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Hayat M, Syed RA, Qaiser H, Uzair M, Al-Regaiey K, Khallaf R, Albassam LAM, Kaleem I, Wang X, Wang R, Bhatti MS, Bashir S. Decoding molecular mechanisms: brain aging and Alzheimer's disease. Neural Regen Res 2025; 20:2279-2299. [PMID: 39104174 DOI: 10.4103/nrr.nrr-d-23-01403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 07/04/2024] [Indexed: 08/07/2024] Open
Abstract
The complex morphological, anatomical, physiological, and chemical mechanisms within the aging brain have been the hot topic of research for centuries. The aging process alters the brain structure that affects functions and cognitions, but the worsening of such processes contributes to the pathogenesis of neurodegenerative disorders, such as Alzheimer's disease. Beyond these observable, mild morphological shifts, significant functional modifications in neurotransmission and neuronal activity critically influence the aging brain. Understanding these changes is important for maintaining cognitive health, especially given the increasing prevalence of age-related conditions that affect cognition. This review aims to explore the age-induced changes in brain plasticity and molecular processes, differentiating normal aging from the pathogenesis of Alzheimer's disease, thereby providing insights into predicting the risk of dementia, particularly Alzheimer's disease.
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Affiliation(s)
- Mahnoor Hayat
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Rafay Ali Syed
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hammad Qaiser
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University Islamabad (IIUI), Islamabad, Pakistan
| | - Mohammad Uzair
- Department of Bioengineering, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Khalid Al-Regaiey
- Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Roaa Khallaf
- Department of Neurology, Neuroscience Center, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | | | - Imdad Kaleem
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South (COMSATS University), Islamabad, Pakistan
| | - Xueyi Wang
- Department of Psychiatry, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
- Mental Health Institute of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Ran Wang
- Department of Psychiatry, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
- Mental Health Institute of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Mehwish S Bhatti
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Shahid Bashir
- Neuroscience Center, King Fahad Specialist Hospital Dammam, Dammam, Saudi Arabia
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2
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McWilliams MM, Koohestani F, Jefferson WN, Gunewardena S, Shivashankar K, Wertenberger RA, Williams CJ, Kumar TR, Chennathukuzhi VM. Estrogen receptor alpha mediated repression of PRICKLE1 destabilizes REST and promotes uterine fibroid pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612036. [PMID: 39314474 PMCID: PMC11419101 DOI: 10.1101/2024.09.09.612036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Uterine fibroids (leiomyomas), benign tumors of the myometrial smooth muscle layer, are present in over 75% of women, often causing severe pain, menorrhagia and reproductive dysfunction. The molecular pathogenesis of fibroids is poorly understood. We previously showed that the loss of REST (RE-1 Silencing Transcription factor), a tumor suppressor, in fibroids leads to activation of PI3K/AKT-mTOR pathway. We report here a critical link between estrogen receptor alpha (ERα) and the loss of REST, via PRICKLE1. PRICKLE1 expression is markedly lower in leiomyomas, and the suppression of PRICKLE1 significantly down regulates REST protein levels. Conversely, overexpression of PRICKLE1 resulted in the restoration of REST in cultured primary leiomyoma smooth muscle cells (LSMCs). Crucially, mice exposed neonatally to environmental estrogens, proven risk factors for fibroids, expressed lower levels of PRICKLE1 and REST in the myometrium. Using mice that lack either endogenous estrogen (Lhb -/- mice) or ERα (Esr1 -/- mice), we demonstrate that Prickle1 expression in the myometrium is suppressed by estrogen through ERα. Enhancer of zeste homolog 2 (EZH2) is known to participate in the repression of specific ERα target genes. Uterine leiomyomas express increased levels of EZH2 that inversely correlate with the expression of PRICKLE1. Using chromatin immunoprecipitation, we provide evidence for association of EZH2 with the PRICKLE1 promoter and for hypermethylation of H3K27 within the regulatory region of PRICKLE1 in leiomyomas. Additionally, siRNA mediated knockdown of EZH2 leads to restoration of PRICKLE1 in LSMCs. Collectively, our results identify a novel link between estrogen exposure and PRICKLE1/REST-regulated tumorigenic pathways in leiomyomas.
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Affiliation(s)
- Michelle M McWilliams
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Faezeh Koohestani
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Wendy N Jefferson
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Sumedha Gunewardena
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Kavya Shivashankar
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Riley A Wertenberger
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - T Rajendra Kumar
- Division of Reproductive Sciences, Department of Obstetrics & Gynecology, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO 80045
| | - Vargheese M Chennathukuzhi
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
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Zeng W, Dou Y, Pan L, Xu L, Peng S. Improving prediction performance of general protein language model by domain-adaptive pretraining on DNA-binding protein. Nat Commun 2024; 15:7838. [PMID: 39244557 PMCID: PMC11380688 DOI: 10.1038/s41467-024-52293-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 08/29/2024] [Indexed: 09/09/2024] Open
Abstract
DNA-protein interactions exert the fundamental structure of many pivotal biological processes, such as DNA replication, transcription, and gene regulation. However, accurate and efficient computational methods for identifying these interactions are still lacking. In this study, we propose a method ESM-DBP through refining the DNA-binding protein sequence repertory and domain-adaptive pretraining based the general protein language model. Our method considers the lacking exploration of general language model for DNA-binding protein domain-specific knowledge, so we screen out 170,264 DNA-binding protein sequences to construct the domain-adaptive language model. Experimental results on four downstream tasks show that ESM-DBP provides a better feature representation of DNA-binding protein compared to the original language model, resulting in improved prediction performance and outperforming the state-of-the-art methods. Moreover, ESM-DBP can still perform well even for those sequences with only a few homologous sequences. ChIP-seq on two predicted cases further support the validity of the proposed method.
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Affiliation(s)
- Wenwu Zeng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Yutao Dou
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Liangrui Pan
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Liwen Xu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
| | - Shaoliang Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
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Sarahian N, Khodagholi F, Valian N, Ahmadiani A. Interplay of MeCP2/REST/Synaptophysin-BDNF and intranasal oxytocin influence on Aβ-induced memory and cognitive impairments. Behav Brain Res 2024; 476:115235. [PMID: 39236931 DOI: 10.1016/j.bbr.2024.115235] [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: 05/07/2024] [Revised: 09/01/2024] [Accepted: 09/01/2024] [Indexed: 09/07/2024]
Abstract
BACKGROUND Alzheimer's disease (AD) is linked to the accumulation of Aβ, increased tau hyperphosphorylation, persistent neuroinflammation, and a decline in neurotrophic factors, neurogenesis, and synaptic plasticity. Oxytocin (OT) has a significant impact on memory and learning. We examined the influence of intranasal (IN) OT on synaptic plasticity, neurogenesis, histone acetylation, and spatial and cognitive memories in rats. METHODS Aβ25-35 (5 µg/2.5 µl) was administered bilaterally in the CA1 of male Wistar rats for four consecutive days. After seven days of recovery, OT (2 µg/µl, 10 µl in each nostril) was administered IN for seven consecutive days. Working, spatial, and cognitive memories, and gene expression of neurogenesis- and synaptic plasticity-involved factors were measured in the hippocampus. Histone acetylation (H3K9 and H4K8) was also measured using western blotting. RESULTS IN administration of OT significantly improved working and spatial memory impairment induced by Aβ and increased the factors involved in synaptic plasticity (MeCP2, REST, synaptophysin, and BDNF) and neurogenesis (Ki67 and DCX). We also found an enhancement in the levels of H3K9ac and H4K8ac following OT administration. CONCLUSION These findings indicated that IN OT could improve hippocampus-related behaviors by increasing synaptic plasticity, stimulating neurogenesis, and chromatin plasticity.
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Affiliation(s)
- Nahid Sarahian
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Fariba Khodagholi
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Neda Valian
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran.
| | - Abolhassan Ahmadiani
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran.
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Logan IE, Nguyen KT, Chatterjee T, Manivannan B, Paul NP, Kim SR, Sixta EM, Bastian LP, Marean-Reardon C, Karajannis MA, Fernández-Valle C, Estevez AG, Franco MC. Selective nitration of Hsp90 acts as a metabolic switch promoting tumor cell proliferation. Redox Biol 2024; 75:103249. [PMID: 38945076 PMCID: PMC11261529 DOI: 10.1016/j.redox.2024.103249] [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: 05/21/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024] Open
Abstract
Tumors develop in an oxidative environment characterized by peroxynitrite production and downstream protein tyrosine (Y) nitration. We showed that tyrosine nitration supports schwannoma cell proliferation and regulates cell metabolism in the inheritable tumor disorder NF2-related Schwannomatosis (NF2-SWN). Here, we identified the chaperone Heat shock protein 90 (Hsp90) as the first nitrated protein that acts as a metabolic switch to promote schwannoma cell proliferation. Doubling the endogenous levels of nitrated Hsp90 in schwannoma cells or supplementing nitrated Hsp90 into normal Schwann cells increased their proliferation. Metabolically, nitration on either Y33 or Y56 conferred Hsp90 distinct functions; nitration at Y33 (Hsp90NY33) down-regulated mitochondrial oxidative phosphorylation, while nitration at Y56 (Hsp90NY56) increased glycolysis by activating the purinergic receptor P2X7 in both schwannoma and normal Schwann cells. Hsp90NY33 and Hsp90NY56 showed differential subcellular and spatial distribution corresponding with their metabolic and proliferative functions in schwannoma three-dimensional cell culture models. Collectively, these results underscore the role of tyrosine nitration as a post-translational modification regulating critical cellular processes. Nitrated proteins, particularly nitrated Hsp90, emerge as a novel category of tumor-directed therapeutic targets.
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Affiliation(s)
- Isabelle E Logan
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA; Center for Translational Science, Florida International University, Florida, 34987, USA
| | - Kyle T Nguyen
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Tilottama Chatterjee
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA
| | | | - Ngozi P Paul
- Center for Translational Science, Florida International University, Florida, 34987, USA
| | - Sharon R Kim
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Evelyn M Sixta
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Lydia P Bastian
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Carrie Marean-Reardon
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Cristina Fernández-Valle
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Alvaro G Estevez
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA; Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, Florida, 33199, USA
| | - Maria Clara Franco
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, 97331, USA; Center for Translational Science, Florida International University, Florida, 34987, USA; Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, Florida, 33199, USA.
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Pajarillo E, Kim S, Digman A, Ajayi I, Nyarko-Danquah I, Son DS, Aschner M, Lee E. Dopaminergic REST/NRSF is protective against manganese-induced neurotoxicity in mice. J Biol Chem 2024; 300:107707. [PMID: 39178947 PMCID: PMC11421342 DOI: 10.1016/j.jbc.2024.107707] [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: 03/05/2024] [Revised: 07/23/2024] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
Chronic exposure to elevated levels of manganese (Mn) may cause a neurological disorder referred to as manganism. The transcription factor REST is dysregulated in several neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. REST upregulated tyrosine hydroxylase and induced protection against Mn toxicity in neuronal cultures. In the present study, we investigated if dopaminergic REST plays a critical role in protecting against Mn-induced toxicity in vivo using dopaminergic REST conditional knockout (REST-cKO) mice and REST loxP mice as wild-type (WT) controls. Restoration of REST in the substantia nigra (SN) with neuronal REST AAV vector infusion was performed to further support the role of REST in Mn toxicity. Mice were exposed to Mn (330 μg, intranasal, daily for 3 weeks), followed by behavioral tests and molecular biology experiments. Results showed that Mn decreased REST mRNA/protein levels in the SN-containing midbrain, as well as locomotor activity and motor coordination in WT mice, which were further decreased in REST-cKO mice. Mn-induced mitochondrial insults, such as impairment of fission/fusion and mitophagy, apoptosis, and oxidative stress, in the midbrain of WT mice were more pronounced in REST-cKO mice. However, REST restoration in the SN of REST-cKO mice attenuated Mn-induced neurotoxicity. REST's molecular target for its protection is unclear, but REST attenuated Mn-induced mitochondrial dysregulation, indicating that it is a primary intracellular target for both Mn and REST. These novel findings suggest that dopaminergic REST in the nigrostriatal pathway is critical in protecting against Mn toxicity, underscoring REST as a potential therapeutic target for treating manganism.
