurogenesis and synapse assembly. DISCUSSION We identified miRNAs associated with cognitive domains, brain regions, and neuronal processes affected by aging and neurodegeneration, making them promising candidate blood-based biomarkers or therapeutic targets of subclinical cognitive dysfunction. HIGHLIGHTS We investigated the association of blood-derived microRNAs with cognitive domains. Five previously identified and 14 novel microRNAs were associated with cognition. Eleven cognition-related microRNAs were also associated with cortical thickness. Identified microRNAs were linked to genes associated with neuronal functions. Results provide putative biomarkers or therapeutic targets of cognitive aging.
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Affiliation(s)
- Konstantinos Melas
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Valentina Talevi
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Mohammed Aslam Imtiaz
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Rika Etteldorf
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Santiago Estrada
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- AI in Medical Imaging, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dennis M Krüger
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Tonatiuh Pena-Centeno
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Bioinformatics Unit, German Centre for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - André Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department for Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence MBExC, University of Göttingen & University Medical Center Goettingen, Göttingen, Germany
| | - Monique M B Breteler
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
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Geigenmüller JN, Tari AR, Wisloff U, Walker TL. The relationship between adult hippocampal neurogenesis and cognitive impairment in Alzheimer's disease. Alzheimers Dement 2024. [PMID: 39166771 DOI: 10.1002/alz.14179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Neurogenesis persists throughout adulthood in the hippocampus and contributes to specific cognitive functions. In Alzheimer's disease (AD), the hippocampus is affected by pathology and functional impairment early in the disease. Human AD patients have reduced adult hippocampal neurogenesis (AHN) levels compared to age-matched healthy controls. Similarly, rodent AD models show a decrease in AHN before the onset of the classical hallmarks of AD pathology. Conversely, enhancement of AHN can protect against AD pathology and ameliorate memory deficits in both rodents and humans. Therefore, impaired AHN may be a contributing factor of AD-associated cognitive decline, rather than an effect of it. In this review we outline the regulation and function of AHN in healthy individuals, and highlight the relationship between AHN dysfunction and cognitive impairments in AD. The existence of AHN in humans and its relevance in AD patients will also be discussed, with an outlook toward future research directions. HIGHLIGHTS: Adult hippocampal neurogenesis occurs in the brains of mammals including humans. Adult hippocampal neurogenesis is reduced in Alzheimer's disease in humans and animal models.
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Affiliation(s)
| | - Atefe R Tari
- The Cardiac Exercise Research Group at Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Neurology and Clinical Neurophysiology, St. Olavs University Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ulrik Wisloff
- The Cardiac Exercise Research Group at Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Tara L Walker
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
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Li J, Capuano AW, Agarwal P, Arvanitakis Z, Wang Y, De Jager PL, Schneider JA, Tasaki S, de Paiva Lopes K, Hu FB, Bennett DA, Liang L, Grodstein F. The MIND diet, brain transcriptomic alterations, and dementia. Alzheimers Dement 2024. [PMID: 39129336 DOI: 10.1002/alz.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 05/01/2024] [Accepted: 05/20/2024] [Indexed: 08/13/2024]
Abstract
INTRODUCTION Dietary patterns are associated with dementia risk, but the underlying molecular mechanisms are largely unknown. METHODS We used RNA sequencing data from post mortem prefrontal cortex tissue and annual cognitive evaluations from 1204 participants in the Religious Orders Study and Memory and Aging Project. We identified a transcriptomic profile correlated with the MIND diet (Mediterranean-Dietary Approaches to Stop Hypertension Intervention for Neurodegenerative Delay) among 482 individuals who completed ante mortem food frequency questionnaires; and examined its associations with cognitive health in the remaining 722 participants. RESULTS We identified a transcriptomic profile, consisting of 50 genes, correlated with the MIND diet score (p = 0.001). Each standard deviation increase in the transcriptomic profile score was associated with a slower annual rate of decline in global cognition (β = 0.011, p = 0.003) and lower odds of dementia (odds ratio = 0.76, p = 0.0002). Expressions of several genes (including TCIM and IGSF5) appeared to mediate the association between MIND diet and dementia. DISCUSSION A brain transcriptomic profile for healthy diets revealed novel genes potentially associated with cognitive health. HIGHLIGHTS Why healthy dietary patterns are associated with lower dementia risk are unknown. We integrated dietary, brain transcriptomic, and cognitive data in older adults. Mediterranean-Dietary Approaches to Stop Hypertension Intervention for Neurodegenerative Delay (MIND) diet intake is correlated with a specific brain transcriptomic profile. This brain transcriptomic profile score is associated with better cognitive health. More data are needed to elucidate the causality and functionality of identified genes.
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Affiliation(s)
- Jun Li
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ana W Capuano
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Puja Agarwal
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Zoe Arvanitakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Francine Grodstein
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
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Zhang N, Westerhaus A, Wilson M, Wang E, Goff L, Sockanathan S. Physiological regulation of neuronal Wnt activity is essential for TDP-43 localization and function. EMBO J 2024; 43:3388-3413. [PMID: 38918634 PMCID: PMC11329687 DOI: 10.1038/s44318-024-00156-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Nuclear exclusion of the RNA- and DNA-binding protein TDP-43 can induce neurodegeneration in different diseases. Diverse processes have been implicated to influence TDP-43 mislocalization, including disrupted nucleocytoplasmic transport (NCT); however, the physiological pathways that normally ensure TDP-43 nuclear localization are unclear. The six-transmembrane enzyme glycerophosphodiester phosphodiesterase 2 (GDE2 or GDPD5) cleaves the glycosylphosphatidylinositol (GPI) anchor that tethers some proteins to the membrane. Here we show that GDE2 maintains TDP-43 nuclear localization by regulating the dynamics of canonical Wnt signaling. Ablation of GDE2 causes aberrantly sustained Wnt activation in adult neurons, which is sufficient to cause NCT deficits, nuclear pore abnormalities, and TDP-43 nuclear exclusion. Disruption of GDE2 coincides with TDP-43 abnormalities in postmortem tissue from patients with amyotrophic lateral sclerosis (ALS). Further, GDE2 deficits are evident in human neural cell models of ALS, which display erroneous Wnt activation that, when inhibited, increases mRNA levels of genes regulated by TDP-43. Our study identifies GDE2 as a critical physiological regulator of Wnt signaling in adult neurons and highlights Wnt pathway activation as an unappreciated mechanism contributing to nucleocytoplasmic transport and TDP-43 abnormalities in disease.
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Affiliation(s)
- Nan Zhang
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Anna Westerhaus
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Macey Wilson
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
- Department of Cellular Biology, University of Georgia, Biological Sciences 302, 120 Cedar St., Athens, GA, 30602, USA
| | - Ethan Wang
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Loyal Goff
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
- McKusick-Nathans Department of Genetic Medicine, Kavli Neurodiscovery Institute, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Shanthini Sockanathan
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA.
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Sharallah OA, Poddar NK, Alwadan OA. Delineation of the role of G6PD in Alzheimer's disease and potential enhancement through microfluidic and nanoparticle approaches. Ageing Res Rev 2024; 99:102394. [PMID: 38950868 DOI: 10.1016/j.arr.2024.102394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/16/2024] [Accepted: 06/21/2024] [Indexed: 07/03/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative pathologic entity characterized by the abnormal presence of tau and macromolecular Aβ deposition that leads to the degeneration or death of neurons. In addition to that, glucose-6-phosphate dehydrogenase (G6PD) has a multifaceted role in the process of AD development, where it can be used as both a marker and a target. G6PD activity is dysregulated due to its contribution to oxidative stress, neuroinflammation, and neuronal death. In this context, the current review presents a vivid depiction of recent findings on the relationship between AD progression and changes in the expression or activity of G6PD. The efficacy of the proposed G6PD-based therapeutics has been demonstrated in multiple studies using AD mouse models as representative animal model systems for cognitive decline and neurodegeneration associated with this disease. Innovative therapeutic insights are made for the boosting of G6PD activity via novel innovative nanotechnology and microfluidics tools in drug administration technology. Such approaches provide innovative methods of surpassing the blood-brain barrier, targeting step-by-step specific neural pathways, and overcoming biochemical disturbances that accompany AD. Using different nanoparticles loaded with G6DP to target specific organs, e.g., G6DP-loaded liposomes, enhances BBB penetration and brain distribution of G6DP. Many nanoparticles, which are used for different purposes, are briefly discussed in the paper. Such methods to mimic BBB on organs on-chip offer precise disease modeling and drug testing using microfluidic chips, requiring lower sample amounts and producing faster findings compared to conventional techniques. There are other contributions to microfluid in AD that are discussed briefly. However, there are some limitations accompanying microfluidics that need to be worked on to be used for AD. This study aims to bridge the gap in understanding AD with the synergistic use of promising technologies; microfluid and nanotechnology for future advancements.
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Affiliation(s)
- Omnya A Sharallah
- PharmD Program, Egypt-Japan University of Science and Technology (EJUST), New Borg El Arab, Alexandria 21934, Egypt
| | - Nitesh Kumar Poddar
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India.
| | - Omnia A Alwadan
- PharmD Program, Egypt-Japan University of Science and Technology (EJUST), New Borg El Arab, Alexandria 21934, Egypt
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12
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Wagner N, Tsai T, Reinehr S, Theile J, Dick HB, Joachim SC. Retinal debris triggers cytotoxic damage in cocultivated primary porcine RPE cells. Front Neurosci 2024; 18:1401571. [PMID: 39114482 PMCID: PMC11303199 DOI: 10.3389/fnins.2024.1401571] [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: 03/15/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction One of the most common causes of vision loss in the elderly population worldwide is age-related macular degeneration (AMD). Subsequently, the number of people affected by AMD is estimated to reach approximately 288 million by the year 2040. The aim of this study was to develop an ex vivo model that simulates various aspects of the complex AMD pathogenesis. Methods For this purpose, primary porcine retinal pigment epithelial cells (ppRPE) were isolated and cultured. One group was exposed to medium containing sodium iodate (NaIO3) to induce degeneration. The others were exposed to different supplemented media, such as bovine serum albumin (BSA), homogenized porcine retinas (HPR), or rod outer segments (ROOS) for eight days to promote retinal deposits. Then, these ppRPE cells were cocultured with porcine neuroretina explants for another eight days. To assess the viability of ppRPE cells, live/dead assay was performed at the end of the study. The positive RPE65 and ZO1 area was evaluated by immunocytochemistry and the expression of RLBP1, RPE65, and TJP1 was analyzed by RT-qPCR. Additionally, drusen (APOE), inflammation (ITGAM, IL6, IL8, NLRP3, TNF), oxidative stress (NFE2L2, SOD1, SOD2), and hypoxia (HIF1A) markers were investigated. The concentration of the inflammatory cytokines IL-6 and IL-8 was determined in medium supernatants from day 16 and 24 via ELISA. Results Live/dead assay suggests that especially exposure to NaIO3 and HPR induced damage to ppRPE cells, leading in a significant ppRPE cell loss. All supplemented media resulted in decreased RPE-characteristic markers (RPE65; ZO-1) and gene expression like RLBP1 and RPE65 in the cultured ppRPE cells. Besides, some inflammatory, oxidative as well as hypoxic stress markers were altered in ppRPE cells cultivated with NaIO3. The application of HPR induced an enhanced APOE expression. Pre-exposure of the ppRPE cells led to a diminished number of cones in all supplemented media groups compared to controls. Discussion Overall, this novel coculture model represents an interesting initial approach to incorporating deposits into coculture to mimic AMD pathogenesis. Nevertheless, the effects of the media used need to be investigated in further studies.
