1
|
Gray NE, Hack W, Brandes MS, Zweig JA, Yang L, Marney L, Choi J, Magana AA, Cerruti N, McFerrin J, Koike S, Nguyen T, Raber J, Quinn JF, Maier CS, Soumyanath A. Amelioration of age-related cognitive decline and anxiety in mice by Centella asiatica extract varies by sex, dose and mode of administration. FRONTIERS IN AGING 2024; 5:1357922. [PMID: 38770167 PMCID: PMC11102990 DOI: 10.3389/fragi.2024.1357922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
Background: A water extract (CAW) of the Ayurvedic plant Centella asiatica administered in drinking water has been shown to improve cognitive deficits in mouse models of aging and neurodegenerative diseases. Here the effects of CAW administered in drinking water or the diet on cognition, measures of anxiety and depression-like behavior in healthy aged mice are compared. Methods: Three- and eighteen-month-old male and female C57BL6 mice were administered rodent AIN-93M diet containing CAW (0, 0.2, 0.5 or 1% w/w) to provide 0, 200 mg/kg/d, 500 mg/kg/d or 1,000 mg/kg/d CAW for a total of 5 weeks. An additional group of eighteen-month-old mice were treated with CAW (10 mg/mL) in their drinking water CAW for a total of 5 weeks to deliver the same exposure of CAW as the highest dietary dose (1,000 mg/kg/d). CAW doses delivered were calculated based on food and water consumption measured in previous experiments. In the fourth and fifth weeks, mice underwent behavioral testing of cognition, anxiety and depression (n = 12 of each sex per treatment group in each test). Results: Aged mice of both sexes showed cognitive deficits relative to young mice while only female aged mice showed increased anxiety compared to the young female mice and no differences in depression were observed between the different ages. CAW (1,000 mg/kg/d) in the drinking water improved deficits in aged mice in learning, executive function and recognition memory in both sexes and attenuated the increased measures of anxiety observed in the aged female mice. However, CAW in the diet only improved executive function in aged mice at the highest dose (1,000 mg/kg/d) in both sexes and did so less robustly than when given in the water. There were no effects of CAW on depression-like behavior in aged animals regardless of whether it was administered in the diet or the water. Conclusions: These results suggest that CAW can ameliorate age-related changes in measures of anxiety and cognition and that the mode of administration is important for the effects of CAW on resilience to these age-related changes.
Collapse
Affiliation(s)
- Nora E. Gray
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
| | - Wyatt Hack
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
| | - Mikah S. Brandes
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
| | - Jonathan A. Zweig
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
| | - Liping Yang
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Luke Marney
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Jaewoo Choi
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Armando Alcazar Magana
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Natasha Cerruti
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Oregon’s Wild Harvest, Redmond, OR, United States
| | - Janis McFerrin
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Oregon’s Wild Harvest, Redmond, OR, United States
| | - Seiji Koike
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, OR, United States
| | - Thuan Nguyen
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, OR, United States
| | - Jacob Raber
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
| | - Joseph F. Quinn
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
- Parkinson’s Disease Research Education and Clinical Care Center, Veterans’ Administration Portland Healthcare System, Portland, OR, United States
| | - Claudia S. Maier
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
- Linus Pauling Institute, Oregon State University, Corvallis, OR, United States
| | - Amala Soumyanath
- BENFRA Botanical Dietary Supplements Research Center, Oregon Health & Science University, Portland, OR, United States
- Department of Neurology, Oregon Health & Science University, Portland, OR, United States
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Hussain MS, Altamimi ASA, Afzal M, Almalki WH, Kazmi I, Alzarea SI, Gupta G, Shahwan M, Kukreti N, Wong LS, Kumarasamy V, Subramaniyan V. Kaempferol: Paving the path for advanced treatments in aging-related diseases. Exp Gerontol 2024; 188:112389. [PMID: 38432575 DOI: 10.1016/j.exger.2024.112389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/17/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Aging-related diseases (ARDs) are a major global health concern, and the development of effective therapies is urgently needed. Kaempferol, a flavonoid found in several plants, has emerged as a promising candidate for ameliorating ARDs. This comprehensive review examines Kaempferol's chemical properties, safety profile, and pharmacokinetics, and highlights its potential therapeutic utility against ARDs. Kaempferol's therapeutic potential is underpinned by its distinctive chemical structure, which confers antioxidative and anti-inflammatory properties. Kaempferol counteracts reactive oxygen species (ROS) and modulates crucial cellular pathways, thereby combating oxidative stress and inflammation, hallmarks of ARDs. Kaempferol's low toxicity and wide safety margins, as demonstrated by preclinical and clinical studies, further substantiate its therapeutic potential. Compelling evidence supports Kaempferol's substantial potential in addressing ARDs through several mechanisms, notably anti-inflammatory, antioxidant, and anti-apoptotic actions. Kaempferol exhibits a versatile neuroprotective effect by modulating various proinflammatory signaling pathways, including NF-kB, p38MAPK, AKT, and the β-catenin cascade. Additionally, it hinders the formation and aggregation of beta-amyloid protein and regulates brain-derived neurotrophic factors. In terms of its anticancer potential, kaempferol acts through diverse pathways, inducing apoptosis, arresting the cell cycle at the G2/M phase, suppressing epithelial-mesenchymal transition (EMT)-related markers, and affecting the phosphoinositide 3-kinase/protein kinase B signaling pathways. Subsequent studies should focus on refining dosage regimens, exploring innovative delivery systems, and conducting comprehensive clinical trials to translate these findings into effective therapeutic applications.
Collapse
Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017 Jaipur, Rajasthan, India
| | | | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Aljouf, Saudi Arabia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, Ajman 346, United Arab Emirates
| | - Moyad Shahwan
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, Ajman 346, United Arab Emirates; Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman 346, United Arab Emirates
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Ling Shing Wong
- Faculty of Health and Life Sciences, INTI International University, Nilai 71800, Malaysia
| | - Vinoth Kumarasamy
- Department of Parasitology and Medical Entomology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, 56000 Kuala Lumpur, Malaysia.
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia.
| |
Collapse
|
4
|
Gray NE, Hack W, Brandes MS, Zweig JA, Yang L, Marney L, Choi J, Magana AA, Cerruti N, McFerrin J, Koike S, Nguyen T, Raber J, Quinn JF, Maier CS, Soumyanath A. Amelioration of age-related cognitive decline and anxiety in mice by Centella asiatica extract varies by sex, dose and mode of administration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576700. [PMID: 38328129 PMCID: PMC10849617 DOI: 10.1101/2024.01.23.576700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
We have previously reported that a water extract (CAW) of the Ayurvedic plant Centella asiatica administered in drinking water can improve cognitive deficits in mouse models of aging and neurodegenerative diseases. Here we compared the effects of CAW administered in drinking water or the diet on cognition, measures of anxiety and depression-like behavior in healthy aged mice. Three- and eighteen-month-old male and female C57BL6 mice were administered rodent AIN-93M diet containing CAW (0, 0.2, 0.5 or 1% w/w) to provide 0, 200 mg/kg/d, 500 mg/kg/d or 1000 mg/kg/d for a total of 5 weeks. An additional group of eighteen-month-old mice were treated with CAW (10 mg/mL) in their drinking water for a total of five weeks to deliver the same exposure of CAW as the highest dietary dose (1000 mg/kg/d). CAW doses delivered were calculated based on food and water consumption measured in previous experiments. In the fourth and fifth weeks, mice underwent behavioral testing of cognition, anxiety and depression (n=12 of each sex per treatment group in each test). Aged mice of both sexes showed cognitive deficits relative to young mice while only female aged mice showed increased anxiety compared to the young female mice and no differences in depression were observed between the different ages. CAW (1000 mg/kg/d) in the drinking water improved deficits in aged mice in learning, executive function and recognition memory in both sexes and attenuated the increased measures of anxiety observed in the aged female mice. However, CAW in the diet only improved executive function in aged mice at the highest dose (1000 mg/kg/d) in both sexes and did so less robustly than when given in the water. There were no effects of CAW on depression-like behavior in aged animals regardless of whether it was administered in the diet or the water. These results suggest that CAW can ameliorate age-related changes in measures of anxiety and cognition and that the mode of administration is important for the effects of CAW on resilience to these age-related changes.
Collapse
|
5
|
Achiro JM, Tao Y, Gao F, Lin CH, Watanabe M, Neumann S, Coppola G, Black DL, Martin KC. Aging differentially alters the transcriptome and landscape of chromatin accessibility in the male and female mouse hippocampus. Front Mol Neurosci 2024; 17:1334862. [PMID: 38318533 PMCID: PMC10839115 DOI: 10.3389/fnmol.2024.1334862] [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: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Aging-related memory impairment and pathological memory disorders such as Alzheimer's disease differ between males and females, and yet little is known about how aging-related changes in the transcriptome and chromatin environment differ between sexes in the hippocampus. To investigate this question, we compared the chromatin accessibility landscape and gene expression/alternative splicing pattern of young adult and aged mouse hippocampus in both males and females using ATAC-seq and RNA-seq. We detected significant aging-dependent changes in the expression of genes involved in immune response and synaptic function and aging-dependent changes in the alternative splicing of myelin sheath genes. We found significant sex-bias in the expression and alternative splicing of hundreds of genes, including aging-dependent female-biased expression of myelin sheath genes and aging-dependent male-biased expression of genes involved in synaptic function. Aging was associated with increased chromatin accessibility in both male and female hippocampus, especially in repetitive elements, and with an increase in LINE-1 transcription. We detected significant sex-bias in chromatin accessibility in both autosomes and the X chromosome, with male-biased accessibility enriched at promoters and CpG-rich regions. Sex differences in gene expression and chromatin accessibility were amplified with aging, findings that may shed light on sex differences in aging-related and pathological memory loss.
Collapse
Affiliation(s)
- Jennifer M. Achiro
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Yang Tao
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Fuying Gao
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, United States
| | - Marika Watanabe
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Sylvia Neumann
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Douglas L. Black
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, United States
| | - Kelsey C. Martin
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| |
Collapse
|
6
|
Mir FA, Amanullah A, Jain BP, Hyderi Z, Gautam A. Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review. Ageing Res Rev 2023; 91:102067. [PMID: 37689143 DOI: 10.1016/j.arr.2023.102067] [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: 04/30/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Gene expression is tremendously altered in the brain during memory acquisition, recall, and forgetfulness. However, non-genetic factors, including environmental elements, epigenetic changes, and lifestyle, have grabbed significant attention in recent years regarding the etiology of neurodegenerative diseases (NDD) and age-associated dementia. Epigenetic modifications are essential in regulating gene expression in all living organisms in a DNA sequence-independent manner. The genes implicated in ageing and NDD-related memory disorders are epigenetically regulated by processes such as DNA methylation, histone acetylation as well as messenger RNA editing machinery. The physiological and optimal state of the epigenome, especially within the CNS of humans, plays an intricate role in helping us adjust to the changing environment, and alterations in it cause many brain disorders, but the mechanisms behind it still need to be well understood. When fully understood, these epigenetic landscapes could act as vital targets for pharmacogenetic rescue strategies for treating several diseases, including neurodegeneration- and age-induced dementia. Keeping this objective in mind, this updated review summarises the epigenetic changes associated with age and neurodegeneration-associated dementia.
