1
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Fröhlich AS, Gerstner N, Gagliardi M, Ködel M, Yusupov N, Matosin N, Czamara D, Sauer S, Roeh S, Murek V, Chatzinakos C, Daskalakis NP, Knauer-Arloth J, Ziller MJ, Binder EB. Single-nucleus transcriptomic profiling of human orbitofrontal cortex reveals convergent effects of aging and psychiatric disease. Nat Neurosci 2024:10.1038/s41593-024-01742-z. [PMID: 39227716 DOI: 10.1038/s41593-024-01742-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/30/2024] [Indexed: 09/05/2024]
Abstract
Aging is a complex biological process and represents the largest risk factor for neurodegenerative disorders. The risk for neurodegenerative disorders is also increased in individuals with psychiatric disorders. Here, we characterized age-related transcriptomic changes in the brain by profiling ~800,000 nuclei from the orbitofrontal cortex from 87 individuals with and without psychiatric diagnoses and replicated findings in an independent cohort with 32 individuals. Aging affects all cell types, with LAMP5+LHX6+ interneurons, a cell-type abundant in primates, by far the most affected. Disrupted synaptic transmission emerged as a convergently affected pathway in aged tissue. Age-related transcriptomic changes overlapped with changes observed in Alzheimer's disease across multiple cell types. We find evidence for accelerated transcriptomic aging in individuals with psychiatric disorders and demonstrate a converging signature of aging and psychopathology across multiple cell types. Our findings shed light on cell-type-specific effects and biological pathways underlying age-related changes and their convergence with effects driven by psychiatric diagnosis.
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Affiliation(s)
- Anna S Fröhlich
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany.
- International Max Planck Research School for Translational Psychiatry, Munich, Germany.
| | - Nathalie Gerstner
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Miriam Gagliardi
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Maik Ködel
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Natan Yusupov
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Natalie Matosin
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Darina Czamara
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Susann Sauer
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Simone Roeh
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Vanessa Murek
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Chris Chatzinakos
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Nikolaos P Daskalakis
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Janine Knauer-Arloth
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael J Ziller
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Elisabeth B Binder
- Department of Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany.
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA.
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2
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Xu H, Li H, Zhang P, Gao Y, Ma H, Gao T, Liu H, Hua W, Zhang L, Zhang X, Yang P, Liu J. The functions of exosomes targeting astrocytes and astrocyte-derived exosomes targeting other cell types. Neural Regen Res 2024; 19:1947-1953. [PMID: 38227520 DOI: 10.4103/1673-5374.390961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/08/2023] [Indexed: 01/17/2024] Open
Abstract
Astrocytes are the most abundant glial cells in the central nervous system; they participate in crucial biological processes, maintain brain structure, and regulate nervous system function. Exosomes are cell-derived extracellular vesicles containing various bioactive molecules including proteins, peptides, nucleotides, and lipids secreted from their cellular sources. Increasing evidence shows that exosomes participate in a communication network in the nervous system, in which astrocyte-derived exosomes play important roles. In this review, we have summarized the effects of exosomes targeting astrocytes and the astrocyte-derived exosomes targeting other cell types in the central nervous system. We also discuss the potential research directions of the exosome-based communication network in the nervous system. The exosome-based intercellular communication focused on astrocytes is of great significance to the biological and/or pathological processes in different conditions in the brain. New strategies may be developed for the diagnosis and treatment of neurological disorders by focusing on astrocytes as the central cells and utilizing exosomes as communication mediators.
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Affiliation(s)
- Hongye Xu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - He Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Emergency, Naval Hospital of Eastern Theater, Zhoushan, Zhejiang Province, China
| | - Ping Zhang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yuan Gao
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Hongyu Ma
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Tianxiang Gao
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Hanchen Liu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Weilong Hua
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Lei Zhang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xiaoxi Zhang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Pengfei Yang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jianmin Liu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, China
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3
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Swahari V, Nakamura A, Hollville E, Hung YH, Kanke M, Kurtz CL, Caravia XM, Roiz-Valle D, He S, Krishnamurthy J, Kapoor S, Prasad V, Flowers C, Beck M, Baran-Gale J, Sharpless N, López-Otín C, Sethupathy P, Deshmukh M. miR-29 is an important driver of aging-related phenotypes. Commun Biol 2024; 7:1055. [PMID: 39191864 DOI: 10.1038/s42003-024-06735-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/14/2024] [Indexed: 08/29/2024] Open
Abstract
Aging is a consequence of complex molecular changes, but whether a single microRNA (miRNA) can drive aging remains unclear. A miRNA known to be upregulated during both normal and premature aging is miR-29. We find miR-29 to also be among the top miRNAs predicted to drive aging-related gene expression changes. We show that partial loss of miR-29 extends the lifespan of Zmpste24-/- mice, an established model of progeria, indicating that miR-29 is functionally important in this accelerated aging model. To examine whether miR-29 alone is sufficient to promote aging-related phenotypes, we generated mice in which miR-29 can be conditionally overexpressed (miR-29TG). miR-29 overexpression is sufficient to drive many aging-related phenotypes and led to early lethality. Transcriptomic analysis of both young miR-29TG and old WT mice reveals shared downregulation of genes associated with extracellular matrix organization and fatty acid metabolism, and shared upregulation of genes in pathways linked to inflammation. These results highlight the functional importance of miR-29 in controlling a gene expression program that drives aging-related phenotypes.