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Affiliation(s)
| | | | | | | | | | - Stephanie C. Joachim
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
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13
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Arregi A, Vegas O, Lertxundi A, Silva A, Ferreira I, Bereziartua A, Cruz MT, Lertxundi N. Road traffic noise exposure and its impact on health: evidence from animal and human studies-chronic stress, inflammation, and oxidative stress as key components of the complex downstream pathway underlying noise-induced non-auditory health effects. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:46820-46839. [PMID: 38977550 PMCID: PMC11297122 DOI: 10.1007/s11356-024-33973-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/08/2024] [Indexed: 07/10/2024]
Abstract
In heavily urbanized world saturated with environmental pollutants, road traffic noise stands out as a significant factor contributing to widespread public health issues. It contributes in the development of a diverse range of non-communicable diseases, such as cardiovascular diseases, metabolic dysregulation, cognitive impairment, and neurodegenerative disorders. Although the exact mechanisms behind these non-auditory health effects remain unclear, the noise reaction model centres on the stress response to noise. When exposed to noise, the body activates the hypothalamic-pituitary-adrenal axis and the sympathetic nervous system, leading to the secretion of stress hormones like catecholamines and cortisol. Prolonged exposure to noise-induced stress results in chronic inflammation and oxidative stress. This review underscores the role of inflammation and oxidative stress in the progression of noise-induced vascular dysfunction, disruption of the circadian rhythm, accelerated aging, neuroinflammation, and changes in microbiome. Additionally, our focus is on understanding the interconnected nature of these health outcomes: These interconnected factors create a cascade effect, contributing to the accumulation of multiple risk factors that ultimately lead to severe adverse health effects.
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Affiliation(s)
- Ane Arregi
- Faculty of Psychology, University of the Basque Country (UPV/EHU), 20008, San Sebastian, Spain
- Environmental Epidemiology and Child Development Group, Biogipuzkoa Health Research Institute, Paseo Doctor Begiristain S/N, 20014, San Sebastian, Spain
| | - Oscar Vegas
- Faculty of Psychology, University of the Basque Country (UPV/EHU), 20008, San Sebastian, Spain
- Environmental Epidemiology and Child Development Group, Biogipuzkoa Health Research Institute, Paseo Doctor Begiristain S/N, 20014, San Sebastian, Spain
| | - Aitana Lertxundi
- Environmental Epidemiology and Child Development Group, Biogipuzkoa Health Research Institute, Paseo Doctor Begiristain S/N, 20014, San Sebastian, Spain
- Spanish Consortium for Research On Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, C/Monforte de Lemos 3-5, 28029, Madrid, Spain
- Department of Preventive Medicine and Public Health, Faculty of Medicine, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Ana Silva
- Center for Neuroscience and Cell Biology and Institute for Biomedical Imaging and Life Sciences, University of Coimbra, 3000-548, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Isabel Ferreira
- Center for Neuroscience and Cell Biology and Institute for Biomedical Imaging and Life Sciences, University of Coimbra, 3000-548, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Ainhoa Bereziartua
- Environmental Epidemiology and Child Development Group, Biogipuzkoa Health Research Institute, Paseo Doctor Begiristain S/N, 20014, San Sebastian, Spain
| | - Maria Teresa Cruz
- Center for Neuroscience and Cell Biology and Institute for Biomedical Imaging and Life Sciences, University of Coimbra, 3000-548, Coimbra, Portugal.
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.
- Faculty of Pharmacy, University of Coimbra, 3000-548, Coimbra, Portugal.
| | - Nerea Lertxundi
- Faculty of Psychology, University of the Basque Country (UPV/EHU), 20008, San Sebastian, Spain
- Environmental Epidemiology and Child Development Group, Biogipuzkoa Health Research Institute, Paseo Doctor Begiristain S/N, 20014, San Sebastian, Spain
- Spanish Consortium for Research On Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, C/Monforte de Lemos 3-5, 28029, Madrid, Spain
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14
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Soelter TM, Howton TC, Clark AD, Oza VH, Lasseigne BN. Altered glia-neuron communication in Alzheimer's Disease affects WNT, p53, and NFkB Signaling determined by snRNA-seq. Cell Commun Signal 2024; 22:317. [PMID: 38849813 PMCID: PMC11157763 DOI: 10.1186/s12964-024-01686-8] [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: 12/06/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Alzheimer's disease is the most common cause of dementia and is characterized by amyloid-β plaques, tau neurofibrillary tangles, and neuronal loss. Although neuronal loss is a primary hallmark of Alzheimer's disease, it is known that non-neuronal cell populations are ultimately responsible for maintaining brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk. Many signaling pathways have been proposed to be dysregulated in Alzheimer's disease, including WNT, TGFβ, p53, mTOR, NFkB, and Pi3k/Akt signaling. Here, we predict altered cell-cell communication between glia and neurons. METHODS Using public snRNA-sequencing data generated from postmortem human prefrontal cortex, we predicted altered cell-cell communication between glia (astrocytes, microglia, oligodendrocytes, and oligodendrocyte progenitor cells) and neurons (excitatory and inhibitory). We confirmed interactions in a second and third independent orthogonal dataset. We determined cell-type-specificity using Jaccard Similarity Index and investigated the downstream effects of altered interactions in inhibitory neurons through gene expression and transcription factor activity analyses of signaling mediators. Finally, we determined changes in pathway activity in inhibitory neurons. RESULTS Cell-cell communication between glia and neurons is altered in Alzheimer's disease in a cell-type-specific manner. As expected, ligands are more cell-type-specific than receptors and targets. We identified ligand-receptor pairs in three independent datasets and found involvement of the Alzheimer's disease risk genes APP and APOE across datasets. Most of the signaling mediators of these interactions were not significantly differentially expressed, however, the mediators that are also transcription factors had differential activity between AD and control. Namely, MYC and TP53, which are associated with WNT and p53 signaling, respectively, had decreased TF activity in Alzheimer's disease, along with decreased WNT and p53 pathway activity in inhibitory neurons. Additionally, inhibitory neurons had both increased NFkB signaling pathway activity and increased TF activity of NFIL3, an NFkB signaling-associated transcription factor. CONCLUSIONS Cell-cell communication between glia and neurons in Alzheimer's disease is altered in a cell-type-specific manner involving Alzheimer's disease risk genes. Signaling mediators had altered transcription factor activity suggesting altered glia-neuron interactions may dysregulate signaling pathways including WNT, p53, and NFkB in inhibitory neurons.
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Affiliation(s)
- Tabea M Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Timothy C Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Amanda D Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Vishal H Oza
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Brittany N Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America.
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15
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Dutta A, Bhattacharya P, Chutia P, Borah A. Targeting of wnt signalling pathway by small bioactive molecules for the treatment of Alzheimer's disease. In Silico Pharmacol 2024; 12:50. [PMID: 38840665 PMCID: PMC11147993 DOI: 10.1007/s40203-024-00226-z] [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: 10/25/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
Alzheimer's disease (AD) is the most occurring neurodegenerative disorder that destroys learning, memory, and thinking skills. Although the pathophysiology of the disease is least understood, the post-mortem brain of AD patients as well as animal models revealed the part of down regulated Wnt signalling in progression of the disease. The deficit in the Wnt signalling leads to the accumulation of amyloid beta peptides, phosphorylation of tau proteins, and synaptic dysfunctions, which are regarded as the major pathological features of AD. As the available drugs for AD are only able to mitigate the symptoms and are also associated with several side effects, the therapeutic potential of the bioactive compounds is being explored for their efficacies in managing the major pathologies. Consequently, a few bioactive compounds fundamentally isolated from Garcinia species are established as promising neuroprotective agents in AD, however; their potential to regulate the Wnt signalling pathway is yet to be discovered. Considering the neuroprotective properties, in the present study efficiency of six small bioactive compounds viz., amentoflavone, isovitexin, orientin, apigenin, kaempferol, and garcinol have been investigated in modulating the receptor proteins (LRP6, DKK1, WIF1 and GSK3β) of the Wnt signalling pathway by molecular docking technique. While all the bioactive compounds could efficiently interact with the target proteins, amentoflavone, orientin, and isovitexin interact with all the target proteins viz., LRP6, DKK1, WIF1, and GSK3β with higher free energy of binding, more number of interactions, and similar mode of binding in comparison to their known or reported modulators. Thus, the present study set forth the investigated small bioactive molecules as potential drug candidates in AD therapeutics.
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Affiliation(s)
- Ankumoni Dutta
- Department of Life Science and Bioinformatics, Cellular and Molecular Neurobiology Laboratory, Assam University, Silchar, Assam 788011 India
- Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya (PDUAM), Behali, Biswanath, Assam 784184 India
| | - Pallab Bhattacharya
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355 India
| | - Pavitra Chutia
- Department of Life Sciences, Debraj Roy College, Golaghat, Assam 785621 India
| | - Anupom Borah
- Department of Life Science and Bioinformatics, Cellular and Molecular Neurobiology Laboratory, Assam University, Silchar, Assam 788011 India
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Lee CY, Riffle D, Xiong Y, Momtaz N, Lei Y, Pariser JM, Sikdar D, Hwang A, Duan Z, Zhang J. Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes. BMC Neurosci 2024; 25:24. [PMID: 38741048 PMCID: PMC11089696 DOI: 10.1186/s12868-024-00867-y] [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: 12/15/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The recent single-cell sequencing technology has revolutionized genetic and genomic resolution by enabling scientists to explore the diversity of gene expression patterns at the finest resolution. Most existing studies have solely focused on molecular perturbations within each cell, but cells live in microenvironments rather than in isolated entities. Here, we leveraged the large-scale and publicly available single-nucleus RNA sequencing in the human prefrontal cortex to investigate cell-to-cell communication in healthy brains and their perturbations in AD. We uniformly processed the snRNA-seq with strict QCs and labeled canonical cell types consistent with the definitions from the BRAIN Initiative Cell Census Network. From ligand and receptor gene expression, we built a high-confidence cell-to-cell communication network to investigate signaling differences between AD and healthy brains. RESULTS Specifically, we first performed broad communication pattern analyses to highlight that biologically related cell types in normal brains rely on largely overlapping signaling networks and that the AD brain exhibits the irregular inter-mixing of cell types and signaling pathways. Secondly, we performed a more focused cell-type-centric analysis and found that excitatory neurons in AD have significantly increased their communications to inhibitory neurons, while inhibitory neurons and other non-neuronal cells globally decreased theirs to all cells. Then, we delved deeper with a signaling-centric view, showing that canonical signaling pathways CSF, TGFβ, and CX3C are significantly dysregulated in their signaling to the cell type microglia/PVM and from endothelial to neuronal cells for the WNT pathway. Finally, after extracting 23 known AD risk genes, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. CONCLUSIONS In summary, with the novel advances in single-cell sequencing technologies, we show that cellular signaling is regulated in a cell-type-specific manner and that improper regulation of extracellular signaling genes is linked to intracellular risk genes, giving the mechanistic intra- and inter-cellular picture of AD.
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Affiliation(s)
- Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Dylan Riffle
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Yifeng Xiong
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Nadia Momtaz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yutong Lei
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Joseph M Pariser
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Diptanshu Sikdar
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, USA.
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Soelter TM, Howton TC, Clark AD, Oza VH, Lasseigne BN. Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.29.569304. [PMID: 38076822 PMCID: PMC10705421 DOI: 10.1101/2023.11.29.569304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Background Alzheimer's disease is the most common cause of dementia and is characterized by amyloid-β plaques, tau neurofibrillary tangles, and neuronal loss. Although neuronal loss is a primary hallmark of Alzheimer's disease, it is known that non-neuronal cell populations are ultimately responsible for maintaining brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk. Many signaling pathways have been proposed to be dysregulated in Alzheimer's disease, including WNT, TGFβ, p53, mTOR, NFkB, and Pi3k/Akt signaling. Here, we predict altered cell-cell communication between glia and neurons. Methods Using public snRNA-sequencing data generated from postmortem human prefrontal cortex, we predicted altered cell-cell communication between glia (astrocytes, microglia, oligodendrocytes, and oligodendrocyte progenitor cells) and neurons (excitatory and inhibitory). We confirmed interactions in a second and third independent orthogonal dataset. We determined cell-type-specificity using Jaccard Similarity Index and investigated the downstream effects of altered interactions in inhibitory neurons through gene expression and transcription factor activity analyses of signaling mediators. Finally, we determined changes in pathway activity in inhibitory neurons. Results Cell-cell communication between glia and neurons is altered in Alzheimer's disease in a cell-type-specific manner. As expected, ligands are more cell-type-specific than receptors and targets. We identified ligand-receptor pairs in three independent datasets and found involvement of the Alzheimer's disease risk genes APP and APOE across datasets. Most of the signaling mediators of these interactions were not differentially expressed, however, the mediators that are also transcription factors had differential activity between AD and control. Namely, MYC and TP53, which are associated with WNT and p53 signaling, respectively, had decreased TF activity in Alzheimer's disease, along with decreased WNT and p53 pathway activity in inhibitory neurons. Additionally, inhibitory neurons had both increased NFkB signaling pathway activity and increased TF activity of NFIL3, an NFkB signaling-associated transcription factor. Conclusions Cell-cell communication between glia and neurons in Alzheimer's disease is altered in a cell-type-specific manner involving Alzheimer's disease risk genes. Signaling mediators had altered transcription factor activity suggesting altered glia-neuron interactions may dysregulate signaling pathways including WNT, p53, and NFkB in inhibitory neurons.