Collapse
Affiliation(s)
- Fayaz Ahmad Mir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Zeeshan Hyderi
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
| |
Collapse
|
7
|
Nobrega M, Farris K, Andersen E, Donkin I, Versteyhe S, Kristiansen VB, Simpson S, Barres R. Splicing across adipocyte differentiation is highly dynamic and impacted by metabolic phenotype. RESEARCH SQUARE 2023:rs.3.rs-3487148. [PMID: 37961160 PMCID: PMC10635361 DOI: 10.21203/rs.3.rs-3487148/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adipose tissue dysfunction underlies many of the metabolic complications associated with obesity. A better understanding of the gene regulation differences present in metabolically unhealthy adipose tissue can provide insights into the mechanisms underlying adipose tissue dysfunction. Here, we used RNA-seq data collected from a differentiation time course of lean, obese, and obese with type 2 diabetes (T2D) individuals to characterize the role of alterative splicing in adipocyte differentiation and function. We found that splicing was highly dynamic across adipocyte differentiation in all three cohorts, and that the dynamics of splicing were significantly impacted by metabolic phenotype. We also found that there was very little overlap between genes that were differentially spliced in adipocyte differentiation and those that were differentially expressed, positioning alternative splicing as a largely independent gene regulatory mechanism whose impact would be missed when looking at gene expression changes alone. To assess the impact of alternative splicing across adipocyte differentiation on genetic risk for metabolic diseases, we integrated the differential splicing results generated here with genome-wide association study results for body mass index and T2D, and found that variants associated with T2D were enriched in regions that were differentially spliced in early differentiation. These findings provide insight into the role of alternative splicing in adipocyte differentiation and can serve as a resource to guide future variant-to-function studies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Romain Barres
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| |
Collapse
|
8
|
Dam SH, Olsen LR, Vitting-Seerup K. Expression and splicing mediate distinct biological signals. BMC Biol 2023; 21:220. [PMID: 37858135 PMCID: PMC10588054 DOI: 10.1186/s12915-023-01724-w] [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: 12/01/2022] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Through alternative splicing, most human genes produce multiple isoforms in a cell-, tissue-, and disease-specific manner. Numerous studies show that alternative splicing is essential for development, diseases, and their treatments. Despite these important examples, the extent and biological relevance of splicing are currently unknown. RESULTS To solve this problem, we developed pairedGSEA and used it to profile transcriptional changes in 100 representative RNA-seq datasets. Our systematic analysis demonstrates that changes in splicing, on average, contribute to 48.1% of the biological signal in expression analyses. Gene-set enrichment analysis furthermore indicates that expression and splicing both convey shared and distinct biological signals. CONCLUSIONS These findings establish alternative splicing as a major regulator of the human condition and suggest that most contemporary RNA-seq studies likely miss out on critical biological insights. We anticipate our results will contribute to the transition from a gene-centric to an isoform-centric research paradigm.
Collapse
Affiliation(s)
- Søren Helweg Dam
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lars Rønn Olsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kristoffer Vitting-Seerup
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
| |
Collapse
|
9
|
Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
Collapse
Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
| |
Collapse
|
10
|
Zou Y, Guo Q, Chang Y, Zhong Y, Cheng L, Wei W. Alternative splicing affects synapses in the hippocampus of offspring after maternal fructose exposure during gestation and lactation. Chem Biol Interact 2023; 379:110518. [PMID: 37121297 DOI: 10.1016/j.cbi.2023.110518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/15/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
Increased fructose over-intake is a global issue. Maternal fructose exposure during gestation and lactation can impair brain development in offspring. However, the effect on synapses is still unknown. For the diversification of RNA and biological functions, alternative splicing (AS) and alternative polyadenylation (APA) are essential. We constructed a maternal high-fructose diet model by administering 13% and 40% fructose water. The student's t-test analyzed the results of RT-qPCR. All other results were analyzed by one-way analysis of variance. The animal behavior experiment results revealed that conditioning and associative memory had been damaged. The proteins that form synapses were consistently low-expressed. In addition, compared with the control group, the Oxford Nanopore Technologies platform's full-length RNA-sequencing identified 298 different spliced genes (DSGs) and 51 differentially expressed alternative splicing (DEAS) genes in the 13% fructose group. 313 DSGs and 74 DEAS genes were in the 40% fructose group. Enrichment analysis based on these altered genes revealed some enlightening items and pathways. Our findings demonstrated the transcriptome mechanism underlying maternal fructose exposure during gestation and lactation and impaired synapse function during the transcripts' editing.
Collapse
Affiliation(s)
- Yuchen Zou
- Child and Adolescent Health, School of Public Health, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, PR China
| | - Qing Guo
- Child and Adolescent Health, School of Public Health, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, PR China
| | - Yidan Chang
- Child and Adolescent Health, School of Public Health, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, PR China
| | - Yongyong Zhong
- Child and Adolescent Health, School of Public Health, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, PR China
| | - Lin Cheng
- Child and Adolescent Health, School of Public Health, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, PR China
| | - Wei Wei
- Child and Adolescent Health, School of Public Health, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, PR China.
| |
Collapse
|
11
|
Tassinari V, La Rosa P, Guida E, Colopi A, Caratelli S, De Paolis F, Gallo A, Cenciarelli C, Sconocchia G, Dolci S, Cesarini V. Contribution of A-to-I RNA editing, M6A RNA Methylation, and Alternative Splicing to physiological brain aging and neurodegenerative diseases. Mech Ageing Dev 2023; 212:111807. [PMID: 37023929 DOI: 10.1016/j.mad.2023.111807] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Aging is a physiological and progressive phenomenon in all organisms' life cycle, characterized by the accumulation of degenerative processes triggered by several alterations within molecular pathways. These changes compromise cell fate, resulting in the loss of functions in tissues throughout the body, including the brain. Physiological brain aging has been linked to structural and functional alterations, as well as to an increased risk of neurodegenerative diseases. Post-transcriptional RNA modifications modulate mRNA coding properties, stability, translatability, expanding the coding capacity of the genome, and are involved in all cellular processes. Among mRNA post-transcriptional modifications, the A-to-I RNA editing, m6A RNA Methylation and Alternative Splicing play a critical role in all the phases of a neuronal cell life cycle and alterations in their mechanisms of action significantly contribute to aging and neurodegeneration. Here we review our current understanding of the contribution of A-to-I RNA editing, m6A RNA Methylation, and Alternative Splicing to physiological brain aging process and neurodegenerative diseases.
Collapse
Affiliation(s)
- Valentina Tassinari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Eugenia Guida
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Ambra Colopi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Sara Caratelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Francesca De Paolis
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Angela Gallo
- RNA Editing Lab., Oncohaematology Department, Cellular and Gene Therapy Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Cenciarelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Giuseppe Sconocchia
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Susanna Dolci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Valeriana Cesarini
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
| |
Collapse
|
12
|
Gautam P, Ajit K, Das M, Taliyan R, Roy R, Banerjee A. Age-related changes in gonadotropin-releasing hormone (GnRH) splice variants in mouse brain. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2023; 339:193-209. [PMID: 36336790 DOI: 10.1002/jez.2671] [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: 04/12/2022] [Revised: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022]
Abstract
Gonadotropin-releasing hormone (GnRH) is the primary regulator of the mammalian reproductive axis. We investigated the spatiotemporal expression of GnRH splice variants (V1, V2, and V3) and splicing factors (Srsf7, Srsf9, and Tra-2) in the male mice brain. Further, using in silico tools, we predicted protein structure and the reason for the low translational efficiency of V2 and V3. Messenger RNA levels of GnRH variants and splicing factors were quantified using real-time reverse transcription-polymerase chain reaction at different age groups. Our data show that expression of almost all the variants alters with aging in all the brain regions studied; even in comparison to the hypothalamus, several brain areas were found to have higher expression of these variants. Hypothalamic expression of splicing factors such as Srsf7, Srsf9, and Tra-2 also change with aging. Computational studies have translation repressors site on the V3, which probably reduces its translation efficiency. Also, V2 is an intrinsically disordered protein that might have a regulatory or signaling function. In conclusion, this study provides novel crucial information and multiple starting points for future analysis of GnRH splice variants in the brain.
Collapse
Affiliation(s)
- Pooja Gautam
- Department of Biological Sciences, BITS Pilani, KK Birla, Goa Campus, Goa, India
| | - Kamal Ajit
- Department of Biological Sciences, BITS Pilani, KK Birla, Goa Campus, Goa, India
| | - Moitreyi Das
- Department of Zoology, Goa University, Goa, India
| | - Rajeev Taliyan
- Department of Pharmacy, BITS Pilani, Pilani Campus, Rajasthan, India
| | | | - Arnab Banerjee
- Department of Biological Sciences, BITS Pilani, KK Birla, Goa Campus, Goa, India
| |
Collapse
|
13
|
Winsky-Sommerer R, King HA, Iadevaia V, Möller-Levet C, Gerber AP. A post-transcriptional regulatory landscape of aging in the female mouse hippocampus. Front Aging Neurosci 2023; 15:1119873. [PMID: 37122377 PMCID: PMC10135431 DOI: 10.3389/fnagi.2023.1119873] [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: 12/09/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2023] Open
Abstract
Aging is associated with substantial physiological changes and constitutes a major risk factor for neurological disorders including dementia. Alterations in gene expression upon aging have been extensively studied; however, an in-depth characterization of post-transcriptional regulatory events remains elusive. Here, we profiled the age-related changes of the transcriptome and translatome in the female mouse hippocampus by RNA sequencing of total RNA and polysome preparations at four ages (3-, 6-, 12-, 20-month-old); and we implemented a variety of bioinformatics approaches to unravel alterations in transcript abundance, alternative splicing, and polyadenylation site selection. We observed mostly well-coordinated transcriptome and translatome expression signatures across age including upregulation of transcripts related to immune system processes and neuroinflammation, though transcripts encoding ribonucleoproteins or associated with mitochondrial functions, calcium signaling and the cell-cycle displayed substantial discordant profiles, suggesting translational control associated with age-related deficits in hippocampal-dependent behavior. By contrast, alternative splicing was less preserved, increased with age and was associated with distinct functionally-related transcripts encoding proteins acting at synapses/dendrites, RNA-binding proteins; thereby predicting regulatory roles for RBM3 and CIRBP. Only minor changes in polyadenylation site selection were identified, indicating pivotal 3'-end selection in young adults compared to older groups. Overall, our study provides a comprehensive resource of age-associated post-transcriptional regulatory events in the mouse hippocampus, enabling further examination of the molecular features underlying age-associated neurological diseases.