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Affiliation(s)
- Vijay Swahari
- Neuroscience Center; University of North Carolina, Chapel Hill, NC, USA
| | - Ayumi Nakamura
- Neuroscience Center; University of North Carolina, Chapel Hill, NC, USA
- Neurobiology Curriculum; University of North Carolina, Chapel Hill, NC, USA
| | - Emilie Hollville
- Neuroscience Center; University of North Carolina, Chapel Hill, NC, USA
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Yu-Han Hung
- Department of Biomedical Sciences; College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matt Kanke
- Department of Biomedical Sciences; College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - C Lisa Kurtz
- Department of Genetics; University of North Carolina, Chapel Hill, NC, USA
| | - Xurde M Caravia
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - David Roiz-Valle
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Shenghui He
- Department of Genetics; University of North Carolina, Chapel Hill, NC, USA
- The Lineberger Comprehensive Cancer Center; University of North Carolina, Chapel Hill, NC, USA
| | - Janakiraman Krishnamurthy
- Department of Genetics; University of North Carolina, Chapel Hill, NC, USA
- The Lineberger Comprehensive Cancer Center; University of North Carolina, Chapel Hill, NC, USA
| | - Sahil Kapoor
- Neuroscience Center; University of North Carolina, Chapel Hill, NC, USA
| | - Varun Prasad
- Neuroscience Center; University of North Carolina, Chapel Hill, NC, USA
| | - Cornelius Flowers
- Neuroscience Center; University of North Carolina, Chapel Hill, NC, USA
| | - Matt Beck
- Neuroscience Center; University of North Carolina, Chapel Hill, NC, USA
| | - Jeanette Baran-Gale
- Department of Genetics; University of North Carolina, Chapel Hill, NC, USA
- Bioinformatics and Computational Biology Curriculum; University of North Carolina, Chapel Hill, NC, USA
| | - Norman Sharpless
- Department of Genetics; University of North Carolina, Chapel Hill, NC, USA
- The Lineberger Comprehensive Cancer Center; University of North Carolina, Chapel Hill, NC, USA
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Praveen Sethupathy
- Department of Biomedical Sciences; College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - Mohanish Deshmukh
- Neuroscience Center; University of North Carolina, Chapel Hill, NC, USA.
- Neurobiology Curriculum; University of North Carolina, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.
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4
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Kulis K, Tabury K, Benotmane MA, Polanska J. Transcriptomic Profile of Mouse Brain Ageing in Early Developmental Stages. Brain Sci 2024; 14:581. [PMID: 38928581 PMCID: PMC11201909 DOI: 10.3390/brainsci14060581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Ageing is a continuous process that can cause neurodevelopmental changes in the body. Several studies have examined its effects, but few have focused on how time affects biological processes in the early stages of brain development. As studying the changes that occur in the early stages of life is important to prevent age-related neurological and psychiatric disorders, we aim to focus on these changes. The transcriptomic markers of ageing that are common to the analysed brain regions of C57Bl/6J mice were identified after conducting two-way ANOVA tests and effect size analysis on the time courses of gene expression profiles in various mouse brain regions. A total of 16,374 genes (59.9%) significantly changed their expression level, among which 7600 (27.8%) demonstrated tissue-dependent differences only, and 1823 (6.7%) displayed time-dependent and tissue-independent responses. Focusing on genes with at least a large effect size gives the list of potential biomarkers 12,332 (45.1%) and 1670 (6.1%) genes, respectively. There were 305 genes that exhibited similar significant time response trends (independently of the brain region). Samples from an 11-day-old mouse embryo validated the identified early-stage brain ageing markers. The overall functional analysis revealed tRNA and rRNA processing in the mitochondrion and contact activation system (CAS), as well as the kallikrein/kinin system (KKS), together with clotting cascade and defective factor F9 activation being affected by ageing. Most ageing-related pathways were significantly enriched, especially those that are strongly connected to development processes and neurodegenerative diseases.
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Affiliation(s)
- Karolina Kulis
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Kevin Tabury
- Radiobiology Unit, Institute for Nuclear Medical Application, Belgian Nuclear Research Centre, 2400 Mol, Belgium; (K.T.); (M.A.B.)
| | - Mohammed Abderrafi Benotmane
- Radiobiology Unit, Institute for Nuclear Medical Application, Belgian Nuclear Research Centre, 2400 Mol, Belgium; (K.T.); (M.A.B.)
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
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5
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Kakizawa S, Park JJ, Tonoki A. Biology of cognitive aging across species. Geriatr Gerontol Int 2024; 24 Suppl 1:15-24. [PMID: 38126240 DOI: 10.1111/ggi.14782] [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: 08/31/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
Aging is associated with cognitive decline, which can critically affect quality of life. Examining the biology of cognitive aging across species will lead to a better understanding of the fundamental mechanisms involved in this process, and identify potential interventions that could help to improve cognitive function in aging individuals. This minireview aimed to explore the mechanisms and processes involved in cognitive aging across a range of species, from flies to rodents, and covers topics, such as the role of reactive oxygen species and autophagy/mitophagy in cognitive aging. Overall, this literature provides a comprehensive overview of the biology of cognitive aging across species, highlighting the latest research findings and identifying potential avenues for future research. Geriatr Gerontol Int 2024; 24: 15-24.