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Affiliation(s)
- Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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Lou S, Gong D, Yang M, Qiu Q, Luo J, Chen T. Curcumin Improves Neurogenesis in Alzheimer's Disease Mice via the Upregulation of Wnt/β-Catenin and BDNF. Int J Mol Sci 2024; 25:5123. [PMID: 38791161 PMCID: PMC11120842 DOI: 10.3390/ijms25105123] [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: 04/03/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Adult neurogenesis in the dentate gyrus (DG) is impaired during Alzheimer's disease (AD) progression. Curcumin has been reported to reduce cell apoptosis and stimulate neurogenesis. This study aimed to investigate the influence of curcumin on adult neurogenesis in AD mice and its potential mechanism. Two-month-old male C57BL/6J mice were injected with soluble β-amyloid (Aβ1-42) using lateral ventricle stereolocalization to establish AD models. An immunofluorescence assay, including bromodeoxyuridine (BrdU), doublecortin (DCX), and neuron-specific nuclear antigen (NeuN), was used to detect hippocampal neurogenesis. Western blot and an enzyme-linked immunosorbent assay (ELISA) were used to test the expression of related proteins and the secretion of brain-derived neurotrophic factor (BDNF). A Morris water maze was used to detect the cognitive function of the mice. Our results showed that curcumin administration (100 mg/kg) rescued the impaired neurogenesis of Aβ1-42 mice, shown as enhanced BrdU+/DCX+ and BrdU+/NeuN+ cells in DG. In addition, curcumin regulated the phosphatidylinositol 3 kinase (PI3K)/protein kinase B (Akt) -mediated glycogen synthase kinase-3β (GSK3β) /Wingless/Integrated (Wnt)/β-catenin pathway and cyclic adenosine monophosphate response element-binding protein (CREB)/BDNF in Aβ1-42 mice. Inhibiting Wnt/β-catenin and depriving BDNF could reverse both the upregulated neurogenesis and cognitive function of curcumin-treated Aβ1-42 mice. In conclusion, our study indicates that curcumin, through targeting PI3K/Akt, regulates GSK3β/Wnt/β-catenin and CREB/BDNF pathways, improving the adult neurogenesis of AD mice.
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Affiliation(s)
| | | | | | | | - Jialie Luo
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong 226001, China; (S.L.); (D.G.); (M.Y.); (Q.Q.)
| | - Tingting Chen
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong 226001, China; (S.L.); (D.G.); (M.Y.); (Q.Q.)
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Liu J, Wei AH, Liu TT, Ji XH, Zhang Y, Yan F, Chen MX, Hu JB, Zhou SY, Shi JS, Jin H, Jin F. Icariin ameliorates glycolytic dysfunction in Alzheimer's disease models by activating the Wnt/β-catenin signaling pathway. FEBS J 2024; 291:2221-2241. [PMID: 38400523 DOI: 10.1111/febs.17099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/21/2023] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
It was reported that the Wnt/β-catenin pathway is involved in the regulation of aerobic glycolysis and that brain glycolytic dysfunction results in the development of Alzheimer's disease (AD). Icariin (ICA), an active component extracted from Epimedii Folium, has been reported to produce neuroprotective effects in multiple models of AD, but its underlying mechanism remains to be fully described. We aimed to investigate the protective effects of ICA on animal and cell models of AD and confirm whether the Wnt/β-catenin pathway has functions in the neuroprotective function of ICA. The 3 × Tg-AD mice were treated with ICA. HT22 cells, the Aβ25-35 peptide and Dickkopf-1 (DKK1) agent (a specific inhibitor of the Wnt/β-catenin pathway) were used to further explore the underlying mechanism of ICA that produces anti-AD effects. Behavioral examination, western blotting assay, staining analysis, biochemical test, and lactate dehydrogenase (LDH) assays were applied. We first demonstrated that ICA significantly improved cognitive function and autonomous behavior, reduced neuronal damage, and reversed the protein levels and activities of glycolytic key enzymes, and expression of protein molecules of the canonical Wnt signaling pathway, in 3 × Tg-AD mice back to wild-type levels. Next, we further found that ICA increased cell viability and effectively improved the dysfunctional glycolysis in HT22 cells injured by Aβ25-35. However, when canonical Wnt signaling was inhibited by DKK1, the above effects of ICA on glycolysis were abolished. In summary, ICA exerts neuroprotective effects in 3 × Tg-AD animals and AD cellular models by enhancing the function of glycolysis through activation of the Wnt/β-catenin pathway.
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Affiliation(s)
- Ju Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
- Department of Hospital Infection Management, People's Hospital of WeiNing County, Bijie, China
| | - Ai-Hong Wei
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
| | - Ting-Ting Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
| | - Xin-Hao Ji
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
| | - Ying Zhang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
| | - Fei Yan
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
| | - Mei-Xiang Chen
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
| | - Jin-Bo Hu
- Department of Clinical Medicine, Zunyi Medical University, China
| | - Shao-Yu Zhou
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
| | - Jing-Shan Shi
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
| | - Hai Jin
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, China
| | - Feng Jin
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, China
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Chan BWGL, Lynch NB, Tran W, Joyce JM, Savage GP, Meutermans W, Montgomery AP, Kassiou M. Fragment-based drug discovery for disorders of the central nervous system: designing better drugs piece by piece. Front Chem 2024; 12:1379518. [PMID: 38698940 PMCID: PMC11063241 DOI: 10.3389/fchem.2024.1379518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/12/2024] [Indexed: 05/05/2024] Open
Abstract
Fragment-based drug discovery (FBDD) has emerged as a powerful strategy to confront the challenges faced by conventional drug development approaches, particularly in the context of central nervous system (CNS) disorders. FBDD involves the screening of libraries that comprise thousands of small molecular fragments, each no greater than 300 Da in size. Unlike the generally larger molecules from high-throughput screening that limit customisation, fragments offer a more strategic starting point. These fragments are inherently compact, providing a strong foundation with good binding affinity for the development of drug candidates. The minimal elaboration required to transition the hit into a drug-like molecule is not only accelerated, but also it allows for precise modifications to enhance both their activity and pharmacokinetic properties. This shift towards a fragment-centric approach has seen commercial success and holds considerable promise in the continued streamlining of the drug discovery and development process. In this review, we highlight how FBDD can be integrated into the CNS drug discovery process to enhance the exploration of a target. Furthermore, we provide recent examples where FBDD has been an integral component in CNS drug discovery programs, enabling the improvement of pharmacokinetic properties that have previously proven challenging. The FBDD optimisation process provides a systematic approach to explore this vast chemical space, facilitating the discovery and design of compounds piece by piece that are capable of modulating crucial CNS targets.
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Affiliation(s)
| | - Nicholas B. Lynch
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Wendy Tran
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Jack M. Joyce
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Michael Kassiou
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
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21
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Li H, Khang TF. SIEVE: One-stop differential expression, variability, and skewness analyses using RNA-Seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588804. [PMID: 38645120 PMCID: PMC11030344 DOI: 10.1101/2024.04.09.588804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Motivation RNA-Seq data analysis is commonly biased towards detecting differentially expressed genes and insufficiently conveys the complexity of gene expression changes between biological conditions. This bias arises because discrete models of RNA-Seq count data cannot fully characterize the mean, variance, and skewness of gene expression distribution using independent model parameters. A unified framework that simultaneously tests for differential expression, variability, and skewness is needed to realize the full potential of RNA-Seq data analysis in a systems biology context. Results We present SIEVE, a statistical methodology that provides the desired unified framework. SIEVE embraces a compositional data analysis framework that transforms discrete RNA-Seq counts to a continuous form with a distribution that is well-fitted by a skew-normal distribution. Simulation results show that SIEVE controls the false discovery rate and probability of Type II error better than existing methods for differential expression analysis. Analysis of the Mayo RNA-Seq dataset for Alzheimer's disease using SIEVE reveals that a gene set with significant expression difference in mean, standard deviation and skewness between the control and the Alzheimer's disease group strongly predicts a subject's disease state. Furthermore, functional enrichment analysis shows that relying solely on differentially expressed genes detects only a segment of a much broader spectrum of biological aspects associated with Alzheimer's disease. The latter aspects can only be revealed using genes that show differential variability and skewness. Thus, SIEVE enables fresh perspectives for understanding the intricate changes in gene expression that occur in complex diseases. Availability The SIEVE R package and source codes are available at https://github.com/Divo-Lee/SIEVE .
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22
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Soheili-Nezhad S, Ibáñez-Solé O, Izeta A, Hoeijmakers JHJ, Stoeger T. Time is ticking faster for long genes in aging. Trends Genet 2024; 40:299-312. [PMID: 38519330 PMCID: PMC11003850 DOI: 10.1016/j.tig.2024.01.009] [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: 11/21/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 03/24/2024]
Abstract
Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.
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Affiliation(s)
- Sourena Soheili-Nezhad
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Olga Ibáñez-Solé
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ander Izeta
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Tecnun-University of Navarra, 20018 Donostia-San Sebastian, Spain.
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands; University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany; Princess Maxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands.
| | - Thomas Stoeger
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA; Potocsnak Longevity Institute, Northwestern University, Chicago, IL, USA; Simpson Querrey Lung Institute for Translational Science, Chicago, IL, USA.
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23
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Petersen SI, Okolicsanyi RK, Haupt LM. Exploring Heparan Sulfate Proteoglycans as Mediators of Human Mesenchymal Stem Cell Neurogenesis. Cell Mol Neurobiol 2024; 44:30. [PMID: 38546765 PMCID: PMC10978659 DOI: 10.1007/s10571-024-01463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/19/2024] [Indexed: 04/01/2024]
Abstract
Alzheimer's disease (AD) and traumatic brain injury (TBI) are major public health issues worldwide, with over 38 million people living with AD and approximately 48 million people (27-69 million) experiencing TBI annually. Neurodegenerative conditions are characterised by the accumulation of neurotoxic amyloid beta (Aβ) and microtubule-associated protein Tau (Tau) with current treatments focused on managing symptoms rather than addressing the underlying cause. Heparan sulfate proteoglycans (HSPGs) are a diverse family of macromolecules that interact with various proteins and ligands and promote neurogenesis, a process where new neural cells are formed from stem cells. The syndecan (SDC) and glypican (GPC) HSPGs have been implicated in AD pathogenesis, acting as drivers of disease, as well as potential therapeutic targets. Human mesenchymal stem cells (hMSCs) provide an attractive therapeutic option for studying and potentially treating neurodegenerative diseases due to their relative ease of isolation and subsequent extensive in vitro expansive potential. Understanding how HSPGs regulate protein aggregation, a key feature of neurodegenerative disorders, is essential to unravelling the underlying disease processes of AD and TBI, as well as any link between these two neurological disorders. Further research may validate HSPG, specifically SDCs or GPCs, use as neurodegenerative disease targets, either via driving hMSC stem cell therapy or direct targeting.
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Affiliation(s)
- Sofia I Petersen
- Stem Cell and Neurogenesis Group, School of Biomedical Sciences, Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), 60 Musk Ave, Kelvin Grove, QLD, 4059, Australia
| | - Rachel K Okolicsanyi
- Stem Cell and Neurogenesis Group, School of Biomedical Sciences, Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), 60 Musk Ave, Kelvin Grove, QLD, 4059, Australia
- Max Planck Queensland Centre for the Materials Sciences of Extracellular Matrices, Kelvin Grove, Australia
| | - Larisa M Haupt
- Stem Cell and Neurogenesis Group, School of Biomedical Sciences, Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), 60 Musk Ave, Kelvin Grove, QLD, 4059, Australia.
- ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Kelvin Grove, Australia.