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Affiliation(s)
- Edward Pajarillo
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Sanghoon Kim
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Alexis Digman
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Itunu Ajayi
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Ivan Nyarko-Danquah
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Deok-Soo Son
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, New York, USA
| | - Eunsook Lee
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA.
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Duan RN, Liu A, Sun YQ, Xie YF, Wei SJ, Gao S, Liu YM, Li X, Sun WJ, Li JX, Yan CZ, Liu QJ. Loss of Smek1 Induces Tauopathy and Triggers Neurodegeneration by Regulating Microtubule Stability. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400584. [PMID: 39206808 DOI: 10.1002/advs.202400584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/22/2024] [Indexed: 09/04/2024]
Abstract
Suppressor of Mek1 (Smek1) is a regulatory subunit of protein phosphatase 4. Genome-wide association studies have shown the protective effect of SMEK1 in Alzheimer's disease (AD). However, the physiological and pathological roles of Smek1 in AD and other tauopathies are largely unclear. Here, the role of Smek1 in preventing neurodegeneration is investigated in tauopathy. Smek1 is downregulated in the aged human brain. Through single-cell sequencing, a novel neuronal cluster is identified that possesses neurodegenerative characteristics in Smek1-/- mice. Smek1 deficiency caused markedly more severe motor and cognitive impairments in mice, as well as neuronal loss, gliosis, and tau hyperphosphorylation at major glycogen synthase kinase 3β (Gsk3β) sites. Protein-protein interaction analysis revealed that the Ran-binding domain (RanBD) in the N-terminus of Smek1 facilitated binding with kinesin family member 2A (Kif2a). Depletion of Smek1 resulted in cytoplasmic aggregation of Kif2a, axon outgrowth defects, and impaired mitochondrial axonal trafficking. Downregulation of Kif2a markedly attenuated tau hyperphosphorylation and axon outgrowth defects in shSmek1 cells. For the first time, this study demonstrates that Smek1 deficiency progressively induces neurodegeneration by exacerbating tau pathology and mitochondrial dysfunction in an age-dependent manner.
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Affiliation(s)
- Ruo-Nan Duan
- Department of Neurology, Research Institute of Neuromuscular and Neurodegenerative Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107 West Wenhua Road, Jinan, Shandong, 250012, China
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Ai Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Yue-Qing Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Yun-Fang Xie
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Shi-Jun Wei
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Shang Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Yi-Ming Liu
- Department of Neurology, Research Institute of Neuromuscular and Neurodegenerative Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Xi Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Wen-Jie Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Jiang-Xia Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong, 250012, China
| | - Chuan-Zhu Yan
- Department of Neurology, Research Institute of Neuromuscular and Neurodegenerative Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107 West Wenhua Road, Jinan, Shandong, 250012, China
- Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, 266000, China
| | - Qi-Ji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Shandong University, School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266071, China
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Kitani A, Matsui Y. Predicting Alzheimer's Cognitive Resilience Score: A Comparative Study of Machine Learning Models Using RNA-seq Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.25.609610. [PMID: 39253457 PMCID: PMC11383294 DOI: 10.1101/2024.08.25.609610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Alzheimer's disease (AD) is an important research topic. While amyloid plaques and neurofibrillary tangles are hallmark pathological features of AD, cognitive resilience (CR) is a phenomenon where cognitive function remains preserved despite the presence of these pathological features. This study aimed to construct and compare predictive machine learning models for CR scores using RNA-seq data from the Religious Orders Study and Memory and Aging Project (ROSMAP) and Mount Sinai Brain Bank (MSBB) cohorts. We evaluated support vector regression (SVR), random forest, XGBoost, linear, and transformer-based models. The SVR model exhibited the best performance, with contributing genes identified using Shapley additive explanations (SHAP) scores, providing insights into biological pathways associated with CR. Finally, we developed a tool called the resilience gene analyzer (REGA), which visualizes SHAP scores to interpret the contributions of individual genes to CR. REGA is available at https://igcore.cloud/GerOmics/REsilienceGeneAnalyzer/.
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Affiliation(s)
- Akihiro Kitani
- Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Matsui
- Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, 461-8673 Nagoya, Aichi, Japan
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9
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Taylor CA, Maor-Nof M, Metzl-Raz E, Hidalgo A, Yee C, Gitler AD, Shen K. Histone deacetylase inhibition expands cellular proteostasis repertoires to enhance neuronal stress resilience. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.608176. [PMID: 39229034 PMCID: PMC11370365 DOI: 10.1101/2024.08.21.608176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Neurons are long-lived, terminally differentiated cells with limited regenerative capacity. Cellular stressors such as endoplasmic reticulum (ER) protein folding stress and membrane trafficking stress accumulate as neurons age and accompany age-dependent neurodegeneration. Current strategies to improve neuronal resilience are focused on using factors to reprogram neurons or targeting specific proteostasis pathways. We discovered a different approach. In an unbiased screen for modifiers of neuronal membrane trafficking defects, we unexpectedly identified a role for histone deacetylases (HDACs) in limiting cellular flexibility in choosing cellular pathways to respond to diverse types of stress. Genetic or pharmacological inactivation of HDACs resulted in improved neuronal health in response to ER protein folding stress and endosomal membrane trafficking stress in C. elegans and mammalian neurons. Surprisingly, HDAC inhibition enabled neurons to activate latent proteostasis pathways tailored to the nature of the individual stress, instead of generalized transcriptional upregulation. These findings shape our understanding of neuronal stress responses and suggest new therapeutic strategies to enhance neuronal resilience.
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Affiliation(s)
- Caitlin A Taylor
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
| | - Maya Maor-Nof
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
| | - Eyal Metzl-Raz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron Hidalgo
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, 94158, USA
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
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10
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Navakkode S, Kennedy BK. Neural ageing and synaptic plasticity: prioritizing brain health in healthy longevity. Front Aging Neurosci 2024; 16:1428244. [PMID: 39161341 PMCID: PMC11330810 DOI: 10.3389/fnagi.2024.1428244] [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: 05/06/2024] [Accepted: 07/24/2024] [Indexed: 08/21/2024] Open
Abstract
Ageing is characterized by a gradual decline in the efficiency of physiological functions and increased vulnerability to diseases. Ageing affects the entire body, including physical, mental, and social well-being, but its impact on the brain and cognition can have a particularly significant effect on an individual's overall quality of life. Therefore, enhancing lifespan and physical health in longevity studies will be incomplete if cognitive ageing is over looked. Promoting successful cognitive ageing encompasses the objectives of mitigating cognitive decline, as well as simultaneously enhancing brain function and cognitive reserve. Studies in both humans and animal models indicate that cognitive decline related to normal ageing and age-associated brain disorders are more likely linked to changes in synaptic connections that form the basis of learning and memory. This activity-dependent synaptic plasticity reorganises the structure and function of neurons not only to adapt to new environments, but also to remain robust and stable over time. Therefore, understanding the neural mechanisms that are responsible for age-related cognitive decline becomes increasingly important. In this review, we explore the multifaceted aspects of healthy brain ageing with emphasis on synaptic plasticity, its adaptive mechanisms and the various factors affecting the decline in cognitive functions during ageing. We will also explore the dynamic brain and neuroplasticity, and the role of lifestyle in shaping neuronal plasticity.
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Affiliation(s)
- Sheeja Navakkode
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, Centre for Healthy Longevity, National University Health System, National University of Singapore, Singapore, Singapore
- Life Sciences Institute Neurobiology Programme, Centre for Life Sciences, National University of Singapore, Singapore, Singapore
| | - Brian K. Kennedy
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, Centre for Healthy Longevity, National University Health System, National University of Singapore, Singapore, Singapore
- Life Sciences Institute Neurobiology Programme, Centre for Life Sciences, National University of Singapore, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Departments of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Buck Institute for Research on Ageing, Novato, CA, United States
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11
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Latimer CS, Prater KE, Postupna N, Dirk Keene C. Resistance and Resilience to Alzheimer's Disease. Cold Spring Harb Perspect Med 2024; 14:a041201. [PMID: 38151325 PMCID: PMC11293546 DOI: 10.1101/cshperspect.a041201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Dementia is a significant public health crisis; the most common underlying cause of age-related cognitive decline and dementia is Alzheimer's disease neuropathologic change (ADNC). As such, there is an urgent need to identify novel therapeutic targets for the treatment and prevention of the underlying pathologic processes that contribute to the development of AD dementia. Although age is the top risk factor for dementia in general and AD specifically, these are not inevitable consequences of advanced age. Some individuals are able to live to advanced age without accumulating significant pathology (resistance to ADNC), whereas others are able to maintain cognitive function despite the presence of significant pathology (resilience to ADNC). Understanding mechanisms of resistance and resilience will inform therapeutic strategies to promote these processes to prevent or delay AD dementia. This article will highlight what is currently known about resistance and resilience to AD, including our current understanding of possible underlying mechanisms that may lead to candidate preventive and treatment interventions for this devastating neurodegenerative disease.
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Affiliation(s)
- Caitlin S Latimer
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle 98195, Washington, USA
| | - Katherine E Prater
- Department of Neurology, University of Washington, Seattle 98195, Washington, USA
| | - Nadia Postupna
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle 98195, Washington, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle 98195, Washington, USA
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12
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Chujan S, Cholpraipimolrat W, Satayavivad J. Integrated Transcriptomics and Network Analysis Identified Altered Neural Mechanisms in Frontal Aging Brain-Associated Alzheimer's Disease. Biochem Genet 2024; 62:2382-2398. [PMID: 37934339 DOI: 10.1007/s10528-023-10549-9] [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: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease. The late stage of AD typically develops after 60 years of age and AD pathogenesis can be detected predominately in the frontal lobe, which is responsible for memory. Multiple alterations in cellular mechanisms have been associated with AD, but there is no clear information on AD pathogenesis during brain aging. This study aimed to explore the differentially expressed genes (DEGs) in the frontal lobe of aging brains and to identify shared crucial mechanisms in the aging brain linked to AD pathogenesis. Three datasets were downloaded from the Gene Expression Omnibus (GEO). Biological function analysis was performed by DAVID and KEGG databases. An AD patient's cohort (GSE150696) was collected for verification of the enriched pathway. The results demonstrated that multiple neurochemical synapsis and regulation of the cytoskeleton are linked to AD pathogenesis during aging. Taken together, this study contributes to our further understanding of neural alterations during aging in AD that could be used to develop therapeutics for early intervention to prevent or slow progression.
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Affiliation(s)
- Suthipong Chujan
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, 10400, Thailand
| | | | - Jutamaad Satayavivad
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, 10400, Thailand.
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13
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Dash BP, Freischmidt A, Weishaupt JH, Hermann A. An integrative miRNA-mRNA expression analysis identifies miRNA signatures associated with SOD1 and TARDBP patient-derived motor neurons. Hum Mol Genet 2024; 33:1300-1314. [PMID: 38676626 DOI: 10.1093/hmg/ddae072] [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: 01/28/2024] [Revised: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
MicroRNAs (miRNAs) are a subset of small non-coding single-stranded RNA molecules involved in the regulation of post-transcriptional gene expression of a variety of transcript targets. Therefore altered miRNA expression may result in the dysregulation of key genes and biological pathways that has been reported with the onset and progression of neurodegenerative diseases, such as Amyotrophic lateral sclerosis (ALS). ALS is marked by a progressive degeneration of motor neurons (MNs) present in the spinal cord, brain stem and motor cortex. Although the pathomechanism underlying molecular interactions of ALS remains poorly understood, alterations in RNA metabolism, including dysregulation of miRNA expression in familial as well as sporadic forms are still scarcely studied. In this study, we performed combined transcriptomic data and miRNA profiling in MN samples of the same samples of iPSC-derived MNs from SOD1- and TARDBP (TDP-43 protein)-mutant-ALS patients and healthy controls. We report a global upregulation of mature miRNAs, and suggest that differentially expressed (DE) miRNAs have a significant impact on mRNA-level in SOD1-, but not in TARDBP-linked ALS. Furthermore, in SOD1-ALS we identified dysregulated miRNAs such as miR-124-3p, miR-19b-3p and miR-218 and their potential targets previously implicated in important functional process and pathogenic pathways underlying ALS. These miRNAs may play key roles in the neuronal development and cell survival related functions in SOD1-ALS. Altogether, we provide evidence of miRNA regulated genes expression mainly in SOD1 rather than TDP43-ALS.