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Affiliation(s)
- Sho Kakizawa
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Joong-Jean Park
- Department of Physiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Ayako Tonoki
- Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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6
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Zarrella JA, Tsurumi A. Genome-wide transcriptome profiling and development of age prediction models in the human brain. Aging (Albany NY) 2024; 16:4075-4094. [PMID: 38428408 PMCID: PMC10968712 DOI: 10.18632/aging.205609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 03/28/2023] [Indexed: 03/03/2024]
Abstract
Aging-related transcriptome changes in various regions of the healthy human brain have been explored in previous works, however, a study to develop prediction models for age based on the expression levels of specific panels of transcripts is lacking. Moreover, studies that have assessed sexually dimorphic gene activities in the aging brain have reported discrepant results, suggesting that additional studies would be advantageous. The prefrontal cortex (PFC) region was previously shown to have a particularly large number of significant transcriptome alterations during healthy aging in a study that compared different regions in the human brain. We harmonized neuropathologically normal PFC transcriptome datasets obtained from the Gene Expression Omnibus (GEO) repository, ranging in age from 21 to 105 years, and found a large number of differentially regulated transcripts in the old and elderly, compared to young samples overall, and compared female and male-specific expression alterations. We assessed the genes that were associated with age by employing ontology, pathway, and network analyses. Furthermore, we applied various established (least absolute shrinkage and selection operator (Lasso) and Elastic Net (EN)) and recent (eXtreme Gradient Boosting (XGBoost) and Light Gradient Boosting Machine (LightGBM)) machine learning algorithms to develop accurate prediction models for chronological age and validated them. Studies to further validate these models in other large populations and molecular studies to elucidate the potential mechanisms by which the transcripts identified may be related to aging phenotypes would be advantageous.
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Affiliation(s)
- Joseph A. Zarrella
- Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Shriner's Hospitals for Children-Boston, Boston, MA 02114, USA
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7
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McNair LM, Andersen JV, Waagepetersen HS. Stable isotope tracing reveals disturbed cellular energy and glutamate metabolism in hippocampal slices of aged male mice. Neurochem Int 2023; 171:105626. [PMID: 37838084 DOI: 10.1016/j.neuint.2023.105626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/08/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Neurons and astrocytes work in close metabolic collaboration, linking neurotransmission to brain energy and neurotransmitter metabolism. Dysregulated energy metabolism is a hallmark of the aging brain and may underlie the progressive age-dependent cognitive decline. However, astrocyte and neurotransmitter metabolism remains understudied in aging brain research. In particular, how aging affects metabolism of glutamate, being the primary excitatory neurotransmitter, is still poorly understood. Here we investigated critical aspects of cellular energy metabolism in the aging male mouse hippocampus using stable isotope tracing in vitro. Metabolism of [U-13C]glucose demonstrated an elevated glycolytic capacity of aged hippocampal slices, whereas oxidative [U-13C]glucose metabolism in the TCA cycle was significantly reduced with aging. In addition, metabolism of [1,2-13C]acetate, reflecting astrocyte energy metabolism, was likewise reduced in the hippocampal slices of old mice. In contrast, uptake and subsequent metabolism of [U-13C]glutamate was elevated, suggesting increased capacity for cellular glutamate handling with aging. Finally, metabolism of [15N]glutamate was maintained in the aged slices, demonstrating sustained glutamate nitrogen metabolism. Collectively, this study reveals fundamental alterations in cellular energy and neurotransmitter metabolism in the aging brain, which may contribute to age-related hippocampal deficits.
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Affiliation(s)
- Laura Mikél McNair
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Jens Velde Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Helle Sønderby Waagepetersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
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del Valle E, Rubio-Sardón N, Menéndez-Pérez C, Martínez-Pinilla E, Navarro A. Apolipoprotein D as a Potential Biomarker in Neuropsychiatric Disorders. Int J Mol Sci 2023; 24:15631. [PMID: 37958618 PMCID: PMC10650001 DOI: 10.3390/ijms242115631] [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: 10/08/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Neuropsychiatric disorders (NDs) are a diverse group of pathologies, including schizophrenia or bipolar disorders, that directly affect the mental and physical health of those who suffer from them, with an incidence that is increasing worldwide. Most NDs result from a complex interaction of multiple genes and environmental factors such as stress or traumatic events, including the recent Coronavirus Disease (COVID-19) pandemic. In addition to diverse clinical presentations, these diseases are heterogeneous in their pathogenesis, brain regions affected, and clinical symptoms, making diagnosis difficult. Therefore, finding new biomarkers is essential for the detection, prognosis, response prediction, and development of new treatments for NDs. Among the most promising candidates is the apolipoprotein D (Apo D), a component of lipoproteins implicated in lipid metabolism. Evidence suggests an increase in Apo D expression in association with aging and in the presence of neuropathological processes. As a part of the cellular neuroprotective defense machinery against oxidative stress and inflammation, changes in Apo D levels have been demonstrated in neuropsychiatric conditions like schizophrenia (SZ) or bipolar disorders (BPD), not only in some brain areas but in corporal fluids, i.e., blood or serum of patients. What is not clear is whether variation in Apo D quantity could be used as an indicator to detect NDs and their progression. This review aims to provide an updated view of the clinical potential of Apo D as a possible biomarker for NDs.