- Max Planck Queensland Centre for the Materials Sciences of Extracellular Matrices, Kelvin Grove, Australia.
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24
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Perez-Corredor P, Vanderleest TE, Vacano GN, Sanchez JS, Villalba-Moreno ND, Marino C, Krasemann S, Mendivil-Perez MA, Aguillón D, Jiménez-Del-Río M, Baena A, Sepulveda-Falla D, Lopera F, Quiroz YT, Arboleda-Velasquez JF, Mazzarino RC. APOE3 Christchurch modulates β-catenin/Wnt signaling in iPS cell-derived cerebral organoids from Alzheimer's cases. Front Mol Neurosci 2024; 17:1373568. [PMID: 38571814 PMCID: PMC10987717 DOI: 10.3389/fnmol.2024.1373568] [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: 01/20/2024] [Accepted: 02/22/2024] [Indexed: 04/05/2024] Open
Abstract
A patient with the PSEN1 E280A mutation and homozygous for APOE3 Christchurch (APOE3Ch) displayed extreme resistance to Alzheimer's disease (AD) cognitive decline and tauopathy, despite having a high amyloid burden. To further investigate the differences in biological processes attributed to APOE3Ch, we generated induced pluripotent stem (iPS) cell-derived cerebral organoids from this resistant case and a non-protected control, using CRISPR/Cas9 gene editing to modulate APOE3Ch expression. In the APOE3Ch cerebral organoids, we observed a protective pattern from early tau phosphorylation. ScRNA sequencing revealed regulation of Cadherin and Wnt signaling pathways by APOE3Ch, with immunostaining indicating elevated β-catenin protein levels. Further in vitro reporter assays unexpectedly demonstrated that ApoE3Ch functions as a Wnt3a signaling enhancer. This work uncovered a neomorphic molecular mechanism of protection of ApoE3 Christchurch, which may serve as the foundation for the future development of protected case-inspired therapeutics targeting AD and tauopathies.
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Affiliation(s)
- Paula Perez-Corredor
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
| | - Timothy E. Vanderleest
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
| | | | - Justin S. Sanchez
- Massachusetts General Hospital and Department of Neurology at Harvard Medical School, Boston, MA, United States
| | - Nelson D. Villalba-Moreno
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Marino
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - David Aguillón
- The Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
| | | | - Ana Baena
- The Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
| | - Diego Sepulveda-Falla
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Francisco Lopera
- The Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
| | - Yakeel T. Quiroz
- Massachusetts General Hospital and Department of Neurology at Harvard Medical School, Boston, MA, United States
- The Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
- Massachusetts General Hospital and Department of Psychiatry at Harvard Medical School, Boston, MA, United States
| | - Joseph F. Arboleda-Velasquez
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
| | - Randall C. Mazzarino
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
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25
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Afsar A, Zhang L. Putative Molecular Mechanisms Underpinning the Inverse Roles of Mitochondrial Respiration and Heme Function in Lung Cancer and Alzheimer's Disease. BIOLOGY 2024; 13:185. [PMID: 38534454 DOI: 10.3390/biology13030185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
Mitochondria are the powerhouse of the cell. Mitochondria serve as the major source of oxidative stress. Impaired mitochondria produce less adenosine triphosphate (ATP) but generate more reactive oxygen species (ROS), which could be a major factor in the oxidative imbalance observed in Alzheimer's disease (AD). Well-balanced mitochondrial respiration is important for the proper functioning of cells and human health. Indeed, recent research has shown that elevated mitochondrial respiration underlies the development and therapy resistance of many types of cancer, whereas diminished mitochondrial respiration is linked to the pathogenesis of AD. Mitochondria govern several activities that are known to be changed in lung cancer, the largest cause of cancer-related mortality worldwide. Because of the significant dependence of lung cancer cells on mitochondrial respiration, numerous studies demonstrated that blocking mitochondrial activity is a potent strategy to treat lung cancer. Heme is a central factor in mitochondrial respiration/oxidative phosphorylation (OXPHOS), and its association with cancer is the subject of increased research in recent years. In neural cells, heme is a key component in mitochondrial respiration and the production of ATP. Here, we review the role of impaired heme metabolism in the etiology of AD. We discuss the numerous mitochondrial effects that may contribute to AD and cancer. In addition to emphasizing the significance of heme in the development of both AD and cancer, this review also identifies some possible biological connections between the development of the two diseases. This review explores shared biological mechanisms (Pin1, Wnt, and p53 signaling) in cancer and AD. In cancer, these mechanisms drive cell proliferation and tumorigenic functions, while in AD, they lead to cell death. Understanding these mechanisms may help advance treatments for both conditions. This review discusses precise information regarding common risk factors, such as aging, obesity, diabetes, and tobacco usage.
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Affiliation(s)
- Atefeh Afsar
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Li Zhang
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
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26
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Umoh IO, Dos Reis HJ, de Oliveira ACP. Molecular Mechanisms Linking Osteoarthritis and Alzheimer's Disease: Shared Pathways, Mechanisms and Breakthrough Prospects. Int J Mol Sci 2024; 25:3044. [PMID: 38474288 DOI: 10.3390/ijms25053044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease mostly affecting the elderly population. It is characterized by cognitive decline that occurs due to impaired neurotransmission and neuronal death. Even though deposition of amyloid beta (Aβ) peptides and aggregation of hyperphosphorylated TAU have been established as major pathological hallmarks of the disease, other factors such as the interaction of genetic and environmental factors are believed to contribute to the development and progression of AD. In general, patients initially present mild forgetfulness and difficulty in forming new memories. As it progresses, there are significant impairments in problem solving, social interaction, speech and overall cognitive function of the affected individual. Osteoarthritis (OA) is the most recurrent form of arthritis and widely acknowledged as a whole-joint disease, distinguished by progressive degeneration and erosion of joint cartilage accompanying synovitis and subchondral bone changes that can prompt peripheral inflammatory responses. Also predominantly affecting the elderly, OA frequently embroils weight-bearing joints such as the knees, spine and hips leading to pains, stiffness and diminished joint mobility, which in turn significantly impacts the patient's standard of life. Both infirmities can co-occur in older adults as a result of independent factors, as multiple health conditions are common in old age. Additionally, risk factors such as genetics, lifestyle changes, age and chronic inflammation may contribute to both conditions in some individuals. Besides localized peripheral low-grade inflammation, it is notable that low-grade systemic inflammation prompted by OA can play a role in AD pathogenesis. Studies have explored relationships between systemic inflammatory-associated diseases like obesity, hypertension, dyslipidemia, diabetes mellitus and AD. Given that AD is the most common form of dementia and shares similar risk factors with OA-both being age-related and low-grade inflammatory-associated diseases, OA may indeed serve as a risk factor for AD. This work aims to review literature on molecular mechanisms linking OA and AD pathologies, and explore potential connections between these conditions alongside future prospects and innovative treatments.
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Affiliation(s)
- Idiongo Okon Umoh
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Av. Antonio Carlos 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Helton Jose Dos Reis
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Av. Antonio Carlos 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Antonio Carlos Pinheiro de Oliveira
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Av. Antonio Carlos 6627, Belo Horizonte 31270-901, MG, Brazil
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27
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Shi T, Shen S, Shi Y, Wang Q, Zhang G, Lin J, Chen J, Bai F, Zhang L, Wang Y, Gong W, Shao X, Chen G, Yan W, Chen X, Ma Y, Zheng L, Qin J, Lu K, Liu N, Xu Y, Shi YS, Jiang Q, Guo B. Osteocyte-derived sclerostin impairs cognitive function during ageing and Alzheimer's disease progression. Nat Metab 2024; 6:531-549. [PMID: 38409606 DOI: 10.1038/s42255-024-00989-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Ageing increases susceptibility to neurodegenerative disorders, such as Alzheimer's disease (AD). Serum levels of sclerostin, an osteocyte-derived Wnt-β-catenin signalling antagonist, increase with age and inhibit osteoblastogenesis. As Wnt-β-catenin signalling acts as a protective mechanism for memory, we hypothesize that osteocyte-derived sclerostin can impact cognitive function under pathological conditions. Here we show that osteocyte-derived sclerostin can cross the blood-brain barrier of old mice, where it can dysregulate Wnt-β-catenin signalling. Gain-of-function and loss-of-function experiments show that abnormally elevated osteocyte-derived sclerostin impairs synaptic plasticity and memory in old mice of both sexes. Mechanistically, sclerostin increases amyloid β (Aβ) production through β-catenin-β-secretase 1 (BACE1) signalling, indicating a functional role for sclerostin in AD. Accordingly, high sclerostin levels in patients with AD of both sexes are associated with severe cognitive impairment, which is in line with the acceleration of Αβ production in an AD mouse model with bone-specific overexpression of sclerostin. Thus, we demonstrate osteocyte-derived sclerostin-mediated bone-brain crosstalk, which could serve as a target for developing therapeutic interventions against AD.
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Affiliation(s)
- Tianshu Shi
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Siyu Shen
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Yong Shi
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Qianjin Wang
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Guanqun Zhang
- Department of Neurology, the Xuzhou School of Clinical Medicine of Nanjing Medical University, Xuzhou, PR China
| | - Jiaquan Lin
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, PR China
| | - Jiang Chen
- Department of Neurology, Nanjing Drum Tower Hospital of the Affiliated Hospital of Nanjing University Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Institute of Brain Science, Nanjing University, Nanjing, China
| | - Feng Bai
- Department of Neurology, Nanjing Drum Tower Hospital of the Affiliated Hospital of Nanjing University Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Institute of Brain Science, Nanjing University, Nanjing, China
| | - Lei Zhang
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Yangyufan Wang
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Wang Gong
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Xiaoyan Shao
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, PR China
| | - Guiquan Chen
- Key Laboratory of Model Animal for Disease Study, Ministry of Education, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China
| | - Wenjin Yan
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Xiang Chen
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, PR China
| | - Yuze Ma
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Liming Zheng
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Jianghui Qin
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
| | - Ke Lu
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
- Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Na Liu
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, PR China
| | - Yun Xu
- Department of Neurology, Nanjing Drum Tower Hospital of the Affiliated Hospital of Nanjing University Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Institute of Brain Science, Nanjing University, Nanjing, China
| | - Yun Stone Shi
- Key Laboratory of Model Animal for Disease Study, Ministry of Education, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China.
- Institute for Brain Sciences, Nanjing University, Nanjing, China.
| | - Qing Jiang
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China.
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China.
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China.
| | - Baosheng Guo
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, PR China.
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China.
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, PR China.
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, PR China.
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28
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Guarnieri L, Bosco F, Leo A, Citraro R, Palma E, De Sarro G, Mollace V. Impact of micronutrients and nutraceuticals on cognitive function and performance in Alzheimer's disease. Ageing Res Rev 2024; 95:102210. [PMID: 38296163 DOI: 10.1016/j.arr.2024.102210] [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: 07/31/2023] [Revised: 01/10/2024] [Accepted: 01/25/2024] [Indexed: 02/13/2024]
Abstract
Alzheimer's disease (AD) is a major global health problem today and is the most common form of dementia. AD is characterized by the formation of β-amyloid (Aβ) plaques and neurofibrillary clusters, leading to decreased brain acetylcholine levels in the brain. Another mechanism underlying the pathogenesis of AD is the abnormal phosphorylation of tau protein that accumulates at the level of neurofibrillary aggregates, and the areas most affected by this pathological process are usually the cholinergic neurons in cortical, subcortical, and hippocampal areas. These effects result in decreased cognitive function, brain atrophy, and neuronal death. Malnutrition and weight loss are the most frequent manifestations of AD, and these are also associated with greater cognitive decline. Several studies have confirmed that a balanced low-calorie diet and proper nutritional intake may be considered important factors in counteracting or slowing the progression of AD, whereas a high-fat or hypercholesterolemic diet predisposes to an increased risk of developing AD. Especially, fruits, vegetables, antioxidants, vitamins, polyunsaturated fatty acids, and micronutrients supplementation exert positive effects on aging-related changes in the brain due to their antioxidant, anti-inflammatory, and radical scavenging properties. The purpose of this review is to summarize some possible nutritional factors that may contribute to the progression or prevention of AD, understand the role that nutrition plays in the formation of Aβ plaques typical of this neurodegenerative disease, to identify some potential therapeutic strategies that may involve some natural compounds, in delaying the progression of the disease.