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Affiliation(s)
- Banaja P Dash
- Translational Neurodegeneration Section "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, Gehlsheimer Str. 20, Rostock 18147, Germany
| | - Axel Freischmidt
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Jochen H Weishaupt
- Division of Neurodegeneration, Department of Neurology, Mannheim Center for Translational Neurosciences, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, Mannheim 68167, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, Gehlsheimer Str. 20, Rostock 18147, Germany
- Center for Transdisciplinary Neurosciences Rostock, University Medical Center Rostock, Gehlsheimer Str. 20, Rostock 18147, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald, Gehlsheimer Str. 20, Rostock 18147, Germany
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14
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Griñán-Ferré C, Bellver-Sanchis A, Guerrero A, Pallàs M. Advancing personalized medicine in neurodegenerative diseases: The role of epigenetics and pharmacoepigenomics in pharmacotherapy. Pharmacol Res 2024; 205:107247. [PMID: 38834164 DOI: 10.1016/j.phrs.2024.107247] [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: 02/16/2024] [Revised: 04/23/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
About 80 % of brain disorders have a genetic basis. The pathogenesis of most neurodegenerative diseases is associated with a myriad of genetic defects, epigenetic alterations (DNA methylation, histone/chromatin remodeling, miRNA dysregulation), and environmental factors. The emergence of new sequencing technologies and tools to study the epigenome has led to identifying predictive biomarkers for earlier diagnosis, opening up the possibility of prophylactical interventions. As a result, advances in pharmacogenetics and pharmacoepigenomics now allow for personalized treatments based on the profile of each patient and the specific genetic and epigenetic mechanisms involved. This Review highlights the complexity of neurodegenerative diseases and the variability in patient responses to pharmacotherapy, emphasizing the influence of genetic polymorphisms on the pharmacokinetics and pharmacodynamics of drugs used to treat those conditions. We specifically discuss the potential modulatory effect of several genetic polymorphisms associated with an increased risk of developing different neurodegenerative diseases. We explore genetic and genomic technologies and the potential of analyzing individual-specific drug metabolism to predict and influence drug response and associated clinical outcomes. We also provide insights into the mechanism of action of the drugs under investigation and their potential impact on disease-modifying pathways. Finally, the Review underscores the great potential of this field to enhance the effectiveness and safety of drug treatments through personalized medicine.
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Affiliation(s)
- Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
| | - Aina Bellver-Sanchis
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain
| | - Ana Guerrero
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain
| | - Mercè Pallàs
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
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15
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Maksour S, Ng N, Hulme AJ, Miellet S, Engel M, Muñoz SS, Balez R, Rollo B, Finol-Urdaneta RK, Ooi L, Dottori M. REST and RCOR genes display distinct expression profiles in neurons and astrocytes using 2D and 3D human pluripotent stem cell models. Heliyon 2024; 10:e32680. [PMID: 38975076 PMCID: PMC11226837 DOI: 10.1016/j.heliyon.2024.e32680] [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: 11/29/2023] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/09/2024] Open
Abstract
Repressor element-1 silencing transcription factor (REST) is a transcriptional repressor involved in neurodevelopment and neuroprotection. REST forms a complex with the REST corepressors, CoREST1, CoREST2, or CoREST3 (encoded by RCOR1, RCOR2, and RCOR3, respectively). Emerging evidence suggests that the CoREST family can target unique genes independently of REST, in various neural and glial cell types during different developmental stages. However, there is limited knowledge regarding the expression and function of the CoREST family in human neurodevelopment. To address this gap, we employed 2D and 3D human pluripotent stem cell (hPSC) models to investigate REST and RCOR gene expression levels. Our study revealed a significant increase in RCOR3 expression in glutamatergic cortical and GABAergic ventral forebrain neurons, as well as mature functional NGN2-induced neurons. Additionally, a simplified astrocyte transdifferentiation protocol resulted in a significant decrease in RCOR2 expression following differentiation. REST expression was notably reduced in mature neurons and cerebral organoids. In summary, our findings provide the first insights into the cell-type-specific expression patterns of RCOR genes in human neuronal and glial differentiation. Specifically, RCOR3 expression increases in neurons, while RCOR2 levels decrease in astrocytes. The dynamic expression patterns of REST and RCOR genes during hPSC neuronal and glial differentiation underscore the potential distinct roles played by REST and CoREST proteins in regulating the development of these cell types in humans.
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Affiliation(s)
- Simon Maksour
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Neville Ng
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Amy J. Hulme
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Sara Miellet
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Martin Engel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Sonia Sanz Muñoz
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Rachelle Balez
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Ben Rollo
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Rocio K. Finol-Urdaneta
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Lezanne Ooi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Mirella Dottori
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
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16
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Singh PP, Reeves GA, Contrepois K, Papsdorf K, Miklas JW, Ellenberger M, Hu CK, Snyder MP, Brunet A. Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape. Cell 2024; 187:3338-3356.e30. [PMID: 38810644 DOI: 10.1016/j.cell.2024.04.048] [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: 11/24/2021] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.
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Affiliation(s)
| | - G Adam Reeves
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | | | - Jason W Miklas
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA; Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
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17
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Singh A, Cheng D, Swaminathan J, Yang Y, Zheng Y, Gordon N, Gopalakrishnan V. REST-dependent downregulation of von Hippel-Lindau tumor suppressor promotes autophagy in SHH-medulloblastoma. Sci Rep 2024; 14:13596. [PMID: 38866867 PMCID: PMC11169471 DOI: 10.1038/s41598-024-63371-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
The RE1 silencing transcription factor (REST) is a driver of sonic hedgehog (SHH) medulloblastoma genesis. Our previous studies showed that REST enhances cell proliferation, metastasis and vascular growth and blocks neuronal differentiation to drive progression of SHH medulloblastoma tumors. Here, we demonstrate that REST promotes autophagy, a pathway that is found to be significantly enriched in human medulloblastoma tumors relative to normal cerebella. In SHH medulloblastoma tumor xenografts, REST elevation is strongly correlated with increased expression of the hypoxia-inducible factor 1-alpha (HIF1α)-a positive regulator of autophagy, and with reduced expression of the von Hippel-Lindau (VHL) tumor suppressor protein - a component of an E3 ligase complex that ubiquitinates HIF1α. Human SHH-medulloblastoma tumors with higher REST expression exhibit nuclear localization of HIF1α, in contrast to its cytoplasmic localization in low-REST tumors. In vitro, REST knockdown promotes an increase in VHL levels and a decrease in cytoplasmic HIF1α protein levels, and autophagy flux. In contrast, REST elevation causes a decline in VHL levels, as well as its interaction with HIF1α, resulting in a reduction in HIF1α ubiquitination and an increase in autophagy flux. These data suggest that REST elevation promotes autophagy in SHH medulloblastoma cells by modulating HIF1α ubiquitination and stability in a VHL-dependent manner. Thus, our study is one of the first to connect VHL to REST-dependent control of autophagy in a subset of medulloblastomas.
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Affiliation(s)
- Ashutosh Singh
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 853, Houston, TX, 77030, USA
| | - Donghang Cheng
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 853, Houston, TX, 77030, USA
| | - Jyothishmathi Swaminathan
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 853, Houston, TX, 77030, USA
| | - Yanwen Yang
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 853, Houston, TX, 77030, USA
| | - Yan Zheng
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 853, Houston, TX, 77030, USA
| | - Nancy Gordon
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 853, Houston, TX, 77030, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 853, Houston, TX, 77030, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
- Brain Tumor Center, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
- The University of Texas MD Anderson Cancer Center and UTHealth Graduate School for Biomedical Sciences, 6767 Bertner Ave, S3.8344 Mitchell BSRB, Houston, TX, 77030, USA.
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18
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Buck SA, Mabry SJ, Glausier JR, Banks-Tibbs T, Ward C, Kozel JG, Fu C, Fish KN, Lewis DA, Logan RW, Freyberg Z. Aging disrupts the coordination between mRNA and protein expression in mouse and human midbrain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596950. [PMID: 38854057 PMCID: PMC11160743 DOI: 10.1101/2024.06.01.596950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Age-related dopamine (DA) neuron loss is a primary feature of Parkinson's disease. However, it remains unclear whether similar biological processes occur during healthy aging, albeit to a lesser degree. We therefore determined whether midbrain DA neurons degenerate during aging in mice and humans. In mice, we identified no changes in midbrain neuron numbers throughout aging. Despite this, we found age-related decreases in midbrain mRNA expression of tyrosine hydroxylase (Th), the rate limiting enzyme of DA synthesis. Among midbrain glutamatergic cells, we similarly identified age-related declines in vesicular glutamate transporter 2 (Vglut2) mRNA expression. In co-transmitting Th +/Vglut2 + neurons, Th and Vglut2 transcripts decreased with aging. Importantly, striatal Th and Vglut2 protein expression remained unchanged. In translating our findings to humans, we found no midbrain neurodegeneration during aging and identified age-related decreases in TH and VGLUT2 mRNA expression similar to mouse. Unlike mice, we discovered diminished density of striatal TH+ dopaminergic terminals in aged human subjects. However, TH and VGLUT2 protein expression were unchanged in the remaining striatal boutons. Finally, in contrast to Th and Vglut2 mRNA, expression of most ribosomal genes in Th + neurons was either maintained or even upregulated during aging. This suggests a homeostatic mechanism where age-related declines in transcriptional efficiency are overcome by ongoing ribosomal translation. Overall, we demonstrate species-conserved transcriptional effects of aging in midbrain dopaminergic and glutamatergic neurons that are not accompanied by marked cell death or lower striatal protein expression. This opens the door to novel therapeutic approaches to maintain neurotransmission and bolster neuronal resilience.
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Affiliation(s)
- Silas A. Buck
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samuel J. Mabry
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jill R. Glausier
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tabitha Banks-Tibbs
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Caroline Ward
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jenesis Gayden Kozel
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chen Fu
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kenneth N. Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A. Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan W. Logan
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
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19
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Gao F, Zhang Z, Xue N, Ma Y, Jiao J, Wang C, Zhang K, Lin Y, Li S, Guo Z, An J, Wang P, Xu B, Lei H. Identification of a novel oligopeptide from defatted walnut meal hydrolysate as a potential neuroprotective agent. Food Funct 2024; 15:5566-5578. [PMID: 38712886 DOI: 10.1039/d3fo05501a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Free radical damage and oxidative stress are thought to play a crucial role in the development of neurodegenerative diseases. Walnut peptides, especially walnut oligopeptides, have been shown to protect nerve cells from oxidative stress and inflammatory damage, as well as improve memory function. In this study, walnut peptides were obtained from walnut meal through enzymatic hydrolysis, ultrafiltration, and gel filtration chromatography. A novel oligopeptide called AQ was successfully isolated and its chemical structure was identified as AASCDQ using ESI-MS/MS. AQ demonstrated remarkable scavenging activity against O2- free radicals (81.00%), DPPH free radicals (79.40%), and ABTS free radicals (67.09%) at a concentration of 1 mg mL-1. Furthermore, AQ exhibited strong neuroprotective effects against hydrogen peroxide-induced damage in SH-SY5Y cells, reducing cell injury and apoptosis. AQ also effectively inhibited the secretion of pro-inflammatory factors NO (IC50 = 46.03 ± 0.32 μM) and suppressed the expression of IL-6 and TNF-α in RAW264.7 cells stimulated by LPS. In vivo experiments demonstrated that AQ promoted angiogenesis in the quail chick chorioallantoic membrane assay and reduced ROS accumulation in Caenorhabditis elegans, thereby extending its lifespan. The anti-inflammatory mechanism of AQ was further confirmed by western blotting. In summary, the novel oligopeptide AQ possesses potential neuroprotective effects, including antioxidant, anti-inflammatory, angiogenic, and anti-aging properties, making it a promising candidate for the development of functional foods and pharmaceutical products.