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Affiliation(s)
- Eva del Valle
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
| | - Nuria Rubio-Sardón
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
| | - Carlota Menéndez-Pérez
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
| | - Eva Martínez-Pinilla
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
| | - Ana Navarro
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
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9
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Ren Y, Wang X, Zhang S, Hu H, Quicksall Z, Lee S, Morganti JM, Johnson LA, Asmann YW, Zhao N. Deconvolution reveals cell-type-specific transcriptomic changes in the aging mouse brain. Sci Rep 2023; 13:16855. [PMID: 37803069 PMCID: PMC10558435 DOI: 10.1038/s41598-023-44183-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023] Open
Abstract
Mounting evidence highlights the crucial role of aging in the pathogenesis of Alzheimer's disease (AD). We have previously explored human apoE-targeted replacement mice across different ages and identified distinct molecular pathways driven by aging. However, the specific contribution of different brain cell types to the gene modules underlying these pathways remained elusive. To bridge this knowledge gap, we employed a computational deconvolution approach to examine cell-type-specific gene expression profiles in major brain cell types, including astrocytes (AS), microglia (MG), oligodendroglia (OG), neurons (NEU), and vascular cells (VC). Our findings revealed that immune module genes were predominantly expressed in MG, OG, and VC. The lipid metabolism module genes were primarily expressed in AS, MG, and OG. The mitochondria module genes showed prominent expression in VC, and the synapse module genes were primarily expressed in NEU and VC. Furthermore, we identified intra- and inter-cell-type interactions among these module genes and validated their aging-associated expression changes using published single cell studies. Our study dissected bulk brain transcriptomics data at the cellular level, providing a closer examination of the cell-type contributions to the molecular pathways driven by aging.
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Affiliation(s)
- Yingxue Ren
- Department of Quantitative Health Sciences, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA.
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Shuwen Zhang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | - Hongru Hu
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Sangderk Lee
- Sanders Brown Center On Aging, University of Kentucky, Lexington, KY40536, USA
| | - Josh M Morganti
- Sanders Brown Center On Aging, University of Kentucky, Lexington, KY40536, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY40536, USA
| | - Lance A Johnson
- Sanders Brown Center On Aging, University of Kentucky, Lexington, KY40536, USA
- Department of Physiology, University of Kentucky, Lexington, KY40536, USA
| | - Yan W Asmann
- Department of Quantitative Health Sciences, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Na Zhao
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA.
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10
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Stein-O’Brien GL, Palaganas R, Meyer EM, Redding-Ochoa J, Pletnikova O, Guo H, Bell WR, Troncoso JC, Huganir RL, Morris M. Transcriptional Signatures of Hippocampal Tau Pathology in Primary Age-Related Tauopathy and Alzheimer's Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295440. [PMID: 37745408 PMCID: PMC10516095 DOI: 10.1101/2023.09.12.23295440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background Tau pathology is common in age-related neurodegenerative diseases. Tau pathology in primary age-related tauopathy (PART) and in Alzheimer's disease (AD) has a similar biochemical structure and anatomic distribution, which is distinct from tau pathology in other diseases. However, the molecular changes associated with intraneuronal tau pathology in PART and AD, and whether these changes are similar in the two diseases, is largely unexplored. Methods Using GeoMx spatial transcriptomics, mRNA was quantified in CA1 pyramidal neurons with tau pathology and adjacent neurons without tau pathology in 6 cases of PART and 6 cases of AD, and compared to 4 control cases without pathology. Transcriptional changes were analyzed for differential gene expression and for coordinated patterns of gene expression associated with both disease state and intraneuronal tau pathology. Results Synaptic gene changes and two novel gene expression signatures associated with intraneuronal tau were identified in PART and AD. Overall, gene expression changes associated with intraneuronal tau pathology were similar in PART and AD. Synaptic gene expression was decreased overall in neurons in AD and PART compared to control cases. However, this decrease was largely driven by neurons lacking tau pathology. Synaptic gene expression was increased in tau-positive neurons compared to tau-negative neurons in disease. Two novel gene expression signatures associated with intraneuronal tau were identified by examining coordinated patterns of gene expression. Genes in the up-regulated expression pattern were enriched in calcium regulation and synaptic function pathways, specifically in synaptic exocytosis. These synaptic gene changes and intraneuronal tau expression signatures were confirmed in a published transcriptional dataset of cortical neurons with tau pathology in AD. Conclusions PART and AD show similar transcriptional changes associated with intraneuronal tau pathology in CA1 pyramidal neurons, raising the possibility of a mechanistic relationship between the tau pathology in the two diseases. Intraneuronal tau pathology was also associated with increased expression of genes associated with synaptic function and calcium regulation compared to tau-negative disease neurons. The findings highlight the power of molecular analysis stratified by pathology in neurodegenerative disease and provide novel insight into common molecular pathways associated with intraneuronal tau in PART and AD.