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Affiliation(s)
- Lorenza Guarnieri
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Francesca Bosco
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy.
| | - Antonio Leo
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy; Research Center FAS@UMG, Department of Health Science, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Rita Citraro
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy; Research Center FAS@UMG, Department of Health Science, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Ernesto Palma
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Giovambattista De Sarro
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy; Research Center FAS@UMG, Department of Health Science, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Vincenzo Mollace
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
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Zhang Q, Liu J, Liu H, Ao L, Xi Y, Chen D. Genome-wide epistasis analysis reveals gene-gene interaction network on an intermediate endophenotype P-tau/Aβ 42 ratio in ADNI cohort. Sci Rep 2024; 14:3984. [PMID: 38368488 PMCID: PMC10874417 DOI: 10.1038/s41598-024-54541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/14/2024] [Indexed: 02/19/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the elderly worldwide. The exact etiology of AD, particularly its genetic mechanisms, remains incompletely understood. Traditional genome-wide association studies (GWAS), which primarily focus on single-nucleotide polymorphisms (SNPs) with main effects, provide limited explanations for the "missing heritability" of AD, while there is growing evidence supporting the important role of epistasis. In this study, we performed a genome-wide SNP-SNP interaction detection using a linear regression model and employed multiple GPUs for parallel computing, significantly enhancing the speed of whole-genome analysis. The cerebrospinal fluid (CSF) phosphorylated tau (P-tau)/amyloid-[Formula: see text] (A[Formula: see text]) ratio was used as a quantitative trait (QT) to enhance statistical power. Age, gender, and clinical diagnosis were included as covariates to control for potential non-genetic factors influencing AD. We identified 961 pairs of statistically significant SNP-SNP interactions, explaining a high-level variance of P-tau/A[Formula: see text] level, all of which exhibited marginal main effects. Additionally, we replicated 432 previously reported AD-related genes and found 11 gene-gene interaction pairs overlapping with the protein-protein interaction (PPI) network. Our findings may contribute to partially explain the "missing heritability" of AD. The identified subnetwork may be associated with synaptic dysfunction, Wnt signaling pathway, oligodendrocytes, inflammation, hippocampus, and neuronal cells.
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Affiliation(s)
- Qiushi Zhang
- School of Computer Science, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China
| | - Junfeng Liu
- School of Computer Science, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China
| | - Hongwei Liu
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong Street, Harbin, China
| | - Lang Ao
- School of Computer Science, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China
| | - Yang Xi
- School of Computer Science, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China
| | - Dandan Chen
- School of Automation Engineering, Northeast Electric Power University, 169 Changchun Street, Jilin, 132012, China.
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong Street, Harbin, China.
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Li L, Wang L, Zhang L. Therapeutic Potential of Natural Compounds from Herbs and Nutraceuticals in Alleviating Neurological Disorders: Targeting the Wnt Signaling Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2411-2433. [PMID: 38284360 DOI: 10.1021/acs.jafc.3c07536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
As an important signaling pathway in multicellular eukaryotes, the Wnt signaling pathway participates in a variety of physiological processes. Recent studies have confirmed that the Wnt signaling pathway plays an important role in neurological disorders such as stroke, Alzheimer's disease, and Parkinson's disease. The regulation of Wnt signaling by natural compounds in herbal medicines and nutraceuticals has emerged as a potential strategy for the development of new drugs for neurological disorders. Purpose: The aim of this review is to evaluate the latest research results on the efficacy of natural compounds derived from herbs and nutraceuticals in the prevention and treatment of neurological disorders by regulating the Wnt pathway in vivo and in vitro. A manual and electronic search was performed for English articles available from PubMed, Web of Science, and ScienceDirect from the January 2010 to February 2023. Keywords used for the search engines were "natural products,″ "plant derived products,″ "Wnt+ clinical trials,″ and "Wnt+,″ and/or paired with "natural products″/″plant derived products", and "neurological disorders." A total of 22 articles were enrolled in this review, and a variety of natural compounds from herbal medicine and nutritional foods have been shown to exert therapeutic effects on neurological disorders through the Wnt pathway, including curcumin, resveratrol, and querctrin, etc. These natural products possess antioxidant, anti-inflammatory, and angiogenic properties, confer neurovascular unit and blood-brain barrier integrity protection, and affect neural stem cell differentiation, synaptic formation, and neurogenesis, to play a therapeutic role in neurological disorders. In various in vivo and in vitro studies and clinical trials, these natural compounds have been shown to be safe and tolerable with few adverse effects. Natural compounds may serve a therapeutic role in neurological disorders by regulating the Wnt pathway. This summary of the research progress of natural compounds targeting the Wnt pathway may provide new insights for the treatment of neurological disorders and potential targets for the development of new drugs.
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Affiliation(s)
- Lei Li
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang 110000, Liaoning PR China
| | - Lin Wang
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang 110000, Liaoning PR China
| | - Lijuan Zhang
- Departments of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 39 Huaxiang Road, Tiexi District, Shenyang 110000, Liaoning PR China
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Yamakawa M, Rexach JE. Cell States and Interactions of CD8 T Cells and Disease-Enriched Microglia in Human Brains with Alzheimer's Disease. Biomedicines 2024; 12:308. [PMID: 38397909 PMCID: PMC10886701 DOI: 10.3390/biomedicines12020308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/05/2024] [Accepted: 01/13/2024] [Indexed: 02/25/2024] Open
Abstract
Alzheimer's disease (AD) is a multi-stage neurodegenerative disorder characterized by beta-amyloid accumulation, hyperphosphorylated Tau deposits, neurodegeneration, neuroinflammation, and cognitive impairment. Recent studies implicate CD8 T cells as neuroimmune responders to the accumulation of AD pathology in the brain and potential contributors to toxic neuroinflammation. However, more evidence is needed to understand lymphocytes in disease, including their functional states, molecular mediators, and interacting cell types in diseased brain tissue. The scarcity of lymphocytes in brain tissue samples has limited the unbiased profiling of disease-associated cell types, cell states, drug targets, and relationships to common AD genetic risk variants based on transcriptomic analyses. However, using recent large-scale, high-quality single-nuclear sequencing datasets from over 84 Alzheimer's disease and control cases, we leverage single-nuclear RNAseq data from 800 lymphocytes collected from 70 individuals to complete unbiased molecular profiling. We demonstrate that effector memory CD8 T cells are the major lymphocyte subclass enriched in the brain tissues of individuals with AD dementia. We define disease-enriched interactions involving CD8 T cells and multiple brain cell subclasses including two distinct microglial disease states that correlate, respectively, to beta-amyloid and tau pathology. We find that beta-amyloid-associated microglia are a major hub of multicellular cross-talk gained in disease, including interactions involving both vulnerable neuronal subtypes and CD8 T cells. We reproduce prior reports that amyloid-response microglia are depleted in APOE4 carriers. Overall, these human-based studies provide additional support for the potential relevance of effector memory CD8 T cells as a lymphocyte population of interest in AD dementia and provide new candidate interacting partners and drug targets for further functional study.
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Affiliation(s)
| | - Jessica E. Rexach
- Department of Neurology, University of California Los Angeles, Los Angeles, CA 90095, USA;
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Sanajou S, Yirün A, Demirel G, Çakir DA, Şahin G, Erkekoğlu P, Baydar T. Antioxidant dihydrolipolic acid protects against in vitro aluminum-induced toxicity. J Appl Toxicol 2023; 43:1793-1805. [PMID: 37409350 DOI: 10.1002/jat.4513] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Dihydrolipoic acid (DHLA) is a natural antioxidant known for its ability to counteract metal toxicity and oxidative stress. It has shown the potential to safeguard cells from harmful environmental substances. It may hold therapeutic benefits in treating neurodegenerative disorders by defending against oxidative damage and chronic inflammation. Thus, this study aimed to explore the potential neuroprotective effects of DHLA against aluminum (Al)-induced toxicity using an Alzheimer's disease (AD) model in vitro. The study focused on two important pathways: GSK-3β and the Wnt signaling pathways. The SH-SY5Y cell line was differentiated to establish AD, and the study group were as follows: control, Al, DHLA, Al-DHLA, AD, AD-Al, AD-DHLA, and AD-Al-DHLA. The impact of DHLA on parameters related to oxidative stress was assessed. The activity of the GSK-3β pathway was measured by evaluating the levels of PPP1CA, PP2A, GSK-3β, and Akt. The Wnt signaling pathway was assessed by measuring Wnt/β-catenin in the different study groups. Exposure to DHLA significantly reduced oxidative stress by effectively decreasing the levels of reactive oxygen species, thereby protecting against protein oxidation and limiting the production of malonaldehyde. Moreover, the DHLA-treated groups exhibited a remarkable increase in the total antioxidant capacity. Furthermore, the study observed an upregulation of the Wnt signaling pathway and a downregulation of the GSK-3β pathway in the groups treated with DHLA. In summary, the neuroprotective effects of DHLA, primarily achieved by reducing oxidative stress and modulating critical imbalanced pathways associated with AD, indicate its potential as a promising addition to the treatment regimens of AD patients.
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Affiliation(s)
- Sonia Sanajou
- Faculty of Pharmacy, Department of Toxicology, Hacettepe University, Ankara, Turkey
| | - Anil Yirün
- Faculty of Pharmacy, Department of Toxicology, Hacettepe University, Ankara, Turkey
- Faculty of Pharmacy, Department of Toxicology, Cukurova University, Adana, Turkey
| | - Göksun Demirel
- Faculty of Pharmacy, Department of Toxicology, Cukurova University, Adana, Turkey
| | - Deniz Arca Çakir
- Faculty of Pharmacy, Department of Toxicology, Hacettepe University, Ankara, Turkey
- Vaccine Institute, Department of Vaccine Technology, Hacettepe University, Ankara, Turkey
| | - Gönül Şahin
- Faculty of Pharmacy, Department of Toxicology, Hacettepe University, Ankara, Turkey
| | - Pinar Erkekoğlu
- Faculty of Pharmacy, Department of Toxicology, Hacettepe University, Ankara, Turkey
- Vaccine Institute, Department of Vaccine Technology, Hacettepe University, Ankara, Turkey
| | - Terken Baydar
- Faculty of Pharmacy, Department of Toxicology, Hacettepe University, Ankara, Turkey
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Islam M, Behura SK. Role of caveolin-1 in metabolic programming of fetal brain. iScience 2023; 26:107710. [PMID: 37720105 PMCID: PMC10500482 DOI: 10.1016/j.isci.2023.107710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/10/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Mice lacking caveolin-1 (Cav1), a key protein of plasma membrane, exhibit brain aging at an early adult stage. Here, integrative analyses of metabolomics, transcriptomics, epigenetics, and single-cell data were performed to test the hypothesis that metabolic deregulation of fetal brain due to the ablation of Cav1 is linked to brain aging in these mice. The results of this study show that lack of Cav1 caused deregulation in the lipid and amino acid metabolism in the fetal brain, and genes associated with these deregulated metabolites were significantly altered in the brain upon aging. Moreover, ablation of Cav1 deregulated several metabolic genes in specific cell types of the fetal brain and impacted DNA methylation of those genes in coordination with mouse epigenetic clock. The findings of this study suggest that the aging program of brain is confounded by metabolic abnormalities in the fetal stage due to the absence of Cav1.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, 920 East Campus Drive, University of Missouri, Columbia, MO 65211, USA
| | - Susanta K. Behura
- Division of Animal Sciences, 920 East Campus Drive, University of Missouri, Columbia, MO 65211, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Interdisciplinary Reproduction and Health Group, University of Missouri, Columbia, MO, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, USA
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Tang S, Buchman AS, Wang Y, Avey D, Xu J, Tasaki S, Bennett DA, Zheng Q, Yang J. Differential gene expression analysis based on linear mixed model corrects false positive inflation for studying quantitative traits. Sci Rep 2023; 13:16570. [PMID: 37789141 PMCID: PMC10547771 DOI: 10.1038/s41598-023-43686-7] [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: 03/09/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023] Open
Abstract
Differential gene expression (DGE) analysis has been widely employed to identify genes expressed differentially with respect to a trait of interest using RNA sequencing (RNA-Seq) data. Recent RNA-Seq data with large samples pose challenges to existing DGE methods, which were mainly developed for dichotomous traits and small sample sizes. Especially, existing DGE methods are likely to result in inflated false positive rates. To address this gap, we employed a linear mixed model (LMM) that has been widely used in genetic association studies for DGE analysis of quantitative traits. We first applied the LMM method to the discovery RNA-Seq data of dorsolateral prefrontal cortex (DLPFC) tissue (n = 632) with four continuous measures of Alzheimer's Disease (AD) cognitive and neuropathologic traits. The quantile-quantile plots of p-values showed that false positive rates were well calibrated by LMM, whereas other methods not accounting for sample-specific mixed effects led to serious inflation. LMM identified 37 potentially significant genes with differential expression in DLPFC for at least one of the AD traits, 17 of which were replicated in the additional RNA-Seq data of DLPFC, supplemental motor area, spinal cord, and muscle tissues. This application study showed not only well calibrated DGE results by LMM, but also possibly shared gene regulatory mechanisms of AD traits across different relevant tissues.