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Affiliation(s)
- Feng Gao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Zixuan Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Nannan Xue
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Yunnan Ma
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Jingyi Jiao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Cheng Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Keyi Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Yixuan Lin
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Shanlan Li
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Zhuoqian Guo
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Jin An
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Penglong Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Bing Xu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
| | - Haimin Lei
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102400, China.
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20
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Shmal D, Mantero G, Floss T, Benfenati F, Maya-Vetencourt JF. Restoring vision in adult amblyopia by enhancing plasticity through deletion of the transcriptional repressor REST. iScience 2024; 27:109507. [PMID: 38591011 PMCID: PMC11000024 DOI: 10.1016/j.isci.2024.109507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Visual cortical plasticity is high during early life, but gradually decreases with development. This is due to the Otx2-driven maturation of intracortical inhibition that parallels the condensation of extracellular matrix components into perineuronal nets mainly around parvalbumin-positive GABAergic neurons. Repressor Element 1 Silencing Transcription (REST) epigenetically controls the expression of a plethora of neuron-specific genes. We demonstrate that the conditional knockout of REST in the primary visual cortex of adult mice induces a shift of ocular dominance after short-term monocular deprivation and promotes the recovery of vision in long-term deprived animals after reverse suture. These phenomena paralleled a reduction of perineuronal net density and increased expression of REST target genes, but not of the homeoprotein Otx2 in the visual cortex contralateral to the deprived eye. This shows that REST regulates adult visual cortical plasticity and is a potential therapeutic target to restore vision in adult amblyopia by enhancing V1 plasticity.
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Affiliation(s)
- Dmytro Shmal
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Giulia Mantero
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Thomas Floss
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - José Fernando Maya-Vetencourt
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Biology, University of Pisa, Pisa, Italy
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21
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Choi J, Lee EA. Analysis of REST binding sites with canonical and non-canonical motifs in human cell lines. BMC Med Genomics 2024; 17:92. [PMID: 38632583 PMCID: PMC11025195 DOI: 10.1186/s12920-024-01860-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Repressor element 1 (RE1) silencing transcription factor (REST) is a transcriptional repressor abundantly expressed in aging human brains. It is known to regulate genes associated with oxidative stress, inflammation, and neurological disorders by binding to a canonical form of sequence motif and its non-canonical variations. Although analysis of genomic sequence motifs is crucial to understand transcriptional regulation by transcription factors (TFs), a comprehensive characterization of various forms of RE1 motifs in human cell lines has not been performed. RESULTS Here, we analyzed 23 ENCODE REST ChIP-seq datasets from diverse human cell lines and identified a non-redundant set of 68,975 loci with ChIP-seq peaks. Our systematic characterization of these binding sites revealed that the canonical form of REST binding motif was found primarily in ChIP-seq peaks shared across multiple cell lines, while non-canonical forms of motifs were identified in both cell-line-specific binding sites and those shared across cell lines. Remarkably, we observed a notable prevalence of non-canonical motifs that corresponded to half segments of the canonical motif. Furthermore, our analysis unveiled the presence of cell-line-specific REST binding patterns, as evidenced by the clustering of ChIP-seq experiments according to their respective cell lines. This observation underscores the cell-line specificity of REST binding at certain genomic loci, implying intricate cell-line-specific regulatory mechanisms. CONCLUSIONS Overall, our study provides a comprehensive characterization of REST binding motifs in human cell lines and genome-wide RE1 motif profiles. These findings contribute to a deeper understanding of REST-mediated transcriptional regulation and highlight the importance of considering cell-line-specific effects in future investigations.
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Affiliation(s)
- Jaejoon Choi
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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22
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Kumar NH, Kluever V, Barth E, Krautwurst S, Furlan M, Pelizzola M, Marz M, Fornasiero EF. Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain. Nucleic Acids Res 2024; 52:2865-2885. [PMID: 38471806 PMCID: PMC11014377 DOI: 10.1093/nar/gkae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/18/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive understanding of molecular changes during brain aging is essential to mitigate cognitive decline and delay neurodegenerative diseases. The interpretation of mRNA alterations during brain aging is influenced by the health and age of the animal cohorts studied. Here, we carefully consider these factors and provide an in-depth investigation of mRNA splicing and dynamics in the aging mouse brain, combining short- and long-read sequencing technologies with extensive bioinformatic analyses. Our findings encompass a spectrum of age-related changes, including differences in isoform usage, decreased mRNA dynamics and a module showing increased expression of neuronal genes. Notably, our results indicate a reduced abundance of mRNA isoforms leading to nonsense-mediated RNA decay and suggest a regulatory role for RNA-binding proteins, indicating that their regulation may be altered leading to the reshaping of the aged brain transcriptome. Collectively, our study highlights the importance of studying mRNA splicing events during brain aging.
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Affiliation(s)
- Nisha Hemandhar Kumar
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Verena Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Emanuel Barth
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
- Bioinformatics Core Facility, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Sebastian Krautwurst
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Manja Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
- Leibniz Institute for Age Research, FLI, Beutenbergstraße 11, Jena 07743, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University, Leutragraben 1, Jena 07743, Germany
- German Center for Integrative Biodiversity Research (iDiv), Puschstraße 4, Leipzig 04103, Germany
- Michael Stifel Center Jena, Friedrich Schiller University, Ernst-Abbe-Platz 2, Jena 07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fuerstengraben 1, Jena 07743, Germany
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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23
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Russell AF, Currie MF, Chatterjee C. Covalent hitchhikers guide proteins to the nucleus. Cell Chem Biol 2024; 31:383-386. [PMID: 38518744 PMCID: PMC11193548 DOI: 10.1016/j.chembiol.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/24/2024]
Abstract
In this issue of Cell Chemical Biology, Peng and Weerapana1 report the combination of chemoproteomic and proximity-based labeling approaches to identify cysteines in nuclear proteins that are reactive toward electrophilic probe compounds. They apply this novel technology to identify proteins that are localized to the nucleus and chromatin upon probe labeling.
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Affiliation(s)
| | - Madeline F Currie
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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24
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Mi J, Liu C, Chen H, Qian Y, Zhu J, Zhang Y, Liang Y, Wang L, Ta D. Light on Alzheimer's disease: from basic insights to preclinical studies. Front Aging Neurosci 2024; 16:1363458. [PMID: 38566826 PMCID: PMC10986738 DOI: 10.3389/fnagi.2024.1363458] [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: 12/30/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Alzheimer's disease (AD), referring to a gradual deterioration in cognitive function, including memory loss and impaired thinking skills, has emerged as a substantial worldwide challenge with profound social and economic implications. As the prevalence of AD continues to rise and the population ages, there is an imperative demand for innovative imaging techniques to help improve our understanding of these complex conditions. Photoacoustic (PA) imaging forms a hybrid imaging modality by integrating the high-contrast of optical imaging and deep-penetration of ultrasound imaging. PA imaging enables the visualization and characterization of tissue structures and multifunctional information at high resolution and, has demonstrated promising preliminary results in the study and diagnosis of AD. This review endeavors to offer a thorough overview of the current applications and potential of PA imaging on AD diagnosis and treatment. Firstly, the structural, functional, molecular parameter changes associated with AD-related brain imaging captured by PA imaging will be summarized, shaping the diagnostic standpoint of this review. Then, the therapeutic methods aimed at AD is discussed further. Lastly, the potential solutions and clinical applications to expand the extent of PA imaging into deeper AD scenarios is proposed. While certain aspects might not be fully covered, this mini-review provides valuable insights into AD diagnosis and treatment through the utilization of innovative tissue photothermal effects. We hope that it will spark further exploration in this field, fostering improved and earlier theranostics for AD.
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Affiliation(s)
- Jie Mi
- Yiwu Research Institute, Fudan University, Yiwu, China
| | - Chao Liu
- Yiwu Research Institute, Fudan University, Yiwu, China
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai, China
| | - Honglei Chen
- Yiwu Research Institute, Fudan University, Yiwu, China
| | - Yan Qian
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai, China
| | - Jingyi Zhu
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yachao Zhang
- Medical Ultrasound Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yizhi Liang
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou, China
| | - Lidai Wang
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Dean Ta
- Yiwu Research Institute, Fudan University, Yiwu, China
- Department of Electronic Engineering, Fudan University, Shanghai, China
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25
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Zhang W, Liu Q, Wang J, Liu L. Anaesthesia and brain development: a review of propofol-induced neurotoxicity in pediatric populations. J Dev Orig Health Dis 2024; 15:e2. [PMID: 38450456 DOI: 10.1017/s2040174424000059] [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] [Indexed: 03/08/2024]
Abstract
With the advancement of medical technology, there are increasing opportunities for new-borns, infants, and pregnant women to be exposed to general anaesthesia. Propofol is commonly used for the induction of anaesthesia, maintenance of general intravenous anaesthesia and sedation of intensive-care children. Many previous studies have found that propofol has organ-protective effects, but growing evidence suggests that propofol interferes with brain development, affecting learning and cognitive function. The purpose of this review is to summarize the latest progress in understanding the neurotoxicity of propofol. Evidence from case studies and clinical studies suggests that propofol has neurotoxicity on the developing brain. We classify the findings on propofol-induced neurotoxicity based on its damage mechanism. We end by summarizing the current protective strategies against propofol neurotoxicity. Fully understanding the neurotoxic mechanisms of propofol can help us use it at a reasonable dosage, reduce its side effects, and increase patient safety.
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Affiliation(s)
- Weixin Zhang
- Department of Anesthesiology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Qi Liu
- Department of Anesthesiology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Junli Wang
- Department of Anesthesiology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Li Liu
- Department of Anesthesiology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
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26
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Zarrella JA, Tsurumi A. Genome-wide transcriptome profiling and development of age prediction models in the human brain. Aging (Albany NY) 2024; 16:4075-4094. [PMID: 38428408 PMCID: PMC10968712 DOI: 10.18632/aging.205609] [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: 05/02/2022] [Accepted: 03/28/2023] [Indexed: 03/03/2024]
Abstract
Aging-related transcriptome changes in various regions of the healthy human brain have been explored in previous works, however, a study to develop prediction models for age based on the expression levels of specific panels of transcripts is lacking. Moreover, studies that have assessed sexually dimorphic gene activities in the aging brain have reported discrepant results, suggesting that additional studies would be advantageous. The prefrontal cortex (PFC) region was previously shown to have a particularly large number of significant transcriptome alterations during healthy aging in a study that compared different regions in the human brain. We harmonized neuropathologically normal PFC transcriptome datasets obtained from the Gene Expression Omnibus (GEO) repository, ranging in age from 21 to 105 years, and found a large number of differentially regulated transcripts in the old and elderly, compared to young samples overall, and compared female and male-specific expression alterations. We assessed the genes that were associated with age by employing ontology, pathway, and network analyses. Furthermore, we applied various established (least absolute shrinkage and selection operator (Lasso) and Elastic Net (EN)) and recent (eXtreme Gradient Boosting (XGBoost) and Light Gradient Boosting Machine (LightGBM)) machine learning algorithms to develop accurate prediction models for chronological age and validated them. Studies to further validate these models in other large populations and molecular studies to elucidate the potential mechanisms by which the transcripts identified may be related to aging phenotypes would be advantageous.