Collapse
|
14
|
Huang H, Song R, Wong JJ, Anggono V, Widagdo J. The N6-methyladenosine RNA landscape in the aged mouse hippocampus. Aging Cell 2022; 22:e13755. [PMID: 36495001 PMCID: PMC9835576 DOI: 10.1111/acel.13755] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/13/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
The aged brain is associated with an inevitable decline in cognitive function and increased vulnerability to neurodegenerative disorders. Multiple molecular hallmarks have been associated with the aging nervous system through transcriptomics and proteomic studies. Recently, epitranscriptomic analysis has highlighted the role of RNA chemical modification in various biological processes. In particular, N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNAs, has been functionally linked to multiple aspects of RNA metabolism with the roles of m6A in processes such as learning and memory, leading to our current investigation of how the m6A-transcriptomic landscape is shaped during aging. Using the inbred C57BL/6 line, we compared the m6A-transcriptomic profiles from the hippocampi of young (3-month-old) and aged (20-month-old) mice. Methylated RNA immunoprecipitation (MeRIP)-sequencing analysis revealed hyper- and hypomethylation in 426 and 102 genes, respectively, in the aged hippocampus (fold change >1.5, false discovery rate <0.05). By correlating the methylation changes to their steady-state transcript levels in the RNA-Seq data, we found a significant concordance between m6A and transcript levels in both directions. Notably, the myelin regulator gene Gpr17 was downregulated in the aged hippocampus concomitant with reduced m6A levels in its 3'UTR. Using reporter constructs and mutagenesis analysis, we demonstrated that the putative m6A sites in the 3'UTR of Gpr17 are important for mRNA translation but not for regulating transcript stability. Overall, the positive correlation between m6A and the transcript expression levels indicates a co-transcriptional regulation of m6A with gene expression changes that occur in the aged mouse hippocampus.
Collapse
Affiliation(s)
- He Huang
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain Institute, The University of QueenslandBrisbaneQueenslandAustralia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary InstituteThe University of SydneyCamperdownNew South WalesAustralia,The University of SydneyFaculty of Medicine and HealthCamperdownNew South WalesAustralia
| | - Justin J.‐L. Wong
- Epigenetics and RNA Biology Program Centenary InstituteThe University of SydneyCamperdownNew South WalesAustralia,The University of SydneyFaculty of Medicine and HealthCamperdownNew South WalesAustralia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain Institute, The University of QueenslandBrisbaneQueenslandAustralia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain Institute, The University of QueenslandBrisbaneQueenslandAustralia
| |
Collapse
|
15
|
Lu Y, Xu K, Lin D, Wang S, Fu R, Deng X, Croppi G, Zhang J. Multi-omics analysis reveals neuroinflammation, activated glial signaling, and dysregulated synaptic signaling and metabolism in the hippocampus of aged mice. Front Aging Neurosci 2022; 14:964429. [PMID: 36408109 PMCID: PMC9669972 DOI: 10.3389/fnagi.2022.964429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Aging is an intricate biological event that occurs in both vertebrates and invertebrates. During the aging process, the brain, a vulnerable organ, undergoes structural and functional alterations, resulting in behavioral changes. The hippocampus has long been known to be critically associated with cognitive impairment, dementia, and Alzheimer’s disease during aging; however, the underlying mechanisms remain largely unknown. In this study, we hypothesized that altered metabolic and gene expression profiles promote the aging process in the hippocampus. Behavioral tests showed that exploration, locomotion, learning, and memory activities were reduced in aged mice. Metabolomics analysis identified 69 differentially abundant metabolites and showed that the abundance of amino acids, lipids, and microbiota-derived metabolites (MDMs) was significantly altered in hippocampal tissue of aged animals. Furthermore, transcriptomic analysis identified 376 differentially expressed genes in the aged hippocampus. A total of 35 differentially abundant metabolites and 119 differentially expressed genes, constituting the top 200 correlations, were employed for the co-expression network. The multi-omics analysis showed that pathways related to inflammation, microglial activation, synapse, cell death, cellular/tissue homeostasis, and metabolism were dysregulated in the aging hippocampus. Our data revealed that metabolic perturbations and gene expression alterations in the aged hippocampus were possibly linked to their behavioral changes in aged mice; we also provide evidence that altered MDMs might mediate the interaction between gut and brain during the aging process.
Collapse
Affiliation(s)
- Yinzhong Lu
- Department of Anesthesiology and Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Yinzhong Lu,
| | - Kejia Xu
- Department of Anesthesiology and Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongyang Lin
- Department of Anesthesiology and Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuyan Wang
- Department of Anesthesiology and Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rao Fu
- Department of Neurology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobei Deng
- Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Junjie Zhang
- Department of Anesthesiology and Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Junjie Zhang,
| |
Collapse
|
16
|
Liu Y, Senatore A, Sorce S, Nuvolone M, Guo J, Gümüş ZH, Aguzzi A. Brain aging is faithfully modelled in organotypic brain slices and accelerated by prions. Commun Biol 2022; 5:557. [PMID: 35676449 PMCID: PMC9177860 DOI: 10.1038/s42003-022-03496-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Mammalian models are essential for brain aging research. However, the long lifespan and poor amenability to genetic and pharmacological perturbations have hindered the use of mammals for dissecting aging-regulatory molecular networks and discovering new anti-aging interventions. To circumvent these limitations, we developed an ex vivo model system that faithfully mimics the aging process of the mammalian brain using cultured mouse brain slices. Genome-wide gene expression analyses showed that cultured brain slices spontaneously upregulated senescence-associated genes over time and reproduced many of the transcriptional characteristics of aged brains. Treatment with rapamycin, a classical anti-aging compound, largely abolished the time-dependent transcriptional changes in naturally aged brain slice cultures. Using this model system, we discovered that prions drastically accelerated the development of age-related molecular signatures and the pace of brain aging. We confirmed this finding in mouse models and human victims of Creutzfeldt-Jakob disease. These data establish an innovative, eminently tractable mammalian model of brain aging, and uncover a surprising acceleration of brain aging in prion diseases.
Collapse
Affiliation(s)
- Yingjun Liu
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland.
| | - Assunta Senatore
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Silvia Sorce
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Mario Nuvolone
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
- Amyloidosis Research and Treatment Center, Foundation IRCCS Policlinico San Matteo, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Jingjing Guo
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Zeynep H Gümüş
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
17
|
The signaling pathway of levamisole-sensitive-acetylcholine receptors involved in short-term forgetting of Caenorhabditis elegans. Mol Genet Genomics 2022; 297:1027-1038. [PMID: 35585325 DOI: 10.1007/s00438-022-01901-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/16/2022] [Indexed: 10/18/2022]
Abstract
In contrast to the popular opinion that forgetting is only the opposite of learning and memory, active forgetting explains the intrinsic instability of a labile memory that lasts for hours and has its own signal transduction pathways. However, the detailed mechanisms underlying forgetting are still lacking, though the investigations available in this field offer the first insights into their regulation. To identify the alternative signaling pathways that control the process of forgetting, we used the short-term forgetting model of Caenorhabditis elegans and discovered the involvement of lev-10, a scaffolded transmembrane protein of L-AChR, by screening the candidate genes that potentially functioned in synaptic plasticity. The LEV-9/LEV-10/L-AChR functional complex was confirmed to participate in forgetting occurrence. Furthermore, EGL-9 functioned upstream of LEV-10 and negatively regulated the latter during forgetting. Meanwhile, EGL-9 was also the target of miR-51, and hence the mutation of miR-51 similarly affected the function of L-AChR and delayed the short-term forgetting. Our findings have identified an integrated signaling pathway responsible for active forgetting, which provides the new experimental evidence on the cholinergic forgetting signal.
Collapse
|
18
|
Sándor S, Jónás D, Tátrai K, Czeibert K, Kubinyi E. Poly(A) RNA sequencing reveals age-related differences in the prefrontal cortex of dogs. GeroScience 2022; 44:1269-1293. [PMID: 35288843 PMCID: PMC9213612 DOI: 10.1007/s11357-022-00533-3] [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: 08/24/2021] [Accepted: 02/17/2022] [Indexed: 12/02/2022] Open
Abstract
Dogs may possess a unique translational potential to investigate neural aging and dementia because they are prone to age-related cognitive decline, including an Alzheimer’s disease–like pathological condition. Yet very little is known about the molecular mechanisms underlying canine cognitive decline. The goal of the current study was to explore the transcriptomic differences between young and old dogs’ frontal cortex, which is a brain region often affected by various forms of age-related dementia in humans. RNA isolates from the frontal cortical brain area of 13 pet dogs, which represented 7 different breeds and crossbreds, were analyzed. The dogs were euthanized for medical reasons, and their bodies had been donated by their owners for scientific purposes. The poly(A) tail RNA subfraction of the total transcriptome was targeted in the sequencing analysis. Cluster analyses, differential gene expression analyses, and gene ontology analyses were carried out to assess which genes and genetic regulatory mechanisms were mostly affected by aging. Age was the most prominent factor in the clustering of the animals, indicating the presence of distinct gene expression patterns related to aging in a genetically variable population. A total of 3436 genes were found to be differentially expressed between the age groups, many of which were linked to neural function, immune system, and protein synthesis. These findings are in accordance with previous human brain aging RNA sequencing studies. Some genes were found to behave more similarly to humans than to rodents, further supporting the applicability of dogs in translational aging research.
Collapse
Affiliation(s)
- Sára Sándor
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.
| | - Dávid Jónás
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kitti Tátrai
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.,Department of Genetics, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kálmán Czeibert
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| |
Collapse
|
19
|
Trauma-like exposure alters neuronal apoptosis, Bin1, Fkbp5 and NR2B expression in an amyloid-beta (1-42) rat model of Alzheimer's disease. Neurobiol Learn Mem 2022; 190:107611. [DOI: 10.1016/j.nlm.2022.107611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/01/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022]
|
20
|
Faborode OS, Dalle E, Mabandla MV. Inescapable footshocks induce molecular changes in the prefrontal cortex of rats in an amyloid-beta-42 model of Alzheimer's disease. Behav Brain Res 2022; 419:113679. [PMID: 34826515 DOI: 10.1016/j.bbr.2021.113679] [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: 08/09/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022]
Abstract
Alzheimer's disease (AD) affects several brain areas, including the prefrontal cortex (PFC) involved in execution, working memory, and fear extinction. Despite these critical roles, the PFC is understudied in AD pathology. People with post-traumatic stress disorder (PTSD) have twice the risk of developing AD, and the underlying mechanisms linking these two diseases are less understood. Here, we investigated the effect of footshock stress on behavioural vis-a-vis molecular changes in the PFC of an amyloid-beta (Aβ)-42 lesion rat model of AD. Trauma-like conditions were induced by exposing the animals to several footshocks. AD-like condition was induced via intra-hippocampal injection of Aβ-42 peptide. Following Aβ-42 injections, animals were tested for behavioural changes using the Open Field Test (OFT) and Y-maze test. The PFC was later harvested for neurochemical analyses. Our results showed an interactive effect of footshocks and Aβ-42 lesion on: reduced percentage alternation in the Y-maze test, suggesting memory impairment; reduced number of line crosses and time spent in the centre square of the OFT, indicating anxiogenic responses. Similarly, there was an interactive effect of footshocks and Aβ-42 lesion on: increased FK506 binding protein 51 (FKBP5) expression, which can be associated with stress-induced anxiogenic behaviours; and increased neuronal apoptosis in the PFC of the animals. In addition, footshocks, as well as Aβ-42 lesion, reduced superoxide dismutase levels and Bridging Integrator-1 (BIN1) expression in the PFC of the animals, which can be linked to the observed memory impairment. In conclusion, our findings indicate that footshocks exaggerate PFC-associated behavioural and molecular changes induced by an AD-like pathology.