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Affiliation(s)
- Shizhen Tang
- Department of Human Genetics, Center for Computational and Quantitative Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA, 30322, USA
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Denis Avey
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Jishu Xu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Qi Zheng
- Department of Bioinformatics and Biostatistics, University of Louisville, 485 E. Gray St, Louisville, KY, 40202, USA.
| | - Jingjing Yang
- Department of Human Genetics, Center for Computational and Quantitative Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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Anand AA, Khan M, V M, Kar D. The Molecular Basis of Wnt/ β-Catenin Signaling Pathways in Neurodegenerative Diseases. Int J Cell Biol 2023; 2023:9296092. [PMID: 37780577 PMCID: PMC10539095 DOI: 10.1155/2023/9296092] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/03/2023] Open
Abstract
Defective Wnt signaling is found to be associated with various neurodegenerative diseases. In the canonical pathway, the Frizzled receptor (Fzd) and the lipoprotein receptor-related proteins 5/6 (LRP5/LRP6) create a seven-pass transmembrane receptor complex to which the Wnt ligands bind. This interaction causes the tumor suppressor adenomatous polyposis coli gene product (APC), casein kinase 1 (CK1), and GSK-3β (glycogen synthase kinase-3 beta) to be recruited by the scaffold protein Dishevelled (Dvl), which in turn deactivates the β-catenin destruction complex. This inactivation stops the destruction complex from phosphorylating β-catenin. As a result, β-catenin first builds up in the cytoplasm and then migrates into the nucleus, where it binds to the Lef/Tcf transcription factor to activate the transcription of more than 50 Wnt target genes, including those involved in cell growth, survival, differentiation, neurogenesis, and inflammation. The treatments that are currently available for neurodegenerative illnesses are most commonly not curative in nature but are only symptomatic. According to all available research, restoring Wnt/β-catenin signaling in the brains of patients with neurodegenerative disorders, particularly Alzheimer's and Parkinson's disease, would improve the condition of several patients with neurological disorders. The importance of Wnt activators and modulators in patients with such illnesses is to mainly restore rather than overstimulate the Wnt/β-catenin signaling, thereby reestablishing the equilibrium between Wnt-OFF and Wnt-ON states. In this review, we have tried to summarize the significance of the Wnt canonical pathway in the pathophysiology of certain neurodegenerative diseases, such as Alzheimer's disease, cerebral ischemia, Parkinson's disease, Huntington's disease, multiple sclerosis, and other similar diseases, and as to how can it be restored in these patients.
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Affiliation(s)
- Ananya Anurag Anand
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad 211012, India
| | - Misbah Khan
- Department of Biotechnology, Ramaiah University of Applied Sciences, Bengaluru 560054, India
| | - Monica V
- Department of Biotechnology, Ramaiah University of Applied Sciences, Bengaluru 560054, India
| | - Debasish Kar
- Department of Biotechnology, Ramaiah University of Applied Sciences, Bengaluru 560054, India
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Chen D, Wang J, Li Y, Xu C, Fanzheng M, Zhang P, Liu L. LncRNA NEAT1 suppresses cellular senescence in hepatocellular carcinoma via KIF11-dependent repression of CDKN2A. Clin Transl Med 2023; 13:e1418. [PMID: 37752791 PMCID: PMC10522973 DOI: 10.1002/ctm2.1418] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. Therapeutic options for advanced HCC are limited, which is due to a lack of full understanding of pathogenesis. Cellular senescence is a state of cell cycle arrest, which plays important roles in the pathogenesis of HCC. Mechanisms underlying hepatocellular senescence are not fully understood. LncRNA NEAT1 acts as an oncogene and contributes to the development of HCC. Whether NEAT1 modulates hepatocellular senescence in HCC is unknown. METHODS The role of NEAT1 and KIF11 in cellular senescence and tumor growth in HCC was assessed both in vitro and in vivo. RNA pulldown, mass spectrometry, Chromatin immunoprecipitation (ChIP), luciferase reporter assays, RNA FISH and immunofluorescence (IF) staining were used to explore the detailed molecular mechanism of NEAT1 and KIF11 in cellular senescence of HCC. RESULTS We found that NEAT1 was upregulated in tumor tissues and hepatoma cells, which negatively correlated with a senescence biomarker CDKN2A encoding p16INK4a and p14ARF proteins. NEAT1 was reduced in senescent hepatoma cells induced by doxorubicin (DOXO) or serum starvation. Furthermore, NEAT1 deficiency caused senescence in cultured hepatoma cells, and protected against the progression of HCC in a mouse model. During senescence, NEAT1 translocated into cytosol and interacted with a motor protein KIF11, resulting in KIF11 protein degradation and subsequent increased expression of CDKN2A in cultured hepatoma cells. Furthermore, KIF11 knockdown caused senescence in cultured hepatoma cells. Genetic deletion of Kif11 in hepatocytes inhibited the development of HCC in a mouse model. CONCLUSIONS Conclusively, NEAT1 overexpression reduces senescence and promotes tumor progression in HCC tissues and hepatoma cells, whereas NEAT1 deficiency causes senescence and inhibits tumor progression in HCC. This is associated with KIF11-dependent repression of CDKN2A. These findings lay the foundation to develop potential therapies for HCC by inhibiting NEAT1 and KIF11 or inducing senescence.
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Affiliation(s)
- Danlei Chen
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhuiChina
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhuiChina
| | - Jinghao Wang
- Zhejiang Cancer HospitalHangzhou Institute of MedicineChinese Academy of SciencesHangzhouZhejiangChina
| | - Yang Li
- Zhejiang Cancer HospitalHangzhou Institute of MedicineChinese Academy of SciencesHangzhouZhejiangChina
| | - Chenglin Xu
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Meng Fanzheng
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhuiChina
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhuiChina
| | - Pengfei Zhang
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Zhejiang Cancer HospitalHangzhou Institute of MedicineChinese Academy of SciencesHangzhouZhejiangChina
| | - Lianxin Liu
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhuiChina
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhuiChina
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Moon YJ, Cui B, Cho SY, Hwang JW, Chung HC, Kwon J, Kim D, Jang KY, Kim JR, Wang SI. Sirtuin 6 Overexpression Improves Rotator Cuff Tendon-to-Bone Healing in the Aged. Cells 2023; 12:2035. [PMID: 37626845 PMCID: PMC10453227 DOI: 10.3390/cells12162035] [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: 05/24/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Aging is an independent risk factor for recurrent tearing after surgical repair of rotator cuff ruptures around the tendon-to-bone area. However, aging signature factors and related mechanisms involved in the healing of the rotator cuff are still unknown. We hypothesized that differences in proteins involved in the rotator cuff according to age may affect tendon-to-bone healing. The proteome analysis performed to identify the signature aging proteins of the rotator cuff confirmed the sirtuin signal as an age-specific protein. In particular, the expression of SIRT6 was markedly down-regulated with age. Ingenuity pathway analysis of omics data from age-dependent rat rotator cuffs and linear regression from human rotator cuffs showed SIRT6 to be closely related to the Wnt/β-catenin signal. We confirmed that overexpression of SIRT6 in the rotator cuff and primary tenocyte regulated canonical Wnt signaling by inhibiting the transcriptional expression of sclerostin, a Wnt antagonist. Finally, SIRT6 overexpression promoted tendon-to-bone healing after tenotomy with reconstruction in elderly rats. This approach is considered an effective treatment method for recovery from recurrent rotator cuff tears, which frequently occur in the elderly.
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Affiliation(s)
- Young Jae Moon
- Department of Biochemistry and Orthopaedic Surgery, Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea
| | - Baoning Cui
- Department of Orthopaedic Surgery, Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea; (B.C.)
| | - Se-Young Cho
- Department of Food Science and Technology, Foodborne Virus Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jae Won Hwang
- Department of Orthopaedic Surgery, Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea; (B.C.)
| | - Hee-Chung Chung
- Department of BioChemical Analysis, Korea Basic Science Institute, Daejeon 30147, Republic of Korea
| | - Joseph Kwon
- Department of BioChemical Analysis, Korea Basic Science Institute, Daejeon 30147, Republic of Korea
| | - Duwoon Kim
- Department of Food Science and Technology, Foodborne Virus Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kyu Yun Jang
- Department of Pathology, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea
| | - Jung Ryul Kim
- Department of Orthopaedic Surgery, Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea; (B.C.)
| | - Sung Il Wang
- Department of Orthopaedic Surgery, Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea; (B.C.)
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Yoon M, Kim H, Shin H, Lee H, Kang MJ, Park SH, Han G, Kim Y, Choi KY. Inhibition of CXXC5 function rescues Alzheimer's disease phenotypes by restoring Wnt/β-catenin signaling pathway. Pharmacol Res 2023; 194:106836. [PMID: 37355147 DOI: 10.1016/j.phrs.2023.106836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent type of dementia and is characterized by cognitive deficits and accumulation of pathological plaques. Owing to the complexity of AD development, paradigms for AD research and drug discovery have shifted to target factors that mediate multiple pathogenesis in AD. Increasing evidence suggests that the suppression of the Wnt/β-catenin signaling pathway plays substantial roles in AD progression. However, the underlying mechanism for the suppression of Wnt/β-catenin pathway associated with AD pathogenesis remains unexplored. In this study, we identified that CXXC5, a negative feedback regulator of the Wnt/β-catenin pathway, was overexpressed in the tissues of AD patients and 5xFAD transgenic mice paired with the suppression of Wnt/β-catenin pathway and its target genes related to AD. The level of CXXC5 was upregulated, upon aging of 5xFAD mice. AD characteristics including cognitive deficits, amyloid-β (Aβ) plaques, neuronal inflammation, and age-dependent increment of AD-related markers were rescued in Cxxc5-/-/5xFAD mice. 5-methoxyindirubin-3'-oxime (KY19334), a small molecule that restores the suppressed Wnt/β-catenin pathway via interference of the CXXC5-Dvl interaction, significantly improved the overall pathogenic phenotypes of 5xFAD mice. Collectively, our findings revealed that CXXC5 plays a key role in AD pathogenesis and suggest inhibition of CXXC5-Dvl interaction as a new therapeutic approach for AD.
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Affiliation(s)
- Minguen Yoon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Heejene Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Heewon Shin
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - HeeYang Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | | | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Gyoonhee Han
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - YoungSoo Kim
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea.
| | - Kang-Yell Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea; CK Regeon Inc, Seoul 03722, Republic of Korea.
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Shama Bhat G, Shaik Mohammad F. Computational Fragment-Based Design of Phytochemical Derivatives as EGFR Inhibitors. Chem Biodivers 2023; 20:e202300681. [PMID: 37399183 DOI: 10.1002/cbdv.202300681] [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: 05/10/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
Epidermal growth factor receptor (EGFR) is a potential target with disease modifying benefits against Alzheimer's disease (AD). Repurposing of FDA approved drugs against EGFR have shown beneficial effect against AD but are confined to quinazoline, quinoline and aminopyrimidines. Futuristically, the possibility of acquiring drug resistance mutation as seen in the case of cancer could also hamper AD treatment. To identify novel chemical scaffolds, we rooted on phytochemicals identified from plants such as Acorus calamus, Bacopa monnieri, Convolvulus pluricaulis, Tinospora cordifloia, and Withania somnifera that have well-established records in the treatment of brain disorders. The rationale was to mimic the biosynthetic metabolite extension process observed in the plants for synthesizing new phytochemical derivates. Thus, novel compounds were designed computationally by fragment-based method followed by extensive in silico analysis to pick potential phytochemical derivates. PCD1, 8 and 10 were predicted to have better blood brain barrier permeability. ADMET and SoM analysis suggested that these PCDs exhibited druglike properties. Further simulation studies showed that PCD1 and PCD8 stably interact with EGFR and have the potential to be used even in cases of drug-resistance mutations. With further experimental evidence, these PCDs could be leveraged as potential inhibitors of EGFR.