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Affiliation(s)
- Genevieve L Stein-O’Brien
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Single Cell Training and Analysis Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Baltimore, MD
| | - Ryan Palaganas
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ernest M. Meyer
- UPMC Hillman Cancer Center Cytometry Facility, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY
| | - Haidan Guo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William R Bell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Richard L Huganir
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Baltimore, MD
| | - Meaghan Morris
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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11
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Lautrup S, Myrup Holst C, Yde A, Asmussen S, Thinggaard V, Larsen K, Laursen LS, Richner M, Vægter CB, Prieto GA, Berchtold N, Cotman CW, Stevnsner T. The role of aging and brain-derived neurotrophic factor signaling in expression of base excision repair genes in the human brain. Aging Cell 2023; 22:e13905. [PMID: 37334527 PMCID: PMC10497833 DOI: 10.1111/acel.13905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/20/2023] Open
Abstract
DNA damage is a central contributor to the aging process. In the brain, a major threat to the DNA is the considerable amount of reactive oxygen species produced, which can inflict oxidative DNA damage. This type of damage is removed by the base excision repair (BER) pathway, an essential DNA repair mechanism, which contributes to genome stability in the brain. Despite the crucial role of the BER pathway, insights into how this pathway is affected by aging in the human brain and the underlying regulatory mechanisms are very limited. By microarray analysis of four cortical brain regions from humans aged 20-99 years (n = 57), we show that the expression of core BER genes is largely downregulated during aging across brain regions. Moreover, we find that expression of many BER genes correlates positively with the expression of the neurotrophin brain-derived neurotrophic factor (BDNF) in the human brain. In line with this, we identify binding sites for the BDNF-activated transcription factor, cyclic-AMP response element-binding protein (CREB), in the promoter of most BER genes and confirm the ability of BDNF to regulate several BER genes by BDNF treatment of mouse primary hippocampal neurons. Together, these findings uncover the transcriptional landscape of BER genes during aging of the brain and suggest BDNF as an important regulator of BER in the human brain.
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Affiliation(s)
- Sofie Lautrup
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
- Department of Clinical Molecular BiologyUniversity of Oslo and Akershus University HospitalLørenskogNorway
| | | | - Anne Yde
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Stine Asmussen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Vibeke Thinggaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Knud Larsen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | - Mette Richner
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience – DANDRITE, Nordic EMBL Partnership for Molecular MedicineAarhus UniversityAarhusDenmark
| | - Christian B. Vægter
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience – DANDRITE, Nordic EMBL Partnership for Molecular MedicineAarhus UniversityAarhusDenmark
| | - G. Aleph Prieto
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
- Instituto de NeurobiologíaUNAM‐JuriquillaJuriquillaMexico
| | - Nicole Berchtold
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Carl W. Cotman
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Tinna Stevnsner
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
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12
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Zhang B, Lee DE, Trapp A, Tyshkovskiy A, Lu AT, Bareja A, Kerepesi C, McKay LK, Shindyapina AV, Dmitriev SE, Baht GS, Horvath S, Gladyshev VN, White JP. Multi-omic rejuvenation and life span extension on exposure to youthful circulation. NATURE AGING 2023; 3:948-964. [PMID: 37500973 PMCID: PMC11095548 DOI: 10.1038/s43587-023-00451-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/06/2023] [Indexed: 07/29/2023]
Abstract
Heterochronic parabiosis (HPB) is known for its functional rejuvenation effects across several mouse tissues. However, its impact on biological age and long-term health is unknown. Here we performed extended (3-month) HPB, followed by a 2-month detachment period of anastomosed pairs. Old detached mice exhibited improved physiological parameters and lived longer than control isochronic mice. HPB drastically reduced the epigenetic age of blood and liver based on several clock models using two independent platforms. Remarkably, this rejuvenation effect persisted even after 2 months of detachment. Transcriptomic and epigenomic profiles of anastomosed mice showed an intermediate phenotype between old and young, suggesting a global multi-omic rejuvenation effect. In addition, old HPB mice showed gene expression changes opposite to aging but akin to several life span-extending interventions. Altogether, we reveal that long-term HPB results in lasting epigenetic and transcriptome remodeling, culminating in the extension of life span and health span.
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Affiliation(s)
- Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David E Lee
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Retro Biosciences, Redwood City, CA, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Akshay Bareja
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Csaba Kerepesi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Computer Science and Control (SZTAKI), Eötvös Loránd Research Network, Budapest, Hungary
| | - Lauren K McKay
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anastasia V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Retro Biosciences, Redwood City, CA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - James P White
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA.
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA.
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13
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Chowdhury MAR, An J, Jeong S. The Pleiotropic Face of CREB Family Transcription Factors. Mol Cells 2023; 46:399-413. [PMID: 37013623 PMCID: PMC10336275 DOI: 10.14348/molcells.2023.2193] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 04/05/2023] Open
Abstract
cAMP responsive element-binding protein (CREB) is one of the most intensively studied phosphorylation-dependent transcription factors that provide evolutionarily conserved mechanisms of differential gene expression in vertebrates and invertebrates. Many cellular protein kinases that function downstream of distinct cell surface receptors are responsible for the activation of CREB. Upon functional dimerization of the activated CREB to cis-acting cAMP responsive elements within the promoters of target genes, it facilitates signal-dependent gene expression. From the discovery of CREB, which is ubiquitously expressed, it has been proven to be involved in a variety of cellular processes that include cell proliferation, adaptation, survival, differentiation, and physiology, through the control of target gene expression. In this review, we highlight the essential roles of CREB proteins in the nervous system, the immune system, cancer development, hepatic physiology, and cardiovascular function and further discuss a wide range of CREB-associated diseases and molecular mechanisms underlying the pathogenesis of these diseases.