Collapse
MESH Headings
- Alzheimer Disease/chemically induced
- Alzheimer Disease/etiology
- Alzheimer Disease/metabolism
- Alzheimer Disease/physiopathology
- Amyloid beta-Peptides/pharmacology
- Animals
- Anxiety/chemically induced
- Anxiety/etiology
- Anxiety/metabolism
- Anxiety/physiopathology
- Apoptosis/drug effects
- Apoptosis/physiology
- Behavior, Animal/drug effects
- Behavior, Animal/physiology
- Disease Models, Animal
- Electroshock
- Male
- Memory Disorders/chemically induced
- Memory Disorders/etiology
- Memory Disorders/metabolism
- Memory Disorders/physiopathology
- Memory, Short-Term/drug effects
- Memory, Short-Term/physiology
- Peptide Fragments/pharmacology
- Prefrontal Cortex/metabolism
- Prefrontal Cortex/physiopathology
- Rats
- Rats, Sprague-Dawley
- Stress Disorders, Post-Traumatic/chemically induced
- Stress Disorders, Post-Traumatic/etiology
- Stress Disorders, Post-Traumatic/metabolism
- Stress Disorders, Post-Traumatic/physiopathology
- Tacrolimus Binding Proteins/metabolism
Collapse
Affiliation(s)
- Oluwaseun Samuel Faborode
- Discipline of Human Physiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa.
| | - Ernest Dalle
- Discipline of Human Physiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa.
| | - Musa Vuyisile Mabandla
- Discipline of Human Physiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa.
| |
Collapse
|
21
|
Wang J, Qi W, Shi H, Huang L, Ning F, Wang F, Wang K, Bai H, Wu H, Zhuang J, Hong H, Zhou H, Feng H, Zhou Y, Dong N, Liu L, Kong Y, Xie J, Zhao RC. MiR-4763-3p targeting RASD2as a Potential Biomarker and Therapeutic Target for Schizophrenia. Aging Dis 2022; 13:1278-1292. [PMID: 35855328 PMCID: PMC9286908 DOI: 10.14336/ad.2022.0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/03/2021] [Indexed: 11/06/2022] Open
Abstract
Existing diagnostic methods are limited to observing appearance and demeanor, even though genetic factors play important roles in the pathology of schizophrenia. Indeed, no molecular-level test exists to assist diagnosis, which has limited treatment strategies. To address this serious shortcoming, we used a bioinformatics approach to identify 61 genes that are differentially expressed in schizophrenia patients compared with healthy controls. In particular, competing endogenous RNA network revealed the important role of the gene RASD2, which is regulated by miR-4763-3p. Indeed, analysis of blood samples confirmed that RASD2 is downregulated in schizophrenia patients. Moreover, positron emission tomography data collected for 44 human samples identified the prefrontal and temporal lobes as potential key brain regions in schizophrenia patients. Mechanistic studies indicated that miR-4763-3p inhibits RASD2 by base-pairing with the 3’ untranslated region of RASD2 mRNA. Importantly, RASD2 has been shown to interact with β-arrestin2, which contributes to the regulation of the DRD2-dependent CREB response element-binding protein pathway in the dopamine system. Finally, results obtained with a mouse model of schizophrenia revealed that inhibition of miR-4763-3p function alleviated anxiety symptoms and improved memory. The dopamine transporters in the striatal regions were significantly reduced in schizophrenia model mice as compared with wild-type mice, suggesting that inhibition of miR-4763-3p can lessen the symptoms of schizophrenia. Our findings demonstrate that miR-4763-3p may target RASD2 mRNA and thus may serve as a potential biomarker and therapeutic target for schizophrenia, providing a theoretical foundation for further studies of the molecular basis of this disease.
Collapse
Affiliation(s)
- Jiao Wang
- School of Life Sciences, Shanghai University, Shanghai, China.
- Correspondence should be addressed to: Dr. Jiao Wang (), School of Life Sciences, Shanghai University, Shanghai, China; Dr. Yanyan Kong (), PET Center, Huashan Hospital, Fudan University, Shanghai, China; Dr. Jiang Xie (), School of Computer Engineering and Science, Shanghai University, Shanghai, China, and Dr. Robert Chunhua Zhao (), School of Life Sciences, Shanghai University, Shanghai, China
| | - Wenxin Qi
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Hongwei Shi
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Lin Huang
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Fujiang Ning
- Psychological Rehabilitation Hospital of Penglai District, Yantai, Shandong, China
| | - Fushuai Wang
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Kai Wang
- Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Haotian Bai
- School of Computer Engineering and Science, Shanghai University, Shanghai, China.
| | - Hao Wu
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Junyi Zhuang
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Huanle Hong
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Haicong Zhou
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Hu Feng
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Yinping Zhou
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Naijun Dong
- School of Life Sciences, Shanghai University, Shanghai, China.
| | - Li Liu
- Psychological Rehabilitation Hospital of Penglai District, Yantai, Shandong, China
| | - Yanyan Kong
- PET Center, Huashan Hospital, Fudan University, Shanghai, China.
- Correspondence should be addressed to: Dr. Jiao Wang (), School of Life Sciences, Shanghai University, Shanghai, China; Dr. Yanyan Kong (), PET Center, Huashan Hospital, Fudan University, Shanghai, China; Dr. Jiang Xie (), School of Computer Engineering and Science, Shanghai University, Shanghai, China, and Dr. Robert Chunhua Zhao (), School of Life Sciences, Shanghai University, Shanghai, China
| | - Jiang Xie
- School of Computer Engineering and Science, Shanghai University, Shanghai, China.
- Correspondence should be addressed to: Dr. Jiao Wang (), School of Life Sciences, Shanghai University, Shanghai, China; Dr. Yanyan Kong (), PET Center, Huashan Hospital, Fudan University, Shanghai, China; Dr. Jiang Xie (), School of Computer Engineering and Science, Shanghai University, Shanghai, China, and Dr. Robert Chunhua Zhao (), School of Life Sciences, Shanghai University, Shanghai, China
| | - Robert Chunhua Zhao
- School of Life Sciences, Shanghai University, Shanghai, China.
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
- Centre of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences, Beijing, China.
- Beijing Key Laboratory of New Drug Development and Clinical Trial of Stem Cell Therapy (BZ0381), Beijing, China.
- Correspondence should be addressed to: Dr. Jiao Wang (), School of Life Sciences, Shanghai University, Shanghai, China; Dr. Yanyan Kong (), PET Center, Huashan Hospital, Fudan University, Shanghai, China; Dr. Jiang Xie (), School of Computer Engineering and Science, Shanghai University, Shanghai, China, and Dr. Robert Chunhua Zhao (), School of Life Sciences, Shanghai University, Shanghai, China
| |
Collapse
|
22
|
McCauley BS, Sun L, Yu R, Lee M, Liu H, Leeman DS, Huang Y, Webb AE, Dang W. Altered Chromatin States Drive Cryptic Transcription in Aging Mammalian Stem Cells. ACTA ACUST UNITED AC 2021; 1:684-697. [PMID: 34746802 DOI: 10.1038/s43587-021-00091-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A repressive chromatin state featuring trimethylated lysine 36 on histone H3 (H3K36me3) and DNA methylation suppresses cryptic transcription in embryonic stem cells. Cryptic transcription is elevated with age in yeast and nematodes, and reducing it extends yeast lifespan, though whether this occurs in mammals is unknown. We show that cryptic transcription is elevated in aged mammalian stem cells, including murine hematopoietic stem cells (mHSCs) and neural stem cells (NSCs) and human mesenchymal stem cells (hMSCs). Precise mapping allowed quantification of age-associated cryptic transcription in hMSCs aged in vitro. Regions with significant age-associated cryptic transcription have a unique chromatin signature: decreased H3K36me3 and increased H3K4me1, H3K4me3, and H3K27ac with age. Genomic regions undergoing such changes resemble known promoter sequences and are bound by TBP even in young cells. Hence, the more permissive chromatin state at intragenic cryptic promoters likely underlies increased cryptic transcription in aged mammalian stem cells.
Collapse
Affiliation(s)
- Brenna S McCauley
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luyang Sun
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruofan Yu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Minjung Lee
- Center for Epigenetics & Disease Prevention, Institute of Bioscience and Technology, Texas A&M University, Houston, TX 77030, USA.,Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Haiying Liu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dena S Leeman
- Department of Genetics, Stanford University, Stanford, CA, 94305 USA.,Department of Discovery Immunology, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Bioscience and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Ashley E Webb
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
23
|
Islam MR, Kaurani L, Berulava T, Heilbronner U, Budde M, Centeno TP, Elerdashvili V, Zafieriou M, Benito E, Sertel SM, Goldberg M, Senner F, Kalman JL, Burkhardt S, Oepen AS, Sakib MS, Kerimoglu C, Wirths O, Bickeböller H, Bartels C, Brosseron F, Buerger K, Cosma N, Fliessbach K, Heneka MT, Janowitz D, Kilimann I, Kleinedam L, Laske C, Metzger CD, Munk MH, Perneczky R, Peters O, Priller J, Rauchmann BS, Roy N, Schneider A, Spottke A, Spruth EJ, Teipel S, Tscheuschler M, Wagner M, Wiltfang J, Düzel E, Jessen F, Rizzoli SO, Zimmermann W, Schulze TG, Falkai P, Sananbenesi F, Fischer A. A microRNA signature that correlates with cognition and is a target against cognitive decline. EMBO Mol Med 2021; 13:e13659. [PMID: 34633146 PMCID: PMC8573587 DOI: 10.15252/emmm.202013659] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/25/2022] Open
Abstract
While some individuals age without pathological memory impairments, others develop age-associated cognitive diseases. Since changes in cognitive function develop slowly over time in these patients, they are often diagnosed at an advanced stage of molecular pathology, a time point when causative treatments fail. Thus, there is great need for the identification of inexpensive and minimal invasive approaches that could be used for screening with the aim to identify individuals at risk for cognitive decline that can then undergo further diagnostics and eventually stratified therapies. In this study, we use an integrative approach combining the analysis of human data and mechanistic studies in model systems to identify a circulating 3-microRNA signature that reflects key processes linked to neural homeostasis and inform about cognitive status. We furthermore provide evidence that expression changes in this signature represent multiple mechanisms deregulated in the aging and diseased brain and are a suitable target for RNA therapeutics.