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Affiliation(s)
- Gayathri Shama Bhat
- Department of Biotechnology, Manipal Institute of Technology, Manipal, 576104, Karnataka, India
| | - Fayaz Shaik Mohammad
- Department of Biotechnology, Manipal Institute of Technology, Manipal, 576104, Karnataka, India
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Li J, Wang P, Hou M, Zhu BT. Attenuation of amyloid-β-induced mitochondrial dysfunction by active components of anthocyanins in HT22 neuronal cells. MedComm (Beijing) 2023; 4:e301. [PMID: 37346934 PMCID: PMC10279944 DOI: 10.1002/mco2.301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 06/23/2023] Open
Abstract
Alzheimer's disease (AD) is a common form of neurodegenerative disease in the elderly. Amyloid-β (Aβ)-associated neurotoxicity is an important component of the neurodegenerative change in AD. Recent studies have revealed a beneficial effect of anthocyanins in improving learning and memory in AD animal models. Using cultured HT22 mouse hippocampal neuronal cells as an in vitro model, we examined in this study the protective effect of ten pure components of anthocyanins against Aβ 42-induced cytotoxicity and also investigated the mechanism of their protective effects. We found that treatment of HT22 cells with the pure components of anthocyanins dose-dependently rescued Aβ 42-induced cytotoxicity, with slightly different potencies. Using petunidin as a representative compound, we found that it enhanced mitochondrial homeostasis and function in Aβ 42-treated HT22 cells. Mechanistically, petunidin facilitated β-catenin nuclear translocation and enhanced the interaction between β-catenin and TCF7, which subsequently upregulated mitochondrial homeostasis-related protein Mfn2, thereby promoting restoration of mitochondrial homeostasis and function in Aβ 42-treated HT22 cells. Together, these results reveal that the pure components of anthocyanins have a strong protective effect in HT22 cells against Aβ 42-induced cytotoxicity by ameliorating mitochondrial homeostasis and function in a β-catenin/TCF-dependent manner.
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Affiliation(s)
- Jing Li
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of MedicineThe Chinese University of Hong KongShenzhenGuangdongChina
- School of Life SciencesUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Pan Wang
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of MedicineThe Chinese University of Hong KongShenzhenGuangdongChina
| | - Ming‐Jie Hou
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of MedicineThe Chinese University of Hong KongShenzhenGuangdongChina
| | - Bao Ting Zhu
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of MedicineThe Chinese University of Hong KongShenzhenGuangdongChina
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Killick R, Elliott C, Ribe E, Broadstock M, Ballard C, Aarsland D, Williams G. Neurodegenerative Disease Associated Pathways in the Brains of Triple Transgenic Alzheimer's Model Mice Are Reversed Following Two Weeks of Peripheral Administration of Fasudil. Int J Mol Sci 2023; 24:11219. [PMID: 37446396 PMCID: PMC10342807 DOI: 10.3390/ijms241311219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The pan Rho-associated coiled-coil-containing protein kinase (ROCK) inhibitor fasudil acts as a vasodilator and has been used as a medication for post-cerebral stroke for the past 29 years in Japan and China. More recently, based on the involvement of ROCK inhibition in synaptic function, neuronal survival, and processes associated with neuroinflammation, it has been suggested that the drug may be repurposed for neurodegenerative diseases. Indeed, fasudil has demonstrated preclinical efficacy in many neurodegenerative disease models. To facilitate an understanding of the wider biological processes at play due to ROCK inhibition in the context of neurodegeneration, we performed a global gene expression analysis on the brains of Alzheimer's disease model mice treated with fasudil via peripheral IP injection. We then performed a comparative analysis of the fasudil-driven transcriptional profile with profiles generated from a meta-analysis of multiple neurodegenerative diseases. Our results show that fasudil tends to drive gene expression in a reverse sense to that seen in brains with post-mortem neurodegenerative disease. The results are most striking in terms of pathway enrichment analysis, where pathways perturbed in Alzheimer's and Parkinson's diseases are overwhelmingly driven in the opposite direction by fasudil treatment. Thus, our results bolster the repurposing potential of fasudil by demonstrating an anti-neurodegenerative phenotype in a disease context and highlight the potential of in vivo transcriptional profiling of drug activity.
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Affiliation(s)
- Richard Killick
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
- College of Medicine and Health, University of Exeter, Exeter EX1 2UL, UK;
| | - Christina Elliott
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
| | - Elena Ribe
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
| | - Martin Broadstock
- Wolfson CARD, King’s College London, London Bridge, London SE1 1UL, UK;
| | - Clive Ballard
- College of Medicine and Health, University of Exeter, Exeter EX1 2UL, UK;
| | - Dag Aarsland
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
| | - Gareth Williams
- Wolfson CARD, King’s College London, London Bridge, London SE1 1UL, UK;
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Passero M, Zhai T, Huang Z. Investigation of Potential Drug Targets for Cholesterol Regulation to Treat Alzheimer's Disease. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6217. [PMID: 37444065 PMCID: PMC10341567 DOI: 10.3390/ijerph20136217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
Despite extensive research and seven approved drugs, the complex interplay of genes, proteins, and pathways in Alzheimer's disease remains a challenge. This implies the intricacies of the mechanism for Alzheimer's disease, which involves the interaction of hundreds of genes, proteins, and pathways. While the major hallmarks of Alzheimer's disease are the accumulation of amyloid plaques and tau protein tangles, excessive accumulation of cholesterol is reportedly correlated with Alzheimer's disease patients. In this work, protein-protein interaction analysis was conducted based upon the genes from a clinical database to identify the top protein targets with most data-indicated involvement in Alzheimer's disease, which include ABCA1, CYP46A1, BACE1, TREM2, GSK3B, and SREBP2. The reactions and pathways associated with these genes were thoroughly studied for their roles in regulating brain cholesterol biosynthesis, amyloid beta accumulation, and tau protein tangle formation. Existing clinical trials for each protein target were also investigated. The research indicated that the inhibition of SREBP2, BACE1, or GSK3B is beneficial to reduce cholesterol and amyloid beta accumulation, while the activation of ABCA1, CYP46A1, or TREM2 has similar effects. In this study, Sterol Regulatory Element-Binding Protein 2 (SREBP2) emerged as the primary protein target. SREBP2 serves a pivotal role in maintaining cholesterol balance, acting as a transcription factor that controls the expression of several enzymes pivotal for cholesterol biosynthesis. Novel studies suggest that SREBP2 performs a multifaceted role in Alzheimer's disease. The hyperactivity of SREBP2 may lead to heightened cholesterol biosynthesis, which suggested association with the pathogenesis of Alzheimer's disease. Lowering SREBP2 levels in an Alzheimer's disease mouse model results in reduced production of amyloid-beta, a major contributor to Alzheimer's disease progression. Moreover, its thoroughly analyzed crystal structure allows for computer-aided screening of potential inhibitors; SREBP2 is thus selected as a prospective drug target. While more protein targets can be added onto the list in the future, this work provides an overview of key proteins involved in the regulation of brain cholesterol biosynthesis that may be further investigated for Alzheimer's disease intervention.
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Affiliation(s)
| | | | - Zuyi Huang
- Department of Chemical Engineering, Villanova University, Villanova, PA 19085, USA
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Chen D, Li J, Liu H, Liu X, Zhang C, Luo H, Wei Y, Xi Y, Liang H, Zhang Q. Genome-Wide Epistasis Study of Cerebrospinal Fluid Hyperphosphorylated Tau in ADNI Cohort. Genes (Basel) 2023; 14:1322. [PMID: 37510227 PMCID: PMC10379656 DOI: 10.3390/genes14071322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Alzheimer's disease (AD) is the main cause of dementia worldwide, and the genetic mechanism of which is not yet fully understood. Much evidence has accumulated over the past decade to suggest that after the first large-scale genome-wide association studies (GWAS) were conducted, the problem of "missing heritability" in AD is still a great challenge. Epistasis has been considered as one of the main causes of "missing heritability" in AD, which has been largely ignored in human genetics. The focus of current genome-wide epistasis studies is usually on single nucleotide polymorphisms (SNPs) that have significant individual effects, and the amount of heritability explained by which was very low. Moreover, AD is characterized by progressive cognitive decline and neuronal damage, and some studies have suggested that hyperphosphorylated tau (P-tau) mediates neuronal death by inducing necroptosis and inflammation in AD. Therefore, this study focused on identifying epistasis between two-marker interactions at marginal main effects across the whole genome using cerebrospinal fluid (CSF) P-tau as quantitative trait (QT). We sought to detect interactions between SNPs in a multi-GPU based linear regression method by using age, gender, and clinical diagnostic status (cds) as covariates. We then used the STRING online tool to perform the PPI network and identify two-marker epistasis at the level of gene-gene interaction. A total of 758 SNP pairs were found to be statistically significant. Particularly, between the marginal main effect SNP pairs, highly significant SNP-SNP interactions were identified, which explained a relatively high variance at the P-tau level. In addition, 331 AD-related genes were identified, 10 gene-gene interaction pairs were replicated in the PPI network. The identified gene-gene interactions and genes showed associations with AD in terms of neuroinflammation and neurodegeneration, neuronal cells activation and brain development, thereby leading to cognitive decline in AD, which is indirectly associated with the P-tau pathological feature of AD and in turn supports the results of this study. Thus, the results of our study might be beneficial for explaining part of the "missing heritability" of AD.
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Affiliation(s)
- Dandan Chen
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
- School of Automation Engineering, Northeast Electric Power University, Jilin 132012, China
| | - Jin Li
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Hongwei Liu
- School of Computer Science, Northeast Electric Power University, Jilin 132012, China
| | - Xiaolong Liu
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Chenghao Zhang
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Haoran Luo
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Yiming Wei
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Yang Xi
- School of Computer Science, Northeast Electric Power University, Jilin 132012, China
| | - Hong Liang
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Qiushi Zhang
- School of Computer Science, Northeast Electric Power University, Jilin 132012, China
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Li J, Capuano AW, Agarwal P, Arvanitakis Z, Wang Y, De Jager PL, Schneider JA, Tasaki S, de Paiva Lopes K, Hu FB, Bennett DA, Liang L, Grodstein F. The MIND diet, brain transcriptomic alterations, and dementia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.12.23291263. [PMID: 37398494 PMCID: PMC10312892 DOI: 10.1101/2023.06.12.23291263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Identifying novel mechanisms underlying dementia is critical to improving prevention and treatment. As an approach to mechanistic discovery, we investigated whether MIND diet (Mediterranean-DASH Diet Intervention for Neurodegenerative Delay), a consistent risk factor for dementia, is correlated with a specific profile of cortical gene expression, and whether such a transcriptomic profile is associated with dementia, in the Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP). RNA sequencing (RNA-Seq) was conducted in postmortem dorsolateral prefrontal cortex tissue from 1,204 deceased participants; neuropsychological assessments were performed annually prior to death. In a subset of 482 participants, diet was assessed ~6 years before death using a validated food-frequency questionnaire; in these participants, using elastic net regression, we identified a transcriptomic profile, consisting of 50 genes, significantly correlated with MIND diet score (P=0.001). In multivariable analysis of the remaining 722 individuals, higher transcriptomic score of MIND diet was associated with slower annual rate of decline in global cognition (β=0.011 per standard deviation increment in transcriptomic profile score, P=0.003) and lower odds of dementia (odds ratio [OR] =0.76, P=0.0002). Cortical expression of several genes appeared to mediate the association between MIND diet and dementia, including TCIM, whose expression in inhibitory neurons and oligodendrocytes was associated with dementia in a subset of 424 individuals with single-nuclei RNA-seq data. In a secondary Mendelian randomization analysis, genetically predicted transcriptomic profile score was associated with dementia (OR=0.93, P=0.04). Our study suggests that associations between diet and cognitive health may involve brain molecular alterations at the transcriptomic level. Investigating brain molecular alterations related to diet may inform the identification of novel pathways underlying dementia.