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Affiliation(s)
- Joseph A. Zarrella
- Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Shriner's Hospitals for Children-Boston, Boston, MA 02114, USA
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27
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Liu Y, Tan Y, Zhang Z, Yi M, Zhu L, Peng W. The interaction between ageing and Alzheimer's disease: insights from the hallmarks of ageing. Transl Neurodegener 2024; 13:7. [PMID: 38254235 PMCID: PMC10804662 DOI: 10.1186/s40035-024-00397-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Ageing is a crucial risk factor for Alzheimer's disease (AD) and is characterised by systemic changes in both intracellular and extracellular microenvironments that affect the entire body instead of a single organ. Understanding the specific mechanisms underlying the role of ageing in disease development can facilitate the treatment of ageing-related diseases, such as AD. Signs of brain ageing have been observed in both AD patients and animal models. Alleviating the pathological changes caused by brain ageing can dramatically ameliorate the amyloid beta- and tau-induced neuropathological and memory impairments, indicating that ageing plays a crucial role in the pathophysiological process of AD. In this review, we summarize the impact of several age-related factors on AD and propose that preventing pathological changes caused by brain ageing is a promising strategy for improving cognitive health.
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Affiliation(s)
- Yuqing Liu
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, People's Republic of China
- National Clinical Research Center for Metabolic Diseases, Changsha, 410011, People's Republic of China
| | - Yejun Tan
- School of Mathematics, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Zheyu Zhang
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, People's Republic of China
- National Clinical Research Center for Metabolic Diseases, Changsha, 410011, People's Republic of China
| | - Min Yi
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, People's Republic of China
- National Clinical Research Center for Metabolic Diseases, Changsha, 410011, People's Republic of China
| | - Lemei Zhu
- Academician Workstation, Changsha Medical University, Changsha, 410219, People's Republic of China
| | - Weijun Peng
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, People's Republic of China.
- National Clinical Research Center for Metabolic Diseases, Changsha, 410011, People's Republic of China.
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28
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Nassar A, Kodi T, Satarker S, Gurram PC, Fayaz SM, Nampoothiri M. Astrocytic transcription factors REST, YY1, and putative microRNAs in Parkinson's disease and advanced therapeutic strategies. Gene 2024; 892:147898. [PMID: 37832803 DOI: 10.1016/j.gene.2023.147898] [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: 03/13/2023] [Revised: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Transcription factors (TF) and microRNAs are regulatory factors in astrocytes and are linked to several Parkinson's disease (PD) progression causes, such as disruption of glutamine transporters in astrocytes and concomitant disrupted glutamine uptake and inflammation. REST, a crucial TF, has been documented as an epigenetic repressor that limits the expression of neuronal genes in non-neural cells. REST activity is significantly linked to its corepressors in astrocytes, specifically histone deacetylases (HDACs), CoREST, and MECP2. Another REST-regulating TF, YY1, has been studied in astrocytes, and its interaction with REST has been investigated. In this review, the molecular processes that support the astrocytic control of REST and YY1 in terms of the regulation of glutamate transporter EAAT2 were addressed in a more detailed and comprehensive manner. Both TFs' function in astrocytes and how astrocyte abnormalities cause PD is still a mystery. Moreover, microRNAs (short non-coding RNAs) are key regulators that have been correlated to the expression and regulation of numerous genes linked to PD. The identification of numerous miRs that are engaged in astrocyte dysfunction that triggers PD has been shown. The term "Gut-brain axis" refers to the two systems' mutual communication. Gut microbial dysbiosis, which mediates an imbalance of the gut-brain axis, might contribute to neurodegenerative illnesses through altered astrocytic regulation. New treatment approaches to modify the gut-brain axis and prevent astrocytic repercussions have also been investigated in this review.
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Affiliation(s)
- Ajmal Nassar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Triveni Kodi
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Prasada Chowdari Gurram
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - S M Fayaz
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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Zhao Y, Ai W, Zheng J, Hu X, Zhang L. A bibliometric and visual analysis of epigenetic research publications for Alzheimer's disease (2013-2023). Front Aging Neurosci 2024; 16:1332845. [PMID: 38292341 PMCID: PMC10824959 DOI: 10.3389/fnagi.2024.1332845] [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: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
Background Currently, the prevalence of Alzheimer's disease (AD) is progressively rising, particularly in developed nations. There is an escalating focus on the onset and progression of AD. A mounting body of research indicates that epigenetics significantly contributes to AD and holds substantial promise as a novel therapeutic target for its treatment. Objective The objective of this article is to present the AD areas of research interest, comprehend the contextual framework of the subject research, and investigate the prospective direction for future research development. Methods ln Web of Science Core Collection (WOSCC), we searched documents by specific subject terms and their corresponding free words. VOSviewer, CiteSpace and Scimago Graphica were used to perform statistical analysis on measurement metrics such as the number of published papers, national cooperative networks, publishing countries, institutions, authors, co-cited journals, keywords, and visualize networks of related content elements. Results We selected 1,530 articles from WOSCC from January 2013 to June 2023 about epigenetics of AD. Based on visual analysis, we could get that China and United States were the countries with the most research in this field. Bennett DA was the most contributed and prestigious scientist. The top 3 cited journals were Journal of Alzheimer's Disease, Neurobiology of Aging and Molecular Neurobiology. According to the analysis of keywords and the frequency of citations, ncRNAs, transcription factor, genome, histone modification, blood DNA methylation, acetylation, biomarkers were hot research directions in AD today. Conclusion According to bibliometric analysis, epigenetic research in AD was a promising research direction, and epigenetics had the potential to be used as AD biomarkers and therapeutic targets.
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Affiliation(s)
- YaPing Zhao
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - WenJing Ai
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - JingFeng Zheng
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - XianLiang Hu
- Chengdu Eighth People’s Hospital, Geriatric Hospital of Chengdu Medical College, Chengdu, China
| | - LuShun Zhang
- Sichuan Key Laboratory of Development and Regeneration, Department of Neurobiology, Chengdu Medical College, Chengdu, China
- Department of Pathology and Pathophysiology, Chengdu Medical College, Chengdu, China
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30
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Al-Saran N, Subash-Babu P, Al-Harbi LN, Alrfaei BM, Alshatwi AA. Neuroprotective Effect of Solid Lipid Nanoparticles Loaded with Lepidium sativum (L.) Seed Bioactive Components Enhance Bioavailability and Wnt/β-Catenin/Camk-II Signaling Cascade in SH-SY5Y Neuroblastoma Cells. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:199. [PMID: 38251163 PMCID: PMC10819627 DOI: 10.3390/nano14020199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
The primary pathological hallmark of Alzheimer's disease (AD) is the formation and accumulation of neurofibrillary tangles and plaques, which result from the aggregation of amyloid-β (Aβ) induced by oxidative stress. The effectiveness of Alzheimer's disease (AD) therapeutics significantly hinges on the drug's bioavailability and its ability to penetrate neuronal cells. The current investigation was designed as a first attempt to examine bio-fabricated Lepidium sativum (LS) seed-extract-loaded solid lipid nanoparticles (SLNps) to increase bioavailability and bioefficacy for the prevention of undifferentiated SH-SY5Y neuronal cells from oxidative stress induced by H2O2 and amyloid-β peptide (Aβ,1-42). The SLNps were fabricated using LS extract as a water phase and hyaluronic acid and chia seed fatty acids as a lipid phase, then confirmed and characterized using UV, Zeta size, and SEM methods. The biological safety of synthesized LS-SLNps has been determined using MTT assay and PI staining (nuclear damage) in hMSCs. LS-SLNp-pretreated neuronal cells were induced with oxidative stress and 2 µM of beta-amyloid (Aβ,1-42) fibrils; furthermore, the neuroprotective potential of LS-SLNps was determined through the quenching of oxidative stress, enhancing mitochondrial oxidative capacity, and immunoregulatory potential. Observations found that cells treated with both H2O2 and beta-amyloid (Aβ,1-42) fibrils showed decreased neuronal cell growth, nuclear damage, and mitochondrial membrane potential due to oxidative stress. However, SH-SY5Y cells pretreated with LS-SLNps for 24 h showed an increase in cell proliferation with uniform morphology and increased mitochondrial membrane potential compared to cells pretreated with LS alone. Gene expression analysis found that LS-SLNps increased the expression of Wnt 3a and 5a, which stimulated the canonical, β-catenin, and non-canonical Camk-II expressions of nerve cell growth factors, confirming the molecular-level reversal of neurodegenerative diseases.
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Affiliation(s)
- Nada Al-Saran
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia (P.S.-B.)
| | - Pandurangan Subash-Babu
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia (P.S.-B.)
| | - Laila Naif Al-Harbi
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia (P.S.-B.)
| | - Bahauddeen M. Alrfaei
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Minister of National Guard-Health Affairs (MNGHA), P.O. Box 22490, Riyadh 11426, Saudi Arabia
- King Abdullah International Medical Research Center, Minister of National Guard-Health Affairs (MNGHA), P.O. Box 22490, Riyadh 11426, Saudi Arabia
| | - Ali A. Alshatwi
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia (P.S.-B.)
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31
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Meyer K, Ling KH, Yeo PL, Spathopoulou A, Drake D, Choi J, Aron L, Garcia-Corral M, Ko T, Lee EA, Tam JM, Perlis RH, Church GM, Tsai LH, Yankner BA. Impaired neural stress resistance and loss of REST in bipolar disorder. Mol Psychiatry 2024; 29:153-164. [PMID: 37938767 DOI: 10.1038/s41380-023-02313-7] [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: 04/04/2023] [Revised: 07/27/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023]
Abstract
Neurodevelopmental changes and impaired stress resistance have been implicated in the pathogenesis of bipolar disorder (BD), but the underlying regulatory mechanisms are unresolved. Here we describe a human cerebral organoid model of BD that exhibits altered neural development, elevated neural network activity, and a major shift in the transcriptome. These phenotypic changes were reproduced in cerebral organoids generated from iPS cell lines derived in different laboratories. The BD cerebral organoid transcriptome showed highly significant enrichment for gene targets of the transcriptional repressor REST. This was associated with reduced nuclear REST and REST binding to target gene recognition sites. Reducing the oxygen concentration in organoid cultures to a physiological range ameliorated the developmental phenotype and restored REST expression. These effects were mimicked by treatment with lithium. Reduced nuclear REST and derepression of REST targets genes were also observed in the prefrontal cortex of BD patients. Thus, an impaired cellular stress response in BD cerebral organoids leads to altered neural development and transcriptional dysregulation associated with downregulation of REST. These findings provide a new model and conceptual framework for exploring the molecular basis of BD.
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Affiliation(s)
- Katharina Meyer
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - King-Hwa Ling
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Pei-Ling Yeo
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jaejoon Choi
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Liviu Aron
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Mariana Garcia-Corral
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Tak Ko
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Jenny M Tam
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Roy H Perlis
- Center for Quantitative Health, Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Li-Huei Tsai
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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32
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Do BK, Jang JH, Park GH. Effects of Corticosterone on Beta-Amyloid-Induced Cell Death in SH-SY5Y Cells. Biomol Ther (Seoul) 2024; 32:77-83. [PMID: 38148553 PMCID: PMC10762270 DOI: 10.4062/biomolther.2023.133] [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: 07/21/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 12/28/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease characterized by neuronal cell death and memory impairment. Corticosterone (CORT) is a glucocorticoid hormone produced by the hypothalamic-pituitary-adrenal axis in response to a stressful condition. Excessive stress and high CORT levels are known to cause neurotoxicity and aggravate various diseases, whereas mild stress and low CORT levels exert beneficial actions under pathophysiological conditions. However, the effects of mild stress on AD have not been clearly elucidated yet. In this study, the effects of low (3 and 30 nM) CORT concentration on Aβ25-35-induced neurotoxicity in SH-SY5Y cells and underlying molecular mechanisms have been investigated. Cytotoxicity caused by Aβ25-35 was significantly inhibited by the low concentration of CORT treatment in the cells. Furthermore, CORT pretreatment significantly reduced Aβ25-35-mediated pro-apoptotic signals, such as increased Bim/Bcl-2 ratio and caspase-3 cleavage. Moreover, low concentration of CORT treatment inhibited the Aβ25-35-induced cyclooxygenase-2 and pro-inflammatory cytokine expressions, including tumor necrosis factor-α and interleukin-1β. Aβ25-35 resulted in intracellular accumulation of reactive oxygen species and lipid peroxidation, which were effectively reduced by the low CORT concentration. As a molecular mechanism, low CORT concentration activated the nuclear factor-erythroid 2-related factor 2, a redox-sensitive transcription factor mediating cellular defense and upregulating the expression of antioxidant enzymes, such as NAD(P)H:quinone oxidoreductase, glutamylcysteine synthetase, and manganese superoxide dismutase. These findings suggest that low CORT concentration exerts protective actions against Aβ25-35-induced neurotoxicity and might be used to treat and/or prevent AD.