Collapse
|
24
|
Exposure to footshock stress downregulates antioxidant genes and increases neuronal apoptosis in an Aβ(1-42) rat model of Alzheimer's disease. Neurochem Int 2021; 150:105170. [PMID: 34419526 DOI: 10.1016/j.neuint.2021.105170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022]
Abstract
Post-traumatic stress disorder (PTSD) is a neuropsychiatric disorder that develops from exposure to trauma, mostly when normal psychological mechanisms fail. Studies have shown that people who have PTSD are susceptible to developing dementia, mostly Alzheimer's disease (AD), suggesting common underlying risk factors in the comorbidity. However, data elucidating links between these conditions is scarce. Here we show that footshock stress exacerbates AD-like pathology. To induce a trauma-like condition, the rats were exposed to multiple intense footshocks followed by a single reminder. This was followed by bilateral intrahippocampal lesions with amyloid-beta (Aβ) (1-42), to model AD-like pathology. We found that footshocks increased anxiety behavior and impaired fear memory extinction in Aβ(1-42) lesioned rats. We also found a reduced expression of nuclear factor erythroid 2-related factor 2 (Nrf2), NAD (P) H: quinone oxidoreductase 1 (NQO1), heme oxygenase-1 (HO-1), and an increased expression of Kelch-like ECH-associated protein 1 (Keap1) in the amygdala and hippocampus. Furthermore, oxidative stress level was sustained, which was associated with increased apoptosis in the amygdala and hippocampus. Our finding suggests that AD-like pathology can induce oxidative changes in the amygdala and hippocampus, which can be exaggerated by footshock stress.
Collapse
|
25
|
Gupta K, Yadav P, Maryam S, Ahuja G, Sengupta D. Quantification of Age-Related Decline in Transcriptional Homeostasis. J Mol Biol 2021; 433:167179. [PMID: 34339725 DOI: 10.1016/j.jmb.2021.167179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Age-dependent dysregulation of transcription regulatory machinery triggers modulations in the gene expression levels leading to the decline in cellular fitness. Tracking of these transcripts along the temporal axis in multiple species revealed a spectrum of evolutionarily conserved pathways, such as electron transport chain, translation regulation, DNA repair, etc. Recent shreds of evidence suggest that aging deteriorates the transcription machinery itself, indicating the hidden complexity of the aging transcriptomes. This reinforces the need for devising novel computational methods to view aging through the lens of transcriptomics. Here, we present Homeostatic Divergence Score (HDS) to quantify the extent of messenger RNA (mRNA) homeostasis by assessing the balance between spliced and unspliced mRNA repertoire in single cells. We validated its utility in two independent aging datasets, and identified sets of genes undergoing age-related breakdown of transcriptional homeostasis. Moreover, testing of our method on a subpopulation of human embryonic stem cells revealed a set of differentially processed transcripts segregating these subpopulations. Our preliminary analyses in this direction suggest that mRNA processing level information offered by single-cell RNA sequencing (scRNA-seq) data is a superior determinant of chronological age as compared to transcriptional noise.
Collapse
Affiliation(s)
- Krishan Gupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Princey Yadav
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Sidrah Maryam
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India.
| | - Debarka Sengupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Institute of Health and Biomedical Innovation, Queensland University of Technology, Australia.
| |
Collapse
|
26
|
Park J, Farris S. Spatiotemporal Regulation of Transcript Isoform Expression in the Hippocampus. Front Mol Neurosci 2021; 14:694234. [PMID: 34305526 PMCID: PMC8295539 DOI: 10.3389/fnmol.2021.694234] [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: 04/12/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development and plasticity of hippocampal neurons require specific RNA isoforms to be expressed in the right place at the right time. Precise spatiotemporal transcript regulation requires the incorporation of essential regulatory RNA sequences into expressed isoforms. In this review, we describe several RNA processing strategies utilized by hippocampal neurons to regulate the spatiotemporal expression of genes critical to development and plasticity. The works described here demonstrate how the hippocampus is an ideal investigative model for uncovering alternate isoform-specific mechanisms that restrict the expression of transcripts in space and time.
Collapse
Affiliation(s)
- Joun Park
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, United States
| | - Shannon Farris
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
| |
Collapse
|
27
|
Zocher S, Overall RW, Lesche M, Dahl A, Kempermann G. Environmental enrichment preserves a young DNA methylation landscape in the aged mouse hippocampus. Nat Commun 2021; 12:3892. [PMID: 34162876 PMCID: PMC8222384 DOI: 10.1038/s41467-021-23993-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
The decline of brain function during aging is associated with epigenetic changes, including DNA methylation. Lifestyle interventions can improve brain function during aging, but their influence on age-related epigenetic changes is unknown. Using genome-wide DNA methylation sequencing, we here show that experiencing a stimulus-rich environment counteracts age-related DNA methylation changes in the hippocampal dentate gyrus of mice. Specifically, environmental enrichment prevented the aging-induced CpG hypomethylation at target sites of the methyl-CpG-binding protein Mecp2, which is critical to neuronal function. The genes at which environmental enrichment counteracted aging effects have described roles in neuronal plasticity, neuronal cell communication and adult hippocampal neurogenesis and are dysregulated with age-related cognitive decline in the human brain. Our results highlight the stimulating effects of environmental enrichment on hippocampal plasticity at the level of DNA methylation and give molecular insights into the specific aspects of brain aging that can be counteracted by lifestyle interventions.
Collapse
Affiliation(s)
- Sara Zocher
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Rupert W Overall
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Mathias Lesche
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Andreas Dahl
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany.
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.
| |
Collapse
|
28
|
Groh J, Knöpper K, Arampatzi P, Yuan X, Lößlein L, Saliba AE, Kastenmüller W, Martini R. Accumulation of cytotoxic T cells in the aged CNS leads to axon degeneration and contributes to cognitive and motor decline. NATURE AGING 2021; 1:357-367. [PMID: 37117598 DOI: 10.1038/s43587-021-00049-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/23/2021] [Indexed: 04/30/2023]
Abstract
Aging is a major risk factor for the development of nervous system functional decline, even in the absence of diseases or trauma. The axon-myelin units and synaptic terminals are some of the neural structures most vulnerable to aging-related deterioration1-6, but the underlying mechanisms are poorly understood. In the peripheral nervous system, macrophages-important representatives of the innate immune system-are prominent drivers of structural and functional decline of myelinated fibers and motor endplates during aging7. Similarly, in the aging central nervous system (CNS), microglial cells promote damage of myelinated axons and synapses8-20. Here we examine the role of cytotoxic CD8+ T lymphocytes, a type of adaptive immune cells previously identified as amplifiers of axonal perturbation in various models of genetically mediated CNS diseases21 but understudied in the aging CNS22-25. We show that accumulation of CD8+ T cells drives axon degeneration in the normal aging mouse CNS and contributes to age-related cognitive and motor decline. We characterize CD8+ T-cell population heterogeneity in the adult and aged mouse brain by single-cell transcriptomics and identify aging-related changes. Mechanistically, we provide evidence that CD8+ T cells drive axon degeneration in a T-cell receptor- and granzyme B-dependent manner. Cytotoxic neural damage is further aggravated by systemic inflammation in aged but not adult mice. We also find increased densities of T cells in white matter autopsy material from older humans. Our results suggest that targeting CD8+ CNS-associated T cells in older adults might mitigate aging-related decline of brain structure and function.
Collapse
Affiliation(s)
- Janos Groh
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany.
| | - Konrad Knöpper
- Institute for Systems Immunology, University of Würzburg, Würzburg, Germany
| | | | - Xidi Yuan
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Lena Lößlein
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | | | - Rudolf Martini
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| |
Collapse
|
29
|
Sas-Nowosielska H, Magalska A. Long Noncoding RNAs-Crucial Players Organizing the Landscape of the Neuronal Nucleus. Int J Mol Sci 2021; 22:ijms22073478. [PMID: 33801737 PMCID: PMC8037058 DOI: 10.3390/ijms22073478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
The ability to regulate chromatin organization is particularly important in neurons, which dynamically respond to external stimuli. Accumulating evidence shows that lncRNAs play important architectural roles in organizing different nuclear domains like inactive chromosome X, splicing speckles, paraspeckles, and Gomafu nuclear bodies. LncRNAs are abundantly expressed in the nervous system where they may play important roles in compartmentalization of the cell nucleus. In this review we will describe the architectural role of lncRNAs in the nuclei of neuronal cells.
Collapse
|
30
|
Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021. [PMID: 33565261 DOI: 10.1002/wrna.1643.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
| |
Collapse
|
31
|
Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
| |
Collapse
|
32
|
Shah S, Richter JD. Do Fragile X Syndrome and Other Intellectual Disorders Converge at Aberrant Pre-mRNA Splicing? Front Psychiatry 2021; 12:715346. [PMID: 34566717 PMCID: PMC8460907 DOI: 10.3389/fpsyt.2021.715346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
Fragile X Syndrome is a neuro-developmental disorder caused by the silencing of the FMR1 gene, resulting in the loss of its protein product, FMRP. FMRP binds mRNA and represses general translation in the brain. Transcriptome analysis of the Fmr1-deficient mouse hippocampus reveals widespread dysregulation of alternative splicing of pre-mRNAs. Many of these aberrant splicing changes coincide with those found in post-mortem brain tissue from individuals with autism spectrum disorders (ASDs) as well as in mouse models of intellectual disability such as PTEN hamartoma syndrome (PHTS) and Rett Syndrome (RTT). These splicing changes could result from chromatin modifications (e.g., in FXS, RTT) and/or splicing factor alterations (e.g., PTEN, autism). Based on the identities of the RNAs that are mis-spliced in these disorders, it may be that they are at least partly responsible for some shared pathophysiological conditions. The convergence of splicing aberrations among these autism spectrum disorders might be crucial to understanding their underlying cognitive impairments.