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Affiliation(s)
- Md. Arifur Rahman Chowdhury
- Division of Life Sciences (Molecular Biology Major), Department of Bioactive Material Sciences, and Research Center of Bioactive Materials, Jeonbuk National University, Jeonju 54896, Korea
| | - Jungeun An
- Division of Life Sciences (Life Sciences Major), Jeonbuk National University, Jeonju 54896, Korea
| | - Sangyun Jeong
- Division of Life Sciences (Molecular Biology Major), Department of Bioactive Material Sciences, and Research Center of Bioactive Materials, Jeonbuk National University, Jeonju 54896, Korea
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14
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Bang JW, Parra C, Yu K, Wollstein G, Schuman JS, Chan KC. GABA decrease is associated with degraded neural specificity in the visual cortex of glaucoma patients. Commun Biol 2023; 6:679. [PMID: 37386293 PMCID: PMC10310759 DOI: 10.1038/s42003-023-04918-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/05/2023] [Indexed: 07/01/2023] Open
Abstract
Glaucoma is an age-related neurodegenerative disease of the visual system, affecting both the eye and the brain. Yet its underlying metabolic mechanisms and neurobehavioral relevance remain largely unclear. Here, using proton magnetic resonance spectroscopy and functional magnetic resonance imaging, we investigated the GABAergic and glutamatergic systems in the visual cortex of glaucoma patients, as well as neural specificity, which is shaped by GABA and glutamate signals and underlies efficient sensory and cognitive functions. Our study shows that among the older adults, both GABA and glutamate levels decrease with increasing glaucoma severity regardless of age. Further, our study shows that the reduction of GABA but not glutamate predicts the neural specificity. This association is independent of the impairments on the retina structure, age, and the gray matter volume of the visual cortex. Our results suggest that glaucoma-specific decline of GABA undermines neural specificity in the visual cortex and that targeting GABA could improve the neural specificity in glaucoma.
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Affiliation(s)
- Ji Won Bang
- Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10017, USA.
| | - Carlos Parra
- Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10017, USA
| | - Kevin Yu
- Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10017, USA
| | - Gadi Wollstein
- Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10017, USA
- Center for Neural Science, College of Arts and Science, New York University, New York, New York, 10003, USA
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, New York, 11201, USA
| | - Joel S Schuman
- Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10017, USA
- Center for Neural Science, College of Arts and Science, New York University, New York, New York, 10003, USA
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, New York, 11201, USA
- Neuroscience Institute, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10016, USA
| | - Kevin C Chan
- Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10017, USA.
- Center for Neural Science, College of Arts and Science, New York University, New York, New York, 10003, USA.
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, New York, 11201, USA.
- Neuroscience Institute, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10016, USA.
- Department of Radiology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, New York, 10016, USA.
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15
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Xiong M, Roshanbin S, Sehlin D, Hansen HD, Knudsen GM, Rokka J, Eriksson J, Syvänen S. Synaptic density in aging mice measured by [ 18F]SynVesT-1 PET. Neuroimage 2023:120230. [PMID: 37355199 DOI: 10.1016/j.neuroimage.2023.120230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 05/03/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023] Open
Abstract
Synaptic alterations in certain brain structures are related to cognitive decline in neurodegeneration and in aging. Synaptic loss in many neurodegenerative diseases can be visualized by positron emission tomography (PET) imaging of synaptic vesicle glycoprotein 2A (SV2A). However, the use of SV2A PET for studying synaptic changes during aging is not particularly explored. Thus, in the present study, PET ligand [18F]SynVesT-1, which binds to SV2A, was used to investigate synaptic density at different ages in healthy mice. Wild type C57BL/6 mice divided into three age groups (4-5 months (n = 7), 12-14 months (n = 11), 17-19 months (n = 7)) were PET scanned with [18F]SynVesT-1. Brain retention of [18F]SynVesT-1 expressed as the volume of distribution (VIDIF) was calculated using an image-derived input function. Estimates of VIDIF were derived using either a one-tissue compartment model (1TCM), a two-tissue compartment model (2TCM), or the Logan plot with blood input to find the best-fit model for [18F]SynVesT-1. After the PET scans, tissue sections were immunostained for the detection of SV2A and neuronal markers. We found that [18F]SynVesT-1 data acquired 60 min post intravenously injection and analyzed with 1TCM described the brain pharmacokinetics of the radioligand in mice well. [18F]SynVesT-1 brain retention was lower in the oldest group of mice, indicating a decrease in synaptic density in this age group. However, no gradual age-dependent decrease in synaptic density at a region-specific level was observed. Immunostaining indicated that SV2A expression and neuron numbers were similar across all three age groups. In general, these data obtained in healthy aging mice are consistent with previous findings in humans where synaptic density appeared stable during aging up to a certain age, after which a small decrease is observed.
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Affiliation(s)
- Mengfei Xiong
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Sahar Roshanbin
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Dag Sehlin
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Hanne D Hansen
- Neurobiology Research Unit, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark
| | - Gitte M Knudsen
- Neurobiology Research Unit, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Johanna Rokka
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Jonas Eriksson
- PET Centre, Uppsala University Hospital, SE-751 85 Uppsala, Sweden; Department of Medicinal Chemistry, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Stina Syvänen
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, SE-751 85 Uppsala, Sweden.