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Affiliation(s)
- Bo Kyeong Do
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung-Hee Jang
- Department of Pharmacology, School of Medicine, Keimyung University, Daegu 42601, Republic of Korea
| | - Gyu Hwan Park
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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33
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Mu C, Gao M, Xu W, Sun X, Chen T, Xu H, Qiu H. Mechanisms of microRNA-132 in central neurodegenerative diseases: A comprehensive review. Biomed Pharmacother 2024; 170:116029. [PMID: 38128185 DOI: 10.1016/j.biopha.2023.116029] [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: 09/14/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
MicroRNA-132 (miR-132) is a highly conserved molecule that plays a crucial regulatory role in central nervous system (CNS) disorders. The expression levels of miR-132 exhibit variability in various neurological disorders and have been closely linked to disease onset and progression. The expression level of miR-132 in the CNS is regulated by a diverse range of stimuli and signaling pathways, including neuronal migration and integration, dendritic outgrowth, and complexity, synaptogenesis, synaptic plasticity, as well as inflammation and apoptosis activation. The aberrant expression of miR-132 in various central neurodegenerative diseases has garnered widespread attention. Clinical studies have revealed altered miR-132 expression levels in both chronic and acute CNS diseases, positioning miR-132 as a potential biomarker or therapeutic target. An in-depth exploration of miR-132 holds the promise of enhancing our understanding of the mechanisms underlying CNS diseases, thereby offering novel insights and strategies for disease diagnosis and treatment. It is anticipated that this review will assist researchers in recognizing the potential value of miR-132 and in generating innovative ideas for clinical trials related to CNS degenerative diseases.
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Affiliation(s)
- Chenxi Mu
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Meng Gao
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Weijing Xu
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China; School of Public Health, Jiamusi University, Jiamusi 154007, Heilongjiang, China
| | - Xun Sun
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Tianhao Chen
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Hui Xu
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China.
| | - Hongbin Qiu
- School of Public Health, Jiamusi University, Jiamusi 154007, Heilongjiang, China.
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34
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Hosseini L, Shahabi P, Fakhari A, Zangbar HS, Seyedaghamiri F, Sadeghzadeh J, Abolhasanpour N. Aging and age-related diseases with a focus on therapeutic potentials of young blood/plasma. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:1-13. [PMID: 37552316 DOI: 10.1007/s00210-023-02657-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
Aging is accompanied by alterations in the body with time-related to decline of physiological integrity and functionality process, responsible for increasing diseases and vulnerability to death. Several ages associated with biomarkers were observed in red blood cells, and consequently plasma proteins have a critical rejuvenating role in the aging process and age-related disorders. Advanced age is a risk factor for a broad spectrum of diseases and disorders such as cardiovascular diseases, musculoskeletal disorders and liver, chronic kidney disease, neurodegenerative diseases, and cancer because of loss of regenerative capacity, correlated to reduced systemic factors and raise of pro-inflammatory cytokines. Most studies have shown that systemic factors in young blood/plasma can strongly protect against age-related diseases in various tissues by restoring autophagy, increasing neurogenesis, and reducing oxidative stress, inflammation, and apoptosis. Here, we focus on the current advances in using young plasma or blood to combat aging and age-related diseases and summarize the experimental and clinical evidence supporting this approach. Based on reports, young plasma or blood is new a therapeutic approach to aging and age-associated diseases.
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Affiliation(s)
- Leila Hosseini
- Research Center of Psychiatry and Behavioral Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Parviz Shahabi
- Department of Physiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, IR, Iran
| | - Ali Fakhari
- Research Center of Psychiatry and Behavioral Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Soltani Zangbar
- Department of Neurosciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemehsadat Seyedaghamiri
- Department of Neurosciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Sadeghzadeh
- Department of Neurosciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasrin Abolhasanpour
- Research Center for Evidence-Based Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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35
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Islam M, Samal A, Davis DJ, Behura SK. Ablation of placental REST deregulates fetal brain metabolism and impacts gene expression of the offspring brain at the postnatal and adult stages. FASEB J 2024; 38:e23349. [PMID: 38069914 DOI: 10.1096/fj.202301344r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/26/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
In this study, the transcriptional repressor REST (Repressor Element 1 Silencing Transcription factor) was ablated in the mouse placenta to investigate molecular and cellular impacts on the offspring brain at different life stages. Ablation of placental REST deregulated several brain metabolites, including glucose and lactate that fuel brain energy, vitamin C (ascorbic acid) that functions in the epigenetic programming of the brain during postnatal development, and glutamate and creatine that help the brain to respond to stress conditions during adult life. Bulk RNA-seq analysis showed that a lack of placental REST persistently altered multiple transport genes, including those related to oxygen transportation in the offspring brain. While metabolic genes were impacted in the postnatal brain, different stress response genes were activated in the adult brain. DNA methylation was also impacted in the adult brain due to the loss of placental REST, but in a sex-biased manner. Single-nuclei RNA-seq analysis showed that specific cell types of the brain, particularly those of the choroid plexus and ependyma, which play critical roles in producing cerebrospinal fluid and maintaining metabolic homeostasis, were significantly impacted due to the loss of placental REST. These cells showed significant differential expression of genes associated with the metabotropic (G coupled protein) and ionotropic (ligand-gated ion channel) glutamate receptors, suggesting an impact of ablation of placental REST on the glutamatergic signaling of the offspring brain. The study expands our understanding of placental influences on the offspring brain.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Ananya Samal
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Daniel J Davis
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA
- Animal Modeling Core, University of Missouri, Columbia, Missouri, USA
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
- Interdisciplnary Reproductive and Health Group, University of Missouri, Columbia, Missouri, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, Missouri, USA
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36
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Tijms BM, Vromen EM, Mjaavatten O, Holstege H, Reus LM, van der Lee S, Wesenhagen KEJ, Lorenzini L, Vermunt L, Venkatraghavan V, Tesi N, Tomassen J, den Braber A, Goossens J, Vanmechelen E, Barkhof F, Pijnenburg YAL, van der Flier WM, Teunissen CE, Berven FS, Visser PJ. Cerebrospinal fluid proteomics in patients with Alzheimer's disease reveals five molecular subtypes with distinct genetic risk profiles. NATURE AGING 2024; 4:33-47. [PMID: 38195725 PMCID: PMC10798889 DOI: 10.1038/s43587-023-00550-7] [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: 09/11/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Alzheimer's disease (AD) is heterogenous at the molecular level. Understanding this heterogeneity is critical for AD drug development. Here we define AD molecular subtypes using mass spectrometry proteomics in cerebrospinal fluid, based on 1,058 proteins, with different levels in individuals with AD (n = 419) compared to controls (n = 187). These AD subtypes had alterations in protein levels that were associated with distinct molecular processes: subtype 1 was characterized by proteins related to neuronal hyperplasticity; subtype 2 by innate immune activation; subtype 3 by RNA dysregulation; subtype 4 by choroid plexus dysfunction; and subtype 5 by blood-brain barrier impairment. Each subtype was related to specific AD genetic risk variants, for example, subtype 1 was enriched with TREM2 R47H. Subtypes also differed in clinical outcomes, survival times and anatomical patterns of brain atrophy. These results indicate molecular heterogeneity in AD and highlight the need for personalized medicine.
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Affiliation(s)
- Betty M Tijms
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
| | - Ellen M Vromen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Olav Mjaavatten
- Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Henne Holstege
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Lianne M Reus
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sven van der Lee
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Kirsten E J Wesenhagen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Luigi Lorenzini
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neuroimaging, Amsterdam, the Netherlands
| | - Lisa Vermunt
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Neurochemistry Laboratory, Department of Laboratory Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Vikram Venkatraghavan
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Niccoló Tesi
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Jori Tomassen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Anouk den Braber
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | | | | | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Epidemiology & Data Science, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Charlotte E Teunissen
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Neurochemistry Laboratory, Department of Laboratory Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Frode S Berven
- Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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37
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Wu Y, Chen Y, Yu X, Zhang M, Li Z. Towards Understanding Neurodegenerative Diseases: Insights from Caenorhabditis elegans. Int J Mol Sci 2023; 25:443. [PMID: 38203614 PMCID: PMC10778690 DOI: 10.3390/ijms25010443] [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: 12/08/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The elevated occurrence of debilitating neurodegenerative disorders, such as amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD) and Machado-Joseph disease (MJD), demands urgent disease-modifying therapeutics. Owing to the evolutionarily conserved molecular signalling pathways with mammalian species and facile genetic manipulation, the nematode Caenorhabditis elegans (C. elegans) emerges as a powerful and manipulative model system for mechanistic insights into neurodegenerative diseases. Herein, we review several representative C. elegans models established for five common neurodegenerative diseases, which closely simulate disease phenotypes specifically in the gain-of-function aspect. We exemplify applications of high-throughput genetic and drug screenings to illustrate the potential of C. elegans to probe novel therapeutic targets. This review highlights the utility of C. elegans as a comprehensive and versatile platform for the dissection of neurodegenerative diseases at the molecular level.
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Affiliation(s)
| | | | | | | | - Zhaoyu Li
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.W.); (Y.C.); (X.Y.); (M.Z.)
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38
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Younas N, Saleem T, Younas A, Zerr I. Nuclear face of Tau: an inside player in neurodegeneration. Acta Neuropathol Commun 2023; 11:196. [PMID: 38087392 PMCID: PMC10714511 DOI: 10.1186/s40478-023-01702-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Tau (Tubulin associated unit) protein is a major hallmark of Alzheimer's disease (AD) and tauopathies. Tau is predominantly an axonal protein with a crucial role in the stabilization and dynamics of the microtubules. Since the discovery of Tau protein in 1975, research efforts were concentrated on the pathophysiological role of Tau protein in the context of the microtubules. Although, for more than three decades, different localizations of Tau protein have been discovered e.g., in the nuclear compartments. Discovery of the role of Tau protein in various cellular compartments especially in the nucleus opens up a new fold of complexity in tauopathies. Data from cellular models, animal models, and the human brain indicate that nuclear Tau is crucial for genome stability and to cope with cellular distress. Moreover, it's nature of nuclear translocation, its interactions with the nuclear DNA/RNA and proteins suggest it could play multiple roles in the nucleus. To comprehend Tau pathophysiology and efficient Tau-based therapies, there is an urgent need to understand whole repertoire of Tau species (nuclear and cytoplasmic) and their functional relevance. To complete the map of Tau repertoire, understanding of various species of Tau in the nucleus and cytoplasm, identification if specific transcripts of Tau, isoforms and post-translational modifications could foretell Tau's localizations and functions, and how they are modified in neurodegenerative diseases like AD, is urgently required. In this review, we explore the nuclear face of Tau protein, its nuclear localizations and functions and its linkage with Alzheimer's disease.