Collapse
Affiliation(s)
- Sneha Shah
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States
| |
Collapse
|
33
|
Tissue-specific Gene Expression Changes Are Associated with Aging in Mice. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:430-442. [PMID: 33309863 PMCID: PMC8242333 DOI: 10.1016/j.gpb.2020.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/13/2019] [Accepted: 04/10/2019] [Indexed: 12/17/2022]
Abstract
Aging is a complex process that can be characterized by functional and cognitive decline in an individual. Aging can be assessed based on the functional capacity of vital organs and their intricate interactions with one another. Thus, the nature of aging can be described by focusing on a specific organ and an individual itself. However, to fully understand the complexity of aging, one must investigate not only a single tissue or biological process but also its complex interplay and interdependencies with other biological processes. Here, using RNA-seq, we monitored changes in the transcriptome during aging in four tissues (including brain, blood, skin and liver) in mice at 9 months, 15 months, and 24 months, with a final evaluation at the very old age of 30 months. We identified several genes and processes that were differentially regulated during aging in both tissue-dependent and tissue-independent manners. Most importantly, we found that the electron transport chain (ETC) of mitochondria was similarly affected at the transcriptome level in the four tissues during the aging process. We also identified the liver as the tissue showing the largest variety of differentially expressed genes (DEGs) over time. Lcn2 (Lipocalin-2) was found to be similarly regulated among all tissues, and its effect on longevity and survival was validated using its orthologue in Caenorhabditis elegans. Our study demonstrated that the molecular processes of aging are relatively subtle in their progress, and the aging process of every tissue depends on the tissue’s specialized function and environment. Hence, individual gene or process alone cannot be described as the key of aging in the whole organism.
Collapse
|
34
|
Morshed N, Ralvenius WT, Nott A, Watson LA, Rodriguez FH, Akay LA, Joughin BA, Pao P, Penney J, LaRocque L, Mastroeni D, Tsai L, White FM. Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration. Mol Syst Biol 2020; 16:e9819. [PMID: 33289969 PMCID: PMC7722784 DOI: 10.15252/msb.20209819] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the appearance of amyloid-β plaques, neurofibrillary tangles, and inflammation in brain regions involved in memory. Using mass spectrometry, we have quantified the phosphoproteome of the CK-p25, 5XFAD, and Tau P301S mouse models of neurodegeneration. We identified a shared response involving Siglec-F which was upregulated on a subset of reactive microglia. The human paralog Siglec-8 was also upregulated on microglia in AD. Siglec-F and Siglec-8 were upregulated following microglial activation with interferon gamma (IFNγ) in BV-2 cell line and human stem cell-derived microglia models. Siglec-F overexpression activates an endocytic and pyroptotic inflammatory response in BV-2 cells, dependent on its sialic acid substrates and immunoreceptor tyrosine-based inhibition motif (ITIM) phosphorylation sites. Related human Siglecs induced a similar response in BV-2 cells. Collectively, our results point to an important role for mouse Siglec-F and human Siglec-8 in regulating microglial activation during neurodegeneration.
Collapse
Affiliation(s)
- Nader Morshed
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - William T Ralvenius
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Alexi Nott
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain SciencesImperial College LondonUK
- UK Dementia Research Institute at Imperial College LondonLondonUK
| | - L Ashley Watson
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Felicia H Rodriguez
- Department of Chemical and Materials EngineeringNew Mexico State UniversityLas CrucesNMUSA
| | - Leyla A Akay
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Brian A Joughin
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Ping‐Chieh Pao
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Jay Penney
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Lauren LaRocque
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Diego Mastroeni
- ASU‐Banner Neurodegenerative Disease Research CenterTempeAZUSA
| | - Li‐Huei Tsai
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Forest M White
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Precision Cancer MedicineMassachusetts Institute of TechnologyCambridgeMAUSA
| |
Collapse
|
35
|
Szeto RA, Tran T, Truong J, Negraes PD, Trujillo CA. RNA processing in neurological tissue: development, aging and disease. Semin Cell Dev Biol 2020; 114:57-67. [PMID: 33077405 DOI: 10.1016/j.semcdb.2020.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 07/29/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Gene expression comprises a diverse array of enzymes, proteins, non-coding transcripts, and cellular structures to guide the transfer of genetic information to its various final products. In the brain, the coordination among genes, or lack thereof, characterizes individual brain regions, mediates a variety of brain-related disorders, and brings light to fundamental differences between species. RNA processing, occurring between transcription and translation, controls an essential portion of gene expression through splicing, editing, localization, stability, and interference. The machinery to regulate transcripts must operate with precision serving as a blueprint for proteins and non-coding RNAs to derive their identity. Therefore, RNA processing has a broad scope of influence in the brain, as it modulates cell morphogenesis during development and underlies mechanisms behind certain neurological diseases. Here, we present these ideas through recent findings on RNA processing in development and post-developmental maturity to advance therapeutic discoveries and the collective knowledge of the RNA life cycle.
Collapse
Affiliation(s)
- Ryan A Szeto
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Timothy Tran
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Justin Truong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Priscilla D Negraes
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Cleber A Trujillo
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
| |
Collapse
|
36
|
D'Amato A, Di Cesare Mannelli L, Lucarini E, Man AL, Le Gall G, Branca JJV, Ghelardini C, Amedei A, Bertelli E, Regoli M, Pacini A, Luciani G, Gallina P, Altera A, Narbad A, Gulisano M, Hoyles L, Vauzour D, Nicoletti C. Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients. MICROBIOME 2020; 8:140. [PMID: 33004079 PMCID: PMC7532115 DOI: 10.1186/s40168-020-00914-w] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/31/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The gut-brain axis and the intestinal microbiota are emerging as key players in health and disease. Shifts in intestinal microbiota composition affect a variety of systems; however, evidence of their direct impact on cognitive functions is still lacking. We tested whether faecal microbiota transplant (FMT) from aged donor mice into young adult recipients altered the hippocampus, an area of the central nervous system (CNS) known to be affected by the ageing process and related functions. RESULTS Young adult mice were transplanted with the microbiota from either aged or age-matched donor mice. Following transplantation, characterization of the microbiotas and metabolomics profiles along with a battery of cognitive and behavioural tests were performed. Label-free quantitative proteomics was employed to monitor protein expression in the hippocampus of the recipients. We report that FMT from aged donors led to impaired spatial learning and memory in young adult recipients, whereas anxiety, explorative behaviour and locomotor activity remained unaffected. This was paralleled by altered expression of proteins involved in synaptic plasticity and neurotransmission in the hippocampus. Also, a strong reduction of bacteria associated with short-chain fatty acids (SCFAs) production (Lachnospiraceae, Faecalibaculum, and Ruminococcaceae) and disorders of the CNS (Prevotellaceae and Ruminococcaceae) was observed. Finally, the detrimental effect of FMT from aged donors on the CNS was confirmed by the observation that microglia cells of the hippocampus fimbria, acquired an ageing-like phenotype; on the contrary, gut permeability and levels of systemic and local (hippocampus) cytokines were not affected. CONCLUSION These results demonstrate that age-associated shifts of the microbiota have an impact on protein expression and key functions of the CNS. Furthermore, these results highlight the paramount importance of the gut-brain axis in ageing and provide a strong rationale to devise therapies aiming to restore a young-like microbiota to improve cognitive functions and the declining quality of life in the elderly. Video Abstract.
Collapse
Affiliation(s)
| | | | - Elena Lucarini
- NEUROFARBA Department., University of Florence, Florence, Italy
| | | | - Gwenaelle Le Gall
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jacopo J V Branca
- Dept. of Experimental and Clinical Medicine, University of Florence, 50134, Florence, Italy
| | | | - Amedeo Amedei
- Dept. of Experimental and Clinical Medicine, University of Florence, 50134, Florence, Italy
| | - Eugenio Bertelli
- Dept. of Developmental and Molecular Medicine, University of Siena, Siena, Italy
| | - Mari Regoli
- Dept. of Developmental and Molecular Medicine, University of Siena, Siena, Italy
| | - Alessandra Pacini
- Dept. of Experimental and Clinical Medicine, University of Florence, 50134, Florence, Italy
| | - Giulia Luciani
- Dept. of Experimental and Clinical Medicine, University of Florence, 50134, Florence, Italy
| | - Pasquale Gallina
- NEUROFARBA Department., University of Florence, Florence, Italy
- Neurosurgery Unit, Careggi University Hospital, Florence, Italy
| | - Annalisa Altera
- Dept. of Developmental and Molecular Medicine, University of Siena, Siena, Italy
| | | | - Massimo Gulisano
- Dept. of Experimental and Clinical Medicine, University of Florence, 50134, Florence, Italy
| | - Lesley Hoyles
- Dept. of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - David Vauzour
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Claudio Nicoletti
- Dept. of Experimental and Clinical Medicine, University of Florence, 50134, Florence, Italy.
| |
Collapse
|
37
|
Creighton SD, Stefanelli G, Reda A, Zovkic IB. Epigenetic Mechanisms of Learning and Memory: Implications for Aging. Int J Mol Sci 2020; 21:E6918. [PMID: 32967185 PMCID: PMC7554829 DOI: 10.3390/ijms21186918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
The neuronal epigenome is highly sensitive to external events and its function is vital for producing stable behavioral outcomes, such as the formation of long-lasting memories. The importance of epigenetic regulation in memory is now well established and growing evidence points to altered epigenome function in the aging brain as a contributing factor to age-related memory decline. In this review, we first summarize the typical role of epigenetic factors in memory processing in a healthy young brain, then discuss the aspects of this system that are altered with aging. There is general agreement that many epigenetic marks are modified with aging, but there are still substantial inconsistencies in the precise nature of these changes and their link with memory decline. Here, we discuss the potential source of age-related changes in the epigenome and their implications for therapeutic intervention in age-related cognitive decline.
Collapse
Affiliation(s)
- Samantha D. Creighton
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
| | - Gilda Stefanelli
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
| | - Anas Reda
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada;
| | - Iva B. Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada;
| |
Collapse
|
38
|
Effects of age and social isolation on murine hippocampal biochemistry and behavior. Mech Ageing Dev 2020; 191:111337. [PMID: 32866520 DOI: 10.1016/j.mad.2020.111337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/29/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022]
Abstract
Social isolation (SI) is a major health risk in older people leading to cognitive decline. This study examined how SI and age influence performance in the novel object recognition (NOR) and elevated plus maze (EPM) tasks in C57BL/6 mice aged 3 or 24 months. Mice were group-housed (groups of 2-3) or isolated for 2 weeks prior to experimentation. Following NOR and EPM testing hippocampal norepinephrine (NE), 5, hydroxytryptamine (5-HT), 5, hydroxyindole acetic acid (5-HIAA), corticosterone (CORT) and interleukin-6 (IL-6) were determined and serum collected for basal CORT analysis. A separate set of mice were exposed to the forced swim test (FST), sacrificed immediately and serum CORT determined. SI impaired performance in the NOR and the FST, reduced hippocampal 5-HT, increased hippocampal IL-6 and increased serum CORT post-FST in young mice. Aged mice either failed to respond significantly to SI (NOR, FST, hippocampal 5-HT, serum CORT post FST) or SI had synergistic effects with age (hippocampal NE, 5-HIAA:5-HT). In conclusion, the lack of response to SI in the aged mice may affect health by preventing them adapting to new stressors, while the synergistic effects of SI with age would increase allostatic load and enhance the deleterious effects of the ageing process.