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16
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Toker L, Nido GS, Tzoulis C. Not every estimate counts - evaluation of cell composition estimation approaches in brain bulk tissue data. Genome Med 2023; 15:41. [PMID: 37287013 DOI: 10.1186/s13073-023-01195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Variation in cell composition can dramatically impact analyses in bulk tissue samples. A commonly employed approach to mitigate this issue is to adjust statistical models using estimates of cell abundance derived directly from omics data. While an arsenal of estimation methods exists, the applicability of these methods to brain tissue data and whether or not cell estimates can sufficiently account for confounding cellular composition has not been adequately assessed. METHODS We assessed the correspondence between different estimation methods based on transcriptomic (RNA sequencing, RNA-seq) and epigenomic (DNA methylation and histone acetylation) data from brain tissue samples of 49 individuals. We further evaluated the impact of different estimation approaches on the analysis of H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-seq) data from entorhinal cortex of individuals with Alzheimer's disease and controls. RESULTS We show that even closely adjacent tissue samples from the same Brodmann area vary greatly in their cell composition. Comparison across different estimation methods indicates that while different estimation methods applied to the same data produce highly similar outcomes, there is a surprisingly low concordance between estimates based on different omics data modalities. Alarmingly, we show that cell type estimates may not always sufficiently account for confounding variation in cell composition. CONCLUSIONS Our work indicates that cell composition estimation or direct quantification in one tissue sample should not be used as a proxy to the cellular composition of another tissue sample from the same brain region of an individual-even if the samples are directly adjacent. The highly similar outcomes observed among vastly different estimation methods, highlight the need for brain benchmark datasets and better validation approaches. Finally, unless validated through complementary experiments, the interpretation of analyses outcomes based on data confounded by cell composition should be done with great caution, and ideally avoided all together.
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Affiliation(s)
- Lilah Toker
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
| | - Gonzalo S Nido
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway.
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway.
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway.
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17
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LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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18
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Wahl D, Smith ME, McEntee CM, Cavalier AN, Osburn SC, Burke SD, Grant RA, Nerguizian D, Lark DS, Link CD, LaRocca TJ. The reverse transcriptase inhibitor 3TC protects against age-related cognitive dysfunction. Aging Cell 2023; 22:e13798. [PMID: 36949552 PMCID: PMC10186603 DOI: 10.1111/acel.13798] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 03/24/2023] Open
Abstract
Aging is the primary risk factor for most neurodegenerative diseases, including Alzheimer's disease. Major hallmarks of brain aging include neuroinflammation/immune activation and reduced neuronal health/function. These processes contribute to cognitive dysfunction (a key risk factor for Alzheimer's disease), but their upstream causes are incompletely understood. Age-related increases in transposable element (TE) transcripts might contribute to reduced cognitive function with brain aging, as the reverse transcriptase inhibitor 3TC reduces inflammation in peripheral tissues and TE transcripts have been linked with tau pathology in Alzheimer's disease. However, the effects of 3TC on cognitive function with aging have not been investigated. Here, in support of a role for TE transcripts in brain aging/cognitive decline, we show that 3TC: (a) improves cognitive function and reduces neuroinflammation in old wild-type mice; (b) preserves neuronal health with aging in mice and Caenorhabditis elegans; and (c) enhances cognitive function in a mouse model of tauopathy. We also provide insight on potential underlying mechanisms, as well as evidence of translational relevance for these observations by showing that TE transcripts accumulate with brain aging in humans, and that these age-related increases intersect with those observed in Alzheimer's disease. Collectively, our results suggest that TE transcript accumulation during aging may contribute to cognitive decline and neurodegeneration, and that targeting these events with reverse transcriptase inhibitors like 3TC could be a viable therapeutic strategy.
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Affiliation(s)
- Devin Wahl
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Meghan E. Smith
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Cali M. McEntee
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Alyssa N. Cavalier
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Shelby C. Osburn
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Samuel D. Burke
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - Randy A. Grant
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
| | - David Nerguizian
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Daniel S. Lark
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
| | - Christopher D. Link
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Thomas J. LaRocca
- Department of Health and Exercise ScienceColorado State UniversityFort CollinsColoradoUSA
- Center for Healthy AgingColorado State UniversityFort CollinsColoradoUSA
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19
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Gasperi RD, Gama Sosa MA, Perez Garcia GS, Perez GM, Abutarboush R, Kawoos U, Statz JK, Patterson J, Hof PR, Katsel P, Cook DG, Ahlers ST, Elder GA. Progressive Transcriptional Changes in the Amygdala Implicate Neuroinflammation in the Effects of Repetitive Low-Level Blast Exposure in Male Rats. J Neurotrauma 2023; 40:561-577. [PMID: 36262047 PMCID: PMC10040418 DOI: 10.1089/neu.2022.0282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chronic mental health problems are common among military veterans who sustained blast-related traumatic brain injuries. The reasons for this association remain unexplained. Male rats exposed to repetitive low-level blast overpressure (BOP) exposures exhibit chronic cognitive and post-traumatic stress disorder (PTSD)-related traits that develop in a delayed fashion. We examined blast-induced alterations on the transcriptome in four brain areas (anterior cortex, hippocampus, amygdala, and cerebellum) across the time frame over which the PTSD-related behavioral phenotype develops. When analyzed at 6 weeks or 12 months after blast exposure, relatively few differentially expressed genes (DEGs) were found. However, longitudinal analysis of amygdala, hippocampus, and anterior cortex between 6 weeks and 12 months revealed blast-specific DEG patterns. Six DEGs (hyaluronan and proteoglycan link protein 1 [Hapln1], glutamate metabotropic receptor 2 [Grm2], purinergic receptor P2y12 [P2ry12], C-C chemokine receptor type 5 [Ccr5], phenazine biosynthesis-like protein domain containing 1 [Pbld1], and cadherin related 23 [Cdh23]) were found altered in all three brain regions in blast-exposed animals. Pathway enrichment analysis using all DEGs or those uniquely changed revealed different transcription patterns in blast versus sham. In particular, the amygdala in blast-exposed animals had a unique set of enriched pathways related to stress responses, oxidative phosphorylation, and mitochondrial dysfunction. Upstream analysis implicated tumor necrosis factor (TNF)α signaling in blast-related effects in amygdala and anterior cortex. Eukaryotic initiating factor eIF4E (EIF4e), an upstream regulator of P2ry12 and Ccr5, was predicted to be activated in the amygdala. Quantitative polymerase chain reaction (qPCR) validated longitudinal changes in two TNFα regulated genes (cathepsin B [Ctsb], Hapln1), P2ry12, and Grm2. These studies have implications for understanding how blast injury damages the brain and implicates inflammation as a potential therapeutic target.