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Affiliation(s)
- Neelam Younas
- University Medical Center Göttingen, National Reference Center for Surveillance of TSE, Department of Neurology, Robert-Koch strasse 40, 37075, Göttingen, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, 37075, Germany.
| | - Tayyaba Saleem
- University Medical Center Göttingen, National Reference Center for Surveillance of TSE, Department of Neurology, Robert-Koch strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, 37075, Germany
| | - Abrar Younas
- University Medical Center Göttingen, National Reference Center for Surveillance of TSE, Department of Neurology, Robert-Koch strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, 37075, Germany
| | - Inga Zerr
- University Medical Center Göttingen, National Reference Center for Surveillance of TSE, Department of Neurology, Robert-Koch strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, 37075, Germany
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39
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Crews FT, Fisher RP, Qin L, Vetreno RP. HMGB1 neuroimmune signaling and REST-G9a gene repression contribute to ethanol-induced reversible suppression of the cholinergic neuron phenotype. Mol Psychiatry 2023; 28:5159-5172. [PMID: 37402853 PMCID: PMC10764639 DOI: 10.1038/s41380-023-02160-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 06/14/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Adolescent binge drinking increases Toll-like receptor 4 (TLR4), receptor for advanced glycation end products (RAGE), the endogenous TLR4/RAGE agonist high-mobility group box 1 (HMGB1), and proinflammatory neuroimmune signaling in the adult basal forebrain in association with persistent reductions of basal forebrain cholinergic neurons (BFCNs). In vivo preclinical adolescent intermittent ethanol (AIE) studies find anti-inflammatory interventions post-AIE reverse HMGB1-TLR4/RAGE neuroimmune signaling and loss of BFCNs in adulthood, suggesting proinflammatory signaling causes epigenetic repression of the cholinergic neuron phenotype. Reversible loss of BFCN phenotype in vivo is linked to increased repressive histone 3 lysine 9 dimethylation (H3K9me2) occupancy at cholinergic gene promoters, and HMGB1-TLR4/RAGE proinflammatory signaling is linked to epigenetic repression of the cholinergic phenotype. Using an ex vivo basal forebrain slice culture (FSC) model, we report EtOH recapitulates the in vivo AIE-induced loss of ChAT+IR BFCNs, somal shrinkage of the remaining ChAT+ neurons, and reduction of BFCN phenotype genes. Targeted inhibition of EtOH-induced proinflammatory HMGB1 blocked ChAT+IR loss while disulfide HMBG1-TLR4 and fully reduced HMGB1-RAGE signaling decreased ChAT+IR BFCNs. EtOH increased expression of the transcriptional repressor RE1-silencing transcription factor (REST) and the H3K9 methyltransferase G9a that was accompanied by increased repressive H3K9me2 and REST occupancy at promoter regions of the BFCN phenotype genes Chat and Trka as well as the lineage transcription factor Lhx8. REST expression was similarly increased in the post-mortem human basal forebrain of individuals with alcohol use disorder, which is negatively correlated with ChAT expression. Administration of REST siRNA and the G9a inhibitor UNC0642 blocked and reversed the EtOH-induced loss of ChAT+IR BFCNs, directly linking REST-G9a transcriptional repression to suppression of the cholinergic neuron phenotype. These data suggest that EtOH induces a novel neuroplastic process involving neuroimmune signaling and transcriptional epigenetic gene repression resulting in the reversible suppression of the cholinergic neuron phenotype.
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Affiliation(s)
- Fulton T Crews
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rachael P Fisher
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Liya Qin
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ryan P Vetreno
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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40
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Protti G, Rubbi L, Gören T, Sabirli R, Civlan S, Kurt Ö, Türkçüer İ, Köseler A, Pellegrini M. The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties. Physiol Genomics 2023; 55:618-633. [PMID: 37781740 DOI: 10.1152/physiolgenomics.00063.2023] [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: 06/22/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023] Open
Abstract
Epigenetic modifications, particularly DNA methylation, have emerged as regulators of gene expression and are implicated in various biological processes and disease states. Understanding the factors influencing the epigenome is essential for unraveling its complexity. In this study, we aimed to identify how the methylome of buccal epithelial cells, a noninvasive and easily accessible tissue, is associated with demographic and health-related variables commonly used in clinical settings, such as age, sex, blood immune composition, hemoglobin levels, and others. We developed a model to assess the association of multiple factors with the human methylome and identify the genomic loci significantly impacted by each trait. We demonstrated that DNA methylation variation is accurately modeled by several factors. We confirmed the well-known impact of age and sex and unveiled novel clinical factors associated with DNA methylation, such as blood neutrophils, hemoglobin, red blood cell distribution width, high-density lipoprotein cholesterol, and urea. Genomic regions significantly associated with these traits were enriched in relevant transcription factors, drugs, and diseases. Among our findings, we showed that neutrophil-impacted loci were involved in neutrophil functionality and maturation. Similarly, hemoglobin-influenced sites were associated with several diseases, including aplastic anemia, and the genomic loci affected by urea were related to congenital anomalies of the kidney and urinary tract. Our findings contribute to a better understanding of the human methylome plasticity and provide insights into novel factors shaping DNA methylation patterns, highlighting their potential clinical implications as biomarkers and the importance of considering these physiological traits in future medical epigenomic investigations.NEW & NOTEWORTHY We have developed a quantitative model to assess how the human methylome is associated with several factors and to identify the genomic loci significantly impacted by each trait. We reported novel health-related factors driving DNA methylation patterns and new site-specific regulations that further elucidate methylome dynamics. Our study contributes to a better understanding of the plasticity of the human methylome and unveils novel physiological traits with a potential role in future medical epigenomic investigations.
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Affiliation(s)
- Giulia Protti
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
| | - Tarik Gören
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Ramazan Sabirli
- Emergency Department, Bakircay University Faculty of Medicine Cigli Training and Research Hospital, Izmir, Turkey
| | - Serkan Civlan
- Department of Neurosurgery, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Özgür Kurt
- Department of Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - İbrahim Türkçüer
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Aylin Köseler
- Department of Biophysics, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
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Lu YR, Tian X, Sinclair DA. The Information Theory of Aging. NATURE AGING 2023; 3:1486-1499. [PMID: 38102202 DOI: 10.1038/s43587-023-00527-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/02/2023] [Indexed: 12/17/2023]
Abstract
Information storage and retrieval is essential for all life. In biology, information is primarily stored in two distinct ways: the genome, comprising nucleic acids, acts as a foundational blueprint and the epigenome, consisting of chemical modifications to DNA and histone proteins, regulates gene expression patterns and endows cells with specific identities and functions. Unlike the stable, digital nature of genetic information, epigenetic information is stored in a digital-analog format, susceptible to alterations induced by diverse environmental signals and cellular damage. The Information Theory of Aging (ITOA) states that the aging process is driven by the progressive loss of youthful epigenetic information, the retrieval of which via epigenetic reprogramming can improve the function of damaged and aged tissues by catalyzing age reversal.
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Affiliation(s)
- Yuancheng Ryan Lu
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiao Tian
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - David A Sinclair
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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Waziry R, Williams OA. Alzheimer Disease: A Life-Limiting Disease With a Burden of a Terminal Illness. Neurol Clin Pract 2023; 13:e200208. [PMID: 37854176 PMCID: PMC10581074 DOI: 10.1212/cpj.0000000000200208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/15/2023] [Indexed: 10/20/2023]
Abstract
Purpose of Review An estimated 6.5 million Americans live with Alzheimer dementia. Better understanding of advanced stages of Alzheimer disease (AD) and timely monitoring of its preventable complications would translate to improved survival and quality of life in this population. Recent Findings In this perspective review, we proposed shifting the narrative to recognizing AD as a chronic life-limiting illness instead of a terminal disease. In support of this view, we discussed the following: (1) the biochemical, cellular (preclinical), and clinical phases of AD; (2) survival after AD; (3) AD therapeutics and potential implications for the population with AD in the advanced stages. Summary On the bases of the prolonged preclinical phase in AD, promising advances in AD therapeutics and the varying survival after AD, we proposed a new classification for AD and more broadly neurodegenerative disorders to be recognized as chronic life-limiting illnesses rather than terminal diseases with important implications for patients with AD in the advanced stages given the challenges that are specific to this population.
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Affiliation(s)
- Reem Waziry
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia University, NY
| | - Olajide A Williams
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia University, NY
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Cattaneo C, Urakcheeva I, Giacomini G, Stazi MA, Lana S, Arnofi A, Salemi M, Toccaceli V. Attitude and concerns of healthy individuals regarding post-mortem brain donation. A qualitative study on a nation-wide sample in Italy. BMC Med Ethics 2023; 24:104. [PMID: 38012766 PMCID: PMC10683267 DOI: 10.1186/s12910-023-00980-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Collecting post-mortem brain tissue is essential, especially from healthy "control" individuals, to advance knowledge on increasingly common neurological and mental disorders. Yet, healthy individuals, on which this study is focused, are still understudied. The aim of the study was to explore, among healthy potential brain donors and/or donors' relatives, attitude, concerns and opinion about post-mortem brain donation (PMBD). METHODS A convenience sampling of the general population (twins and their non-twin contacts) was adopted. From June 2018 to February 2019, 12 focus groups were conducted in four Italian cities: Milan, Turin, Rome and Naples, stratified according to twin and non-twin status. A qualitative content analysis was performed with both deductive and inductive approaches. Emotional interactions analysis corroborated results. RESULTS One hundred and three individuals (49-91 yrs of age) participated. Female were 60%. Participants had scarse knowledge regarding PMBD. Factors affecting attitude towards donation were: concerns, emotions, and misconceptions about donation and research. Religion, spirituality and secular attitude were implied, as well as trust towards research and medical institutions and a high degree of uncertainty about brain death ascertainment. Family had a very multifaceted central role in decision making. A previous experience with neurodegenerative diseases seems among factors able to favour brain donation. CONCLUSIONS The study sheds light on healthy individuals' attitudes about PMBD. Brain had a special significance for participants, and the ascertainment of brain death was a source of debate and doubt. Our findings emphasise the importance of targeted communication and thorough information to promote this kind of donation, within an ethical framework of conduct. Trust in research and health professionals emerged as an essential factor for a collaborative attitude towards donation and informed decision making in PMBD.
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Affiliation(s)
- Chiara Cattaneo
- National Centre for Disease Prevention and Health Promotion, Istituto Superiore di Sanità, Rome, Italy
| | | | - Gianmarco Giacomini
- Centre of Reference for Mental Health and Behavioural Sciences, Istituto Superiore di Sanità, Rome, Italy
- Department of Public Health Sciences, University of Turin, Turin, Italy
| | - Maria Antonietta Stazi
- Centre of Reference for Mental Health and Behavioural Sciences, Istituto Superiore di Sanità, Rome, Italy
| | - Susanna Lana
- National Centre for Disease Prevention and Health Promotion, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Arnofi
- Centre of Reference for Mental Health and Behavioural Sciences, Istituto Superiore di Sanità, Rome, Italy
| | - Miriam Salemi
- Centre of Reference for Mental Health and Behavioural Sciences, Istituto Superiore di Sanità, Rome, Italy
| | - Virgilia Toccaceli
- Centre of Reference for Mental Health and Behavioural Sciences, Istituto Superiore di Sanità, Rome, Italy.