Collapse
|
39
|
Paterson C, Cumming B, Law AJ. Temporal Dynamics of the Neuregulin-ErbB Network in the Murine Prefrontal Cortex across the Lifespan. Cereb Cortex 2020; 30:3325-3339. [PMID: 31897479 DOI: 10.1093/cercor/bhz312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neuregulin-ErbB signaling is essential for numerous functions in the developing, adult, and aging brain, particularly in the prefrontal cortex (PFC). Mouse models with disrupted Nrg and/or ErbB genes are relevant to psychiatric, developmental, and age-related disorders, displaying a range of abnormalities stemming from cortical circuitry impairment. Many of these models display nonoverlapping phenotypes dependent upon the gene target and timing of perturbation, suggesting that cortical expression of the Nrg-ErbB network undergoes temporal regulation across the lifespan. Here, we report a comprehensive temporal expression mapping study of the Nrg-ErbB signaling network in the mouse PFC across postnatal development through aging. We find that Nrg and ErbB genes display distinct expression profiles; moreover, splice isoforms of these genes are differentially expressed across the murine lifespan. We additionally find a developmental switch in ErbB4 splice isoform expression potentially mediated through coregulation of the lncRNA Miat expression. Our results are the first to comprehensively and quantitatively map the expression patterns of the Nrg-ErbB network in the mouse PFC across the postnatal lifespan and may help disentangle the pathway's involvement in normal cortical sequences of events across the lifespan, as well as shedding light on the pathophysiological mechanisms of abnormal Nrg-ErbB signaling in neurological disease.
Collapse
Affiliation(s)
- Clare Paterson
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Brooke Cumming
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amanda J Law
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Cell and Developmental Biology, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Medicine, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
| |
Collapse
|
40
|
Catana CS, Crișan CA, Opre D, Berindan-Neagoe I. Implications of Long Non-Coding RNAs in Age-Altered Proteostasis. Aging Dis 2020; 11:692-704. [PMID: 32489713 PMCID: PMC7220293 DOI: 10.14336/ad.2019.0814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/14/2019] [Indexed: 12/15/2022] Open
Abstract
This review aims to summarize the current knowledge on how lncRNAs are influencing aging and cancer metabolism. Recent research has shown that senescent cells re-enter cell-cycle depending on intrinsic or extrinsic factors, thus restoring tissue homeostasis in response to age-related diseases (ARDs). Furthermore, maintaining proteostasis or cellular protein homeostasis requires a correct quality control (QC) of protein synthesis, folding, conformational stability, and degradation. Long non-coding RNAs (lncRNAs), transcripts longer than 200 nucleotides, regulate gene expression through RNA-binding protein (RBP) interaction. Their association is linked to aging, an event of proteostasis collapse. The current review examines approaches that lead to recognition of senescence-associated lncRNAs, current methodologies, potential challenges that arise from studying these molecules, and their crucial implications in clinical practice.
Collapse
Affiliation(s)
- Cristina-Sorina Catana
- Department of Medical Biochemistry, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, Cluj-Napoca, Romania
| | - Catalina-Angela Crișan
- Department of Neurosciences, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, Cluj-Napoca, Romania
| | - Dana Opre
- Department of Psychology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- MEDFUTURE - Research Center for Advanced Medicine, Cluj-Napoca, Romania
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Institute of Doctoral Studies, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Experimental Pathology, “Prof. Dr. Ion Chiricuta” Oncology Institute, Cluj-Napoca, Romania
| |
Collapse
|
41
|
Hentrich T, Wassouf Z, Riess O, Schulze-Hentrich JM. SNCA overexpression disturbs hippocampal gene expression trajectories in midlife. Aging (Albany NY) 2019; 10:4024-4041. [PMID: 30543522 PMCID: PMC6326667 DOI: 10.18632/aging.101691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
Synucleinopathies like Parkinson's disease and dementia with Lewy bodies originate from a complex and still largely enigmatic interplay of genetic predisposition, age, and environmental factors. While progressively declining motor functions hallmark late-life symptoms, first signs of the disease often surface already decades earlier during midlife. To better understand early disease stages with respect to the genetic, temporal, and environmental dimension, we interrogated hippocampal transcriptome data obtained during midlife for a mouse model overexpressing human SNCA, a pivotal gene in synucleinopathies, under different environments. To relate differentially expressed genes to human, we integrated expression signatures for aging and Parkinson's disease. We identified two distinctive modes of age-dependent disturbances: First, cellular processes seemingly activated too early that reflected advanced stages of age and, second, typical longitudinal adaptations of the system that no longer occurred during midlife. Environmental enrichment prevented both disturbances modes despite persistent SNCA overload. Together, our results caution the view that expression changes characterising early stages of SNCA-related pathology reflect accelerated aging alone. Instead, we provide evidence that failure to undergo healthy adaptions during midlife represents a second origin of disturbances. This bimodal disturbance principle could inform therapeutic efforts to distinguish between preventive and restorative attempts to target the disease.
Collapse
Affiliation(s)
- Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Zinah Wassouf
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | | |
Collapse
|
42
|
Bhadra M, Howell P, Dutta S, Heintz C, Mair WB. Alternative splicing in aging and longevity. Hum Genet 2019; 139:357-369. [PMID: 31834493 DOI: 10.1007/s00439-019-02094-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/24/2019] [Indexed: 12/13/2022]
Abstract
Alternative pre-mRNA splicing increases the complexity of the proteome that can be generated from the available genomic coding sequences. Dysregulation of the splicing process has been implicated in a vast repertoire of diseases. However, splicing has recently been linked to both the aging process itself and pro-longevity interventions. This review focuses on recent research towards defining RNA splicing as a new hallmark of aging. We highlight dysfunctional alternative splicing events that contribute to the aging phenotype across multiple species, along with recent efforts toward deciphering mechanistic roles for RNA splicing in the regulation of aging and longevity. Further, we discuss recent research demonstrating a direct requirement for specific splicing factors in pro-longevity interventions, and specifically how nutrient signaling pathways interface to splicing factor regulation and downstream splicing targets. Finally, we review the emerging potential of using splicing profiles as a predictor of biological age and life expectancy. Understanding the role of RNA splicing components and downstream targets altered in aging may provide opportunities to develop therapeutics and ultimately extend healthy lifespan in humans.
Collapse
Affiliation(s)
- Malini Bhadra
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Porsha Howell
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Sneha Dutta
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Caroline Heintz
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - William B Mair
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| |
Collapse
|
43
|
Mimicking Age-Associated Gadd45γ Dysregulation Results in Memory Impairments in Young Adult Mice. J Neurosci 2019; 40:1197-1210. [PMID: 31826946 DOI: 10.1523/jneurosci.1621-19.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/08/2019] [Accepted: 12/05/2019] [Indexed: 01/19/2023] Open
Abstract
Age-related memory loss is observed across multiple mammalian species and preferentially affects hippocampus-dependent memory. Memory impairments are characterized by accelerated decay of spatial memories. Nevertheless, the molecular mechanisms underlying these deficits are still largely unknown. Here, we investigated the expression and function of the growth arrest DNA damage (Gadd45) family during aging and cognition, respectively. We report that aging impairs the expression of Gadd45γ in the hippocampus of cognitively impaired male mice. Mimicking this decrease in young adult male mice led to age-like memory deficits in hippocampus-dependent memory tasks. Gadd45γ reduction impaired the activity of key components of the mitogen-activated protein kinase (MAPK) pathway (p38 and JNK) in mouse hippocampal cultures. Furthermore, we found that activation of downstream targets, such as ATF-2, c-Jun, and CREB (cAMP response element-binding protein), was disrupted. Finally, we showed that Gadd45γ is required for induction of key early- and late-response genes that have been associated with aging. Together, these findings indicate that Gadd45γ expression regulates cognitive abilities and synapse-to-nucleus communication and suggest Gadd45γ dysfunction as a potential mechanism contributing to age-related cognitive impairments.SIGNIFICANCE STATEMENT A high percentage of subjects experience age-related memory loss that burdens daily performance. Although many advances have been made, the precise changes in the brain governing these deficits are unclear. Identifying molecular processes that are required for cognition and are altered during old age is crucial to develop preventive or therapeutic strategies. Here, we show that baseline and learning-induced expression of the growth arrest DNA damage (Gadd45) γ is selectively impaired in the hippocampus of aged mice with cognitive deficits. Next, we show that modeling this impairment in young adult mice with normal cognitive performance disrupts long- and short-term memories in an age-like manner. Finally, we demonstrate that Gadd45γ regulates synapse-to-nucleus communication processes that are needed for plasticity-associated gene expression.
Collapse
|
44
|
Urban I, Kerimoglu C, Sakib MS, Wang H, Benito E, Thaller C, Zhou X, Yan J, Fischer A, Eichele G. TIP60/KAT5 is required for neuronal viability in hippocampal CA1. Sci Rep 2019; 9:16173. [PMID: 31700011 PMCID: PMC6838100 DOI: 10.1038/s41598-019-50927-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
Aberrant histone acetylation contributes to age-dependent cognitive decline and neurodegenerative diseases. We analyze the function of lysine acetyltransferase TIP60/KAT5 in neurons of the hippocampus using an inducible mouse model. TIP60-deficiency in the adult forebrain leads within days to extensive transcriptional dysfunction characterized by the presence of a neurodegeneration-related signature in CA1. Cell cycle- and immunity-related genes are upregulated while learning- and neuronal plasticity-related genes are downregulated. The dysregulated genes seen under TIP60-deficiency overlap with those in the well-characterized CK-p25 neurodegeneration model. We found that H4K12 is hypoacetylated at the transcriptional start sites of those genes whose expression is dampened in TIP60-deficient mice. Transcriptional dysregulation is followed over a period of weeks by activation of Caspase 3 and fragmentation of β-actin in CA1 neurites, eventually leading to severe neuronal loss. TIP60-deficient mice also develop mild memory impairment. These phenotypes point to a central role of TIP60 in transcriptional networks that are critical for neuronal viability.