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Affiliation(s)
- Jun Li
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
- Department of Nutrition, Harvard T.H. Chan School of Public Health
| | - Ana W. Capuano
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Neurological Sciences, Rush University Medical Center
| | - Puja Agarwal
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Internal Medicine, Rush University Medical Center
| | - Zoe Arvanitakis
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Neurological Sciences, Rush University Medical Center
| | - Yanling Wang
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Neurological Sciences, Rush University Medical Center
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center
| | - Julie A. Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Neurological Sciences, Rush University Medical Center
- Department of Pathology, Rush University Medical Center
| | - Shinya Tasaki
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Neurological Sciences, Rush University Medical Center
| | - Katia de Paiva Lopes
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Neurological Sciences, Rush University Medical Center
| | - Frank B. Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health
- Department of Epidemiology, Harvard T.H. Chan School of Public Health
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
| | - David A Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Neurological Sciences, Rush University Medical Center
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health
- Department of Biostatistics, Harvard T.H. Chan School of Public Health
| | - Francine Grodstein
- Rush Alzheimer’s Disease Center, Rush University Medical Center
- Department of Internal Medicine, Rush University Medical Center
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45
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Hemedan AA, Schneider R, Ostaszewski M. Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses. FRONTIERS IN BIOINFORMATICS 2023; 3:1189723. [PMID: 37325771 PMCID: PMC10267406 DOI: 10.3389/fbinf.2023.1189723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Computational modeling has emerged as a critical tool in investigating the complex molecular processes involved in biological systems and diseases. In this study, we apply Boolean modeling to uncover the molecular mechanisms underlying Parkinson's disease (PD), one of the most prevalent neurodegenerative disorders. Our approach is based on the PD-map, a comprehensive molecular interaction diagram that captures the key mechanisms involved in the initiation and progression of PD. Using Boolean modeling, we aim to gain a deeper understanding of the disease dynamics, identify potential drug targets, and simulate the response to treatments. Our analysis demonstrates the effectiveness of this approach in uncovering the intricacies of PD. Our results confirm existing knowledge about the disease and provide valuable insights into the underlying mechanisms, ultimately suggesting potential targets for therapeutic intervention. Moreover, our approach allows us to parametrize the models based on omics data for further disease stratification. Our study highlights the value of computational modeling in advancing our understanding of complex biological systems and diseases, emphasizing the importance of continued research in this field. Furthermore, our findings have potential implications for the development of novel therapies for PD, which is a pressing public health concern. Overall, this study represents a significant step forward in the application of computational modeling to the investigation of neurodegenerative diseases, and underscores the power of interdisciplinary approaches in tackling challenging biomedical problems.
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Ehtewish H, Mesleh A, Ponirakis G, De la Fuente A, Parray A, Bensmail I, Abdesselem H, Ramadan M, Khan S, Chandran M, Ayadathil R, Elsotouhy A, Own A, Al Hamad H, Abdelalim EM, Decock J, Alajez NM, Albagha O, Thornalley PJ, Arredouani A, Malik RA, El-Agnaf OMA. Blood-Based Proteomic Profiling Identifies Potential Biomarker Candidates and Pathogenic Pathways in Dementia. Int J Mol Sci 2023; 24:ijms24098117. [PMID: 37175824 PMCID: PMC10179172 DOI: 10.3390/ijms24098117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023] Open
Abstract
Dementia is a progressive and debilitating neurological disease that affects millions of people worldwide. Identifying the minimally invasive biomarkers associated with dementia that could provide insights into the disease pathogenesis, improve early diagnosis, and facilitate the development of effective treatments is pressing. Proteomic studies have emerged as a promising approach for identifying the protein biomarkers associated with dementia. This pilot study aimed to investigate the plasma proteome profile and identify a panel of various protein biomarkers for dementia. We used a high-throughput proximity extension immunoassay to quantify 1090 proteins in 122 participants (22 with dementia, 64 with mild cognitive impairment (MCI), and 36 controls with normal cognitive function). Limma-based differential expression analysis reported the dysregulation of 61 proteins in the plasma of those with dementia compared with controls, and machine learning algorithms identified 17 stable diagnostic biomarkers that differentiated individuals with AUC = 0.98 ± 0.02. There was also the dysregulation of 153 plasma proteins in individuals with dementia compared with those with MCI, and machine learning algorithms identified 8 biomarkers that classified dementia from MCI with an AUC of 0.87 ± 0.07. Moreover, multiple proteins selected in both diagnostic panels such as NEFL, IL17D, WNT9A, and PGF were negatively correlated with cognitive performance, with a correlation coefficient (r2) ≤ -0.47. Gene Ontology (GO) and pathway analysis of dementia-associated proteins implicated immune response, vascular injury, and extracellular matrix organization pathways in dementia pathogenesis. In conclusion, the combination of high-throughput proteomics and machine learning enabled us to identify a blood-based protein signature capable of potentially differentiating dementia from MCI and cognitively normal controls. Further research is required to validate these biomarkers and investigate the potential underlying mechanisms for the development of dementia.
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Affiliation(s)
- Hanan Ehtewish
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Areej Mesleh
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Georgios Ponirakis
- Department of Medicine, Weill Cornell Medicine-Qatar, Qatar Foundation (QF), Doha P.O. Box 24144, Qatar
| | - Alberto De la Fuente
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Aijaz Parray
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation (HMC), Doha P.O. Box 3050, Qatar
| | - Ilham Bensmail
- Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Houari Abdesselem
- Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Marwan Ramadan
- Geriatric and Memory Clinic, Rumailah Hospital, Hamad Medical Corporation (HMC), Doha P.O. Box 3050, Qatar
| | - Shafi Khan
- Geriatric and Memory Clinic, Rumailah Hospital, Hamad Medical Corporation (HMC), Doha P.O. Box 3050, Qatar
| | - Mani Chandran
- Geriatric and Memory Clinic, Rumailah Hospital, Hamad Medical Corporation (HMC), Doha P.O. Box 3050, Qatar
| | - Raheem Ayadathil
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation (HMC), Doha P.O. Box 3050, Qatar
| | - Ahmed Elsotouhy
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation (HMC), Doha P.O. Box 3050, Qatar
- Department of Clinical Radiology, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha P.O. Box 24144, Qatar
| | - Ahmed Own
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation (HMC), Doha P.O. Box 3050, Qatar
- Neuroradiology Department, Hamad General Hospital, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Hanadi Al Hamad
- Geriatric and Memory Clinic, Rumailah Hospital, Hamad Medical Corporation (HMC), Doha P.O. Box 3050, Qatar
| | - Essam M Abdelalim
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Julie Decock
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Nehad M Alajez
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Omar Albagha
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Paul J Thornalley
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Abdelilah Arredouani
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Rayaz A Malik
- Department of Medicine, Weill Cornell Medicine-Qatar, Qatar Foundation (QF), Doha P.O. Box 24144, Qatar
| | - Omar M A El-Agnaf
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
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47
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Azbazdar Y, Poyraz YK, Ozalp O, Nazli D, Ipekgil D, Cucun G, Ozhan G. High-fat diet feeding triggers a regenerative response in the adult zebrafish brain. Mol Neurobiol 2023; 60:2486-2506. [PMID: 36670270 DOI: 10.1007/s12035-023-03210-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) includes a range of liver conditions ranging from excess fat accumulation to liver failure. NAFLD is strongly associated with high-fat diet (HFD) consumption that constitutes a metabolic risk factor. While HFD has been elucidated concerning its several systemic effects, there is little information about its influence on the brain at the molecular level. Here, by using a high-fat diet (HFD)-feeding of adult zebrafish, we first reveal that excess fat uptake results in weight gain and fatty liver. Prolonged exposure to HFD induces a significant increase in the expression of pro-inflammation, apoptosis, and proliferation markers in the liver and brain tissues. Immunofluorescence analyses of the brain tissues disclose stimulation of apoptosis and widespread activation of glial cell response. Moreover, glial activation is accompanied by an initial decrease in the number of neurons and their subsequent replacement in the olfactory bulb and the telencephalon. Long-term consumption of HFD causes activation of Wnt/β-catenin signaling in the brain tissues. Finally, fish fed an HFD induces anxiety, and aggressiveness and increases locomotor activity. Thus, HFD feeding leads to a non-traumatic brain injury and stimulates a regenerative response. The activation mechanisms of a regeneration response in the brain can be exploited to fight obesity and recover from non-traumatic injuries.
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Affiliation(s)
- Yagmur Azbazdar
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, 35340, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, 35340, Izmir, Turkey
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, 90095-1662, USA
| | - Yusuf Kaan Poyraz
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, 35340, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, 35340, Izmir, Turkey
| | - Ozgun Ozalp
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, 35340, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, 35340, Izmir, Turkey
- Department of Molecular Life Sciences, University of Zurich, CH-8057, Zurich, Switzerland
| | - Dilek Nazli
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, 35340, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, 35340, Izmir, Turkey
| | - Dogac Ipekgil
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, 35340, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, 35340, Izmir, Turkey
| | - Gokhan Cucun
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, 35340, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, 35340, Izmir, Turkey
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), 3640 76021, Karlsruhe, Postfach, Germany
| | - Gunes Ozhan
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, 35340, Izmir, Turkey.
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, 35340, Izmir, Turkey.
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, 35430, Izmir, Turkey.
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48
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. Neurobiol Sleep Circadian Rhythms 2023; 14:100092. [PMID: 37020466 PMCID: PMC10068260 DOI: 10.1016/j.nbscr.2023.100092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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Affiliation(s)
- Christine M. Muheim
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
- WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
| | - Kaitlyn Ford
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
| | - Elizabeth Medina
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
| | - Kristan Singletary
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
- WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
| | - Lucia Peixoto
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
| | - Marcos G. Frank
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
- WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA, 99202, USA
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Kostes WW, Brafman DA. The Multifaceted Role of WNT Signaling in Alzheimer's Disease Onset and Age-Related Progression. Cells 2023; 12:1204. [PMID: 37190113 PMCID: PMC10136584 DOI: 10.3390/cells12081204] [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: 03/05/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
The evolutionary conserved WNT signaling pathway orchestrates numerous complex biological processes during development and is critical to the maintenance of tissue integrity and homeostasis in the adult. As it relates to the central nervous system, WNT signaling plays several roles as it relates to neurogenesis, synaptic formation, memory, and learning. Thus, dysfunction of this pathway is associated with multiple diseases and disorders, including several neurodegenerative disorders. Alzheimer's disease (AD) is characterized by several pathologies, synaptic dysfunction, and cognitive decline. In this review, we will discuss the various epidemiological, clinical, and animal studies that demonstrate a precise link between aberrant WNT signaling and AD-associated pathologies. In turn, we will discuss the manner in which WNT signaling influences multiple molecular, biochemical, and cellular pathways upstream of these end-point pathologies. Finally, we will discuss how merging tools and technologies can be used to generate next generation cellular models to dissect the relationship between WNT signaling and AD.
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Affiliation(s)
| | - David A. Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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50
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Banman A, Sakhanenko NA, Kunert-Graf J, Galas DJ. ApoE Modifier Alleles for Alzheimer's Disease Discovered by Information Theory Dependency Measures: MIST Software Package. J Comput Biol 2023; 30:323-336. [PMID: 36322888 PMCID: PMC9993164 DOI: 10.1089/cmb.2022.0185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Information theory-based measures of variable dependency (previously published) have been implemented into a software package, MIST. The design of the software and its potential uses are described, and a demonstration is presented in the discovery of modifier alleles of the ApoE gene in affecting Alzheimer's disease (AD) by analyzing the UK Biobank dataset. The modifier genes uncovered overlap strongly with genes found to be associated with AD. Others include many known to influence AD. We discuss a range of uses of the dependency calculations using MIST that can uncover additional genetic effects in similar complex datasets, like higher degrees of interaction and phenotypic pleiotropy.
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Affiliation(s)
- Andrew Banman
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | | | | | - David J Galas
- Pacific Northwest Research Institute, Seattle, Washington, USA
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