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Shafqat A, Khan S, Omer MH, Niaz M, Albalkhi I, AlKattan K, Yaqinuddin A, Tchkonia T, Kirkland JL, Hashmi SK. Cellular senescence in brain aging and cognitive decline. Front Aging Neurosci 2023; 15:1281581. [PMID: 38076538 PMCID: PMC10702235 DOI: 10.3389/fnagi.2023.1281581] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/01/2023] [Indexed: 10/16/2024] Open
Abstract
Cellular senescence is a biological aging hallmark that plays a key role in the development of neurodegenerative diseases. Clinical trials are currently underway to evaluate the effectiveness of senotherapies for these diseases. However, the impact of senescence on brain aging and cognitive decline in the absence of neurodegeneration remains uncertain. Moreover, patient populations like cancer survivors, traumatic brain injury survivors, obese individuals, obstructive sleep apnea patients, and chronic kidney disease patients can suffer age-related brain changes like cognitive decline prematurely, suggesting that they may suffer accelerated senescence in the brain. Understanding the role of senescence in neurocognitive deficits linked to these conditions is crucial, especially considering the rapidly evolving field of senotherapeutics. Such treatments could help alleviate early brain aging in these patients, significantly reducing patient morbidity and healthcare costs. This review provides a translational perspective on how cellular senescence plays a role in brain aging and age-related cognitive decline. We also discuss important caveats surrounding mainstream senotherapies like senolytics and senomorphics, and present emerging evidence of hyperbaric oxygen therapy and immune-directed therapies as viable modalities for reducing senescent cell burden.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Mahnoor Niaz
- Medical College, Aga Khan University, Karachi, Pakistan
| | | | - Khaled AlKattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Tamara Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, United States
| | - James L. Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, United States
| | - Shahrukh K. Hashmi
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
- Clinical Affairs, Khalifa University, Abu Dhabi, United Arab Emirates
- Department of Medicine, SSMC, Abu Dhabi, United Arab Emirates
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45
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Liu Y, Tian B. Protein-DNA binding sites prediction based on pre-trained protein language model and contrastive learning. Brief Bioinform 2023; 25:bbad488. [PMID: 38171929 PMCID: PMC10782905 DOI: 10.1093/bib/bbad488] [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: 06/30/2023] [Revised: 09/28/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Protein-DNA interaction is critical for life activities such as replication, transcription and splicing. Identifying protein-DNA binding residues is essential for modeling their interaction and downstream studies. However, developing accurate and efficient computational methods for this task remains challenging. Improvements in this area have the potential to drive novel applications in biotechnology and drug design. In this study, we propose a novel approach called Contrastive Learning And Pre-trained Encoder (CLAPE), which combines a pre-trained protein language model and the contrastive learning method to predict DNA binding residues. We trained the CLAPE-DB model on the protein-DNA binding sites dataset and evaluated the model performance and generalization ability through various experiments. The results showed that the area under ROC curve values of the CLAPE-DB model on the two benchmark datasets reached 0.871 and 0.881, respectively, indicating superior performance compared to other existing models. CLAPE-DB showed better generalization ability and was specific to DNA-binding sites. In addition, we trained CLAPE on different protein-ligand binding sites datasets, demonstrating that CLAPE is a general framework for binding sites prediction. To facilitate the scientific community, the benchmark datasets and codes are freely available at https://github.com/YAndrewL/clape.
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Affiliation(s)
- Yufan Liu
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Boxue Tian
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
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46
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Sacco JC, Starr E, Weaver A, Dietz R, Spocter MA. Resequencing of the TMF-1 (TATA Element Modulatory Factor) regulated protein (TRNP1) gene in domestic and wild canids. Canine Med Genet 2023; 10:10. [PMID: 37968761 PMCID: PMC10647097 DOI: 10.1186/s40575-023-00133-0] [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: 07/06/2023] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Cortical folding is related to the functional organization of the brain. The TMF-1 regulated protein (TRNP1) regulates the expansion and folding of the mammalian cerebral cortex, a process that may have been accelerated by the domestication of dogs. The objectives of this study were to sequence the TRNP1 gene in dogs and related canid species, provide evidence of its expression in dog brain and compare the genetic variation within dogs and across the Canidae. The gene was located in silico to dog chromosome 2. The sequence was experimentally confirmed by amplifying and sequencing the TRNP1 exonic and promoter regions in 72 canids (36 purebred dogs, 20 Gy wolves and wolf-dog hybrids, 10 coyotes, 5 red foxes and 1 Gy fox). RESULTS A partial TRNP1 transcript was isolated from several regions in the dog brain. Thirty genetic polymorphisms were found in the Canis sp. with 17 common to both dogs and wolves, and only one unique to dogs. Seven polymorphisms were observed only in coyotes. An additional 9 variants were seen in red foxes. Dogs were the least genetically diverse. Several polymorphisms in the promoter and 3'untranslated region were predicted to alter TRNP1 function by interfering with the binding of transcriptional repressors and miRNAs expressed in neural precursors. A c.259_264 deletion variant that encodes a polyalanine expansion was polymorphic in all species studied except for dogs. A stretch of 15 nucleotides that is found in other mammalian sequences (corresponding to 5 amino acids located between Pro58 and Ala59 in the putative dog protein) was absent from the TRNP1 sequences of all 5 canid species sequenced. Both of these aforementioned coding sequence variations were predicted to affect the formation of alpha helices in the disordered region of the TRNP1 protein. CONCLUSIONS Potentially functionally important polymorphisms in the TRNP1 gene are found within and across various Canis species as well as the red fox, and unique differences in protein structure have evolved and been conserved in the Canidae compared to all other mammalian species.
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Affiliation(s)
- James C Sacco
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA.
| | - Emma Starr
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Alyssa Weaver
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Rachel Dietz
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Muhammad A Spocter
- Department of Anatomy, Des Moines University, 50266, Des Moines, IA, USA
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47
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Liu Y, Tian J. Neuroprotective factors affect the progression of Alzheimer's disease. Biochem Biophys Res Commun 2023; 681:276-282. [PMID: 37797415 DOI: 10.1016/j.bbrc.2023.09.042] [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: 06/29/2023] [Revised: 09/05/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023]
Abstract
Alzheimer's disease(AD) is a neurodegenerative disease that occurs mostly in the elderly and is characterized by chronic progressive cognitive dysfunction, which seriously threatens the health and life-quality of patients. Alterations at the molecular level, which causes pathological changes of AD brain, have impacted the progression of AD. In this review, we illustrate the recent evidence of the alteration of neuroprotective proteins in AD, such as changes in their contents and variants. Furthermore, we elucidate the single nucleotide polymorphism (SNP) and gene changes. Finally, we highlight the epigenetic changes in AD, which helps to display the characteristics of the disease and provides guidance regarding research hot spots in the field against AD.
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Affiliation(s)
- Yan Liu
- Department of Neurology, Dongzhimen Hospital, Beijing University of Chinese Medicine, China
| | - Jinzhou Tian
- Department of Neurology, Dongzhimen Hospital, Beijing University of Chinese Medicine, China.
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48
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Aron L, Qiu C, Ngian ZK, Liang M, Drake D, Choi J, Fernandez MA, Roche P, Bunting EL, Lacey EK, Hamplova SE, Yuan M, Wolfe MS, Bennett DA, Lee EA, Yankner BA. A neurodegeneration checkpoint mediated by REST protects against the onset of Alzheimer's disease. Nat Commun 2023; 14:7030. [PMID: 37919281 PMCID: PMC10622455 DOI: 10.1038/s41467-023-42704-6] [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: 01/31/2022] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Many aging individuals accumulate the pathology of Alzheimer's disease (AD) without evidence of cognitive decline. Here we describe an integrated neurodegeneration checkpoint response to early pathological changes that restricts further disease progression and preserves cognitive function. Checkpoint activation is mediated by the REST transcriptional repressor, which is induced in cognitively-intact aging humans and AD mouse models at the onset of amyloid β-protein (Aβ) deposition and tau accumulation. REST induction is mediated by the unfolded protein response together with β-catenin signaling. A consequence of this response is the targeting of REST to genes involved in key pathogenic pathways, resulting in downregulation of gamma secretase, tau kinases, and pro-apoptotic proteins. Deletion of REST in the 3xTg and J20 AD mouse models accelerates Aβ deposition and the accumulation of misfolded and phosphorylated tau, leading to neurodegeneration and cognitive decline. Conversely, viral-mediated overexpression of REST in the hippocampus suppresses Aβ and tau pathology. Thus, REST mediates a neurodegeneration checkpoint response with multiple molecular targets that may protect against the onset of AD.
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Affiliation(s)
- Liviu Aron
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhen Kai Ngian
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Marianna Liang
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jaejoon Choi
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Marty A Fernandez
- Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Perle Roche
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Emma L Bunting
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ella K Lacey
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sara E Hamplova
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Monlan Yuan
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael S Wolfe
- Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL60612, USA
| | - Eunjung A Lee
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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Dyakonova VE. DNA Instability in Neurons: Lifespan Clock and Driver of Evolution. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1719-1731. [PMID: 38105193 DOI: 10.1134/s0006297923110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 12/19/2023]
Abstract
In the last ten years, the discovery of neuronal DNA postmitotic instability has changed the theoretical landscape in neuroscience and, more broadly, biology. In 2003, A. M. Olovnikov suggested that neuronal DNA is the "initial substrate of aging". Recent experimental data have significantly increased the likelihood of this hypothesis. How does neuronal DNA accumulate damage and in what genome regions? What factors contribute to this process and how are they associated with aging and lifespan? These questions will be discussed in the review. In the course of Metazoan evolution, the instability of neuronal DNA has been accompanied by searching for the pathways to reduce the biological cost of brain activity. Various processes and activities, such as sleep, evolutionary increase in the number of neurons in the vertebrate brain, adult neurogenesis, distribution of neuronal activity, somatic polyploidy, and RNA editing in cephalopods, can be reconsidered in the light of the trade-off between neuronal plasticity and DNA instability in neurons. This topic is of considerable importance for both fundamental neuroscience and translational medicine.
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Affiliation(s)
- Varvara E Dyakonova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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50
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Somsura R, Kamkajon K, Chaimongkolnukul K, Chantip S, Teerapornpuntakit J, Wongdee K, Kamonsutthipaijit N, Tangtrongsup S, Panupinthu N, Tiyasatkulkovit W, Charoenphandhu N. Tissue-specific expression of senescence biomarkers in spontaneously hypertensive rats: evidence of premature aging in hypertension. PeerJ 2023; 11:e16300. [PMID: 37872946 PMCID: PMC10590574 DOI: 10.7717/peerj.16300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
Background Cellular senescence is an age-related physiological process that contributes to tissue dysfunction and accelerated onset of chronic metabolic diseases including hypertension. Indeed, elevation of blood pressure in hypertension coincides with premature vascular aging and dysfunction. In addition, onsets of metabolic disturbance and osteopenia in patients with hypertension have also been reported. It is possible that hypertension enhances premature aging and causes progressive loss of function in multiple organs. However, the landscape of cellular senescence in critical tissues affected by hypertension remains elusive. Materials and Methods Heart, liver, bone, hypothalamus, and kidney were collected from spontaneously hypertensive rats (SHR) and age- and sex-matched normotensive Wistar rats (WT) at 6, 12, 24 and 36 weeks of age (n = 10 animals/group). Changes in mRNA levels of senescence biomarkers namely cyclin-dependent kinase (CDK) inhibitors (CDKIs), i.e., Cdkn2a (encoding p16Ink4a) and Cdkn1a (encoding p21cip1) as well as senescence-associated secretory phenotypes (SASPs), i.e., Timp1, Mmp12, Il6 and Cxcl1, were determined. Additionally, bone collagen alignment and hydroxy apatite crystal dimensions were determined by synchrotron radiation small- and wide-angle X-ray scattering (SAXS/WAXS) techniques. Results Real-time PCR revealed that transcript levels of genes encoding CDKIs and SASPs in the heart and liver were upregulated in SHR from 6 to 36 weeks of age. Expression of Timp1 and Cxcl1 was increased in bone tissues isolated from 36-week-old SHR. In contrast, we found that expression levels of Timp1 and Il6 mRNA were decreased in hypothalamus and kidney of SHR in all age groups. Simultaneous SAXS/WAXS analysis also revealed misalignment of bone collagen fibers in SHR as compared to WT. Conclusion Premature aging was identified in an organ directly affected by high blood pressure (i.e., heart) and those with known functional defects in SHR (i.e., liver and bone). Cellular senescence was not evident in organs with autoregulation of blood pressure (i.e., brain and kidney). Our study suggested that cellular senescence is induced by persistently elevated blood pressure and in part, leading to organ dysfunction. Therefore, interventions that can both lower blood pressure and prevent cellular senescence should provide therapeutic benefits for treatment of cardiovascular and metabolic consequences.
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Affiliation(s)
- Ratthapon Somsura
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Master of Science Program in Zoology, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kanokwan Kamkajon
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Surachai Chantip
- National Laboratory Animal Center, Mahidol University, Nakhon Pathom, Thailand
| | - Jarinthorn Teerapornpuntakit
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Physiology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Kannikar Wongdee
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand
- Faculty of Allied Health Sciences, Burapha University, Chonburi, Thailand
| | | | - Suwimol Tangtrongsup
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Nattapon Panupinthu
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Narattaphol Charoenphandhu
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
- The Academy of Science, The Royal Society of Thailand, Dusit, Bangkok, Thailand
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