Collapse
Affiliation(s)
- Inga Urban
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Cemil Kerimoglu
- Department of Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, 37075, Göttingen, Germany
| | - M Sadman Sakib
- Department of Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, 37075, Göttingen, Germany
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Eva Benito
- Department of Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, 37075, Göttingen, Germany.,European Molecular Biology Organization (EMBO), 69117, Heidelberg, Germany
| | - Christina Thaller
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Xunlei Zhou
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Institute of Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, China
| | - André Fischer
- Department of Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, 37075, Göttingen, Germany. .,Department for Psychiatry and Psychotherapy, University Medical Center Göttingen, 37075, Göttingen, Germany.
| | - Gregor Eichele
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| |
Collapse
|
45
|
Yamauchi A, Tone T, Sugimoto K, Seok Lim H, Kaku T, Tohda C, Shindo T, Tamada K, Mizukami Y, Hirano E. Porcine placental extract facilitates memory and learning in aged mice. Food Sci Nutr 2019; 7:2995-3005. [PMID: 31572593 PMCID: PMC6766592 DOI: 10.1002/fsn3.1156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 05/04/2019] [Indexed: 01/07/2023] Open
Abstract
Aging induces a decline in both memory and learning ability without predisposing an individual to diseases of the central nervous system, such as dementia. This decline can have a variety of adverse effects on daily life, and it can also gradually affect the individual and the people they are surrounded by. Since recent evidence indicated that placental extract has effects on brain function such as memory, we hypothesized that placental extract could ameliorate the age-associated reduction in cognitive function in aging. Here, we investigated the effect of new modified porcine placental extract (SD-F) on memory ability in aged mice at both the behavioral and molecular levels. Our results revealed that SD-F significantly enhanced memory ability in the object recognition and object location tasks in a dose-dependent manner in aged mice relative to controls. The numbers of Nissl-positive cells in the hippocampal cornu ammonis 3 (CA3) and dentate gyrus (DG) regions were increased in SD-F-treated aged mice relative to controls. RNA-seq analysis of the hippocampus of aged mice identified 542 differentially expressed genes, of which 216 were up-regulated and 326 were down-regulated in SD-F-treated mice relative to controls. Of the 216 up-regulated genes, we identified four characteristic genes directly related to memory, including early growth response protein 1 (Egr1), growth arrest and DNA-damage-inducible, beta (Gadd45b), NGFI-A binding protein 2 (Nab2), and vascular endothelial growth factor a (Vegfa). These results suggest that the efficacy of SD-F involves upregulation of these genes.
Collapse
Affiliation(s)
| | - Takahiro Tone
- Research InstituteJapan Bio Products Co., Ltd.KurumeJapan
| | - Koji Sugimoto
- Research InstituteJapan Bio Products Co., Ltd.KurumeJapan
| | | | | | - Chihiro Tohda
- Division of Neuromedical Science, Department of Bioscience, Institute of Natural MedicineUniversity of ToyamaToyamaJapan
| | - Takayuki Shindo
- Department of Cardiovascular ResearchShinshu University Graduate School of MedicineNaganoJapan
| | - Koji Tamada
- Department of Immunology, Graduate School of MedicineYamaguchi UniversityYamaguchiJapan
| | - Yoichi Mizukami
- Institute of Gene ResearchYamaguchi University Science Research CenterYamaguchiJapan
| | - Eiichi Hirano
- Research InstituteJapan Bio Products Co., Ltd.KurumeJapan
| |
Collapse
|
46
|
Age and Sex Influence the Hippocampal Response and Recovery Following Sepsis. Mol Neurobiol 2019; 56:8557-8572. [PMID: 31278440 PMCID: PMC6834928 DOI: 10.1007/s12035-019-01681-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/14/2019] [Indexed: 01/03/2023]
Abstract
Although in-hospital mortality rates for sepsis have decreased, survivors often experience lasting physical and cognitive deficits. Moreover, older adults are more vulnerable to long-term complications associated with sepsis. We employed a murine model to examine the influence of age and sex on the brain’s response and recovery following sepsis. Young (~ 4 months) and old (~ 20 months) mice (C57BL/6) of both sexes underwent cecal ligation and puncture (CLP) with restraint stress. The hippocampal transcriptome was examined in age- and sex-matched controls at 1 and 4 days post-CLP. In general, immune- and stress-related genes increased, while neuronal, synaptic, and glial genes decreased 1 day after CLP-induced sepsis. However, specific age and sex differences were observed for the initial responsiveness to sepsis as well as the rate of recovery examined on day 4. Young females exhibited a muted transcriptional response relative to young males and old females. Old females exhibited a robust shift in gene transcription on day 1, and while most genes recovered, genes linked to neurogenesis and myelination continued to be downregulated by day 4. In contrast, old males exhibited a more delayed or prolonged response to sepsis, such that neuronal and synaptic genes continued to decrease while immune response genes continued to increase on day 4. These results suggest that aging is associated with delayed recovery from sepsis, which is particularly evident in males.
Collapse
|
47
|
Butler AA, Johnston DR, Kaur S, Lubin FD. Long noncoding RNA NEAT1 mediates neuronal histone methylation and age-related memory impairment. Sci Signal 2019; 12:12/588/eaaw9277. [PMID: 31266852 DOI: 10.1126/scisignal.aaw9277] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Histone methylation is critical for the formation and maintenance of long-term memories. Long noncoding RNAs (lncRNAs) are regulators of histone methyltransferases and other chromatin-modifying enzymes (CMEs), thereby epigenetically modifying gene expression. Here, we investigated how the lncRNA NEAT1 may epigenetically contribute to hippocampus-dependent, long-term memory formation using a combination of transcriptomics, RNA-binding protein immunoprecipitation, CRISPR-mediated gene activation (CRISPRa), and behavioral approaches. Knockdown of the lncRNA Neat1 revealed widespread changes in gene transcription, as well as perturbations of histone 3 lysine 9 dimethylation (H3K9me2), a repressive histone modification mark that was increased in the hippocampus of aging rodents. We identified a NEAT1-dependent mechanism of transcriptional repression by H3K9me2 at the c-Fos promoter, corresponding with observed changes in c-Fos mRNA expression. Overexpression of hippocampal NEAT1 using CRISPRa was sufficient to impair memory formation in young adult mice, recapitulating observed memory deficits in old adult mice, whereas knocking down NEAT1 in both young and old adult mice improved behavior test-associated memory. These results suggest that the lncRNA NEAT1 is an epigenetic suppressor of hippocampus-dependent, long-term memory formation.
Collapse
Affiliation(s)
| | | | - Simranjit Kaur
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Farah D Lubin
- University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| |
Collapse
|
48
|
Adusumalli S, Ngian Z, Lin W, Benoukraf T, Ong C. Increased intron retention is a post-transcriptional signature associated with progressive aging and Alzheimer's disease. Aging Cell 2019; 18:e12928. [PMID: 30868713 PMCID: PMC6516162 DOI: 10.1111/acel.12928] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/18/2018] [Indexed: 12/23/2022] Open
Abstract
Intron retention (IR) by alternative splicing is a conserved regulatory mechanism that can affect gene expression and protein function during adult development and age-onset diseases. However, it remains unclear whether IR undergoes spatial or temporal changes during different stages of aging or neurodegeneration like Alzheimer's disease (AD). By profiling the transcriptome of Drosophila head cells at different ages, we observed a significant increase in IR events for many genes during aging. Differential IR affects distinct biological functions at different ages and occurs at several AD-associated genes in older adults. The increased nucleosome occupancy at the differentially retained introns in young animals suggests that it may regulate the level of IR during aging. Notably, an increase in the number of IR events was also observed in healthy older mouse and human brain tissues, as well as in the cerebellum and frontal cortex from independent AD cohorts. Genes with differential IR shared many common features, including shorter intron length, no perturbation in their mRNA level, and enrichment for biological functions that are associated with mRNA processing and proteostasis. The differentially retained introns identified in AD frontal cortex have higher GC content, with many of their mRNA transcripts showing an altered level of protein expression compared to control samples. Taken together, our results suggest that an increased IR is an conserved signature that is associated with aging. By affecting pathways involved in mRNA and protein homeostasis, changes of IR pattern during aging may regulate the transition from healthy to pathological state in late-onset sporadic AD.
Collapse
Affiliation(s)
- Swarnaseetha Adusumalli
- Temasek Life Sciences Laboratory National University of Singapore Singapore
- Department of Biological Sciences National University of Singapore Singapore
| | - Zhen‐Kai Ngian
- Temasek Life Sciences Laboratory National University of Singapore Singapore
| | - Wei‐Qi Lin
- Temasek Life Sciences Laboratory National University of Singapore Singapore
| | - Touati Benoukraf
- Cancer Science Institute of Singapore National University of Singapore Singapore
- Discipline of Genetics, Faculty of Medicine Memorial University of Newfoundland St. John’s Newfoundland and Labrador Canada
| | - Chin‐Tong Ong
- Temasek Life Sciences Laboratory National University of Singapore Singapore
- Department of Biological Sciences National University of Singapore Singapore
| |
Collapse
|
49
|
Nguyen KV. Potential epigenomic co-management in rare diseases and epigenetic therapy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:752-780. [PMID: 31079569 DOI: 10.1080/15257770.2019.1594893] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The purpose of this review is to highlight the impact of the alternative splicing process on human disease. Epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced. The recent progress in the field of epigenetics has important implications for the study of rare diseases. The role of epigenetics in rare diseases is a key issue in molecular physiology and medicine because not only rare diseases can benefit from epigenetic research, but can also provide useful principles for other common and complex disorders such as cancer, cardiovascular, type 2 diabetes, obesity, and neurological diseases. Predominantly, epigenetic modifications include DNA methylation, histone modification, and RNA-associated silencing. These modifications in the genome regulate numerous cellular activities. Disruption of epigenetic regulation process can contribute to the etiology of numerous diseases during both prenatal and postnatal life. Here, I discuss current knowledge about this matter including some current epigenetic therapies and future directions in the field by emphasizing on the RNA-based therapy via antisense oligonucleotides to correct splicing defects.
Collapse
Affiliation(s)
- Khue Vu Nguyen
- a Department of Medicine, Biochemical Genetics and Metabolism, The Mitochondrial and Metabolic Disease Center, School of Medicine, University of California, San Diego , San Diego , CA , USA.,b Department of Pediatrics, UC San Diego School of Medicine , La Jolla , CA , USA
| |
Collapse
|
50
|
Lai RW, Lu R, Danthi PS, Bravo JI, Goumba A, Sampathkumar NK, Benayoun BA. Multi-level remodeling of transcriptional landscapes in aging and longevity. BMB Rep 2019. [PMID: 30526773 PMCID: PMC6386224 DOI: 10.5483/bmbrep.2019.52.1.296] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and gene expression has been observed to be deregulated with aging. In this review, we discuss the current knowledge on the transcriptional alterations that have been described to occur with age in metazoans. First, we discuss age-related transcriptional changes in protein-coding genes, the expected functional impact of such changes, and how known pro-longevity interventions impact these changes. Second, we discuss the changes and impact of emerging aspects of transcription in aging, including age-related changes in splicing, lncRNAs and circRNAs. Third, we discuss the changes and potential impact of transcription of transposable elements with aging. Fourth, we highlight small ncRNAs and their potential impact on the regulation of aging phenotypes. Understanding the aging transcriptome will be key to identify important regulatory targets, and ultimately slow-down or reverse aging and extend healthy lifespan in humans.
Collapse
Affiliation(s)
- Rochelle W Lai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexandre Goumba
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089; USC Stem Cell Initiative, Los Angeles, CA 90089, USA
| |
Collapse
|