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Affiliation(s)
- Rita De Gasperi
- Research and Development Service, James J. Peters Department of Veterans Affairs Medical Center, Bronx, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Miguel A. Gama Sosa
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- General Medical Research Service, James J. Peters Department of Veterans Affairs Medical Center, Bronx, New York, USA
- Department of Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Georgina S. Perez Garcia
- Research and Development Service, James J. Peters Department of Veterans Affairs Medical Center, Bronx, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gissel M. Perez
- Research and Development Service, James J. Peters Department of Veterans Affairs Medical Center, Bronx, New York, USA
| | - Rania Abutarboush
- Department of Neurotrauma, Naval Medical Research Center, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Usmah Kawoos
- Department of Neurotrauma, Naval Medical Research Center, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Jonathan K. Statz
- Department of Neurotrauma, Naval Medical Research Center, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Jacob Patterson
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Parsons Corporation, Centreville, Virginia, USA
| | - Patrick R. Hof
- Department of Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Geriatrics and Palliative Care, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Mount Sinai Alzheimer's Disease Research Center and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pavel Katsel
- Research and Development Service, James J. Peters Department of Veterans Affairs Medical Center, Bronx, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David G. Cook
- Geriatric Research Education and Clinical Center, VA Puget Sound Health Care System, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Stephen T. Ahlers
- Department of Neurotrauma, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Gregory A. Elder
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Mount Sinai Alzheimer's Disease Research Center and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neurology Service, James J. Peters Department of Veterans Affairs Medical Center, Bronx, New York, USA
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20
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Rigby Dames BA, Kilili H, Charvet CJ, Díaz-Barba K, Proulx MJ, de Sousa AA, Urrutia AO. Evolutionary and genomic perspectives of brain aging and neurodegenerative diseases. PROGRESS IN BRAIN RESEARCH 2023; 275:165-215. [PMID: 36841568 PMCID: PMC11191546 DOI: 10.1016/bs.pbr.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This chapter utilizes genomic concepts and evolutionary perspectives to further understand the possible links between typical brain aging and neurodegenerative diseases, focusing on the two most prevalent of these: Alzheimer's disease and Parkinson's disease. Aging is the major risk factor for these neurodegenerative diseases. Researching the evolutionary and molecular underpinnings of aging helps to reveal elements of the typical aging process that leave individuals more vulnerable to neurodegenerative pathologies. Very little is known about the prevalence and susceptibility of neurodegenerative diseases in nonhuman species, as only a few individuals have been observed with these neuropathologies. However, several studies have investigated the evolution of lifespan, which is closely connected with brain size in mammals, and insights can be drawn from these to enrich our understanding of neurodegeneration. This chapter explores the relationship between the typical aging process and the events in neurodegeneration. First, we examined how age-related processes can increase susceptibility to neurodegenerative diseases. Second, we assessed to what extent neurodegeneration is an accelerated form of aging. We found that while at the phenotypic level both neurodegenerative diseases and the typical aging process share some characteristics, at the molecular level they show some distinctions in their profiles, such as variation in genes and gene expression. Furthermore, neurodegeneration of the brain is associated with an earlier onset of cellular, molecular, and structural age-related changes. In conclusion, a more integrative view of the aging process, both from a molecular and an evolutionary perspective, may increase our understanding of neurodegenerative diseases.
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Affiliation(s)
- Brier A Rigby Dames
- Department of Computer Science, University of Bath, Bath, United Kingdom; Department of Psychology, University of Bath, Bath, United Kingdom.
| | - Huseyin Kilili
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Christine J Charvet
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Karina Díaz-Barba
- Licenciatura en Ciencias Genómicas, UNAM, CP62210, Cuernavaca, México; Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Michael J Proulx
- Department of Psychology, University of Bath, Bath, United Kingdom
| | | | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom; Licenciatura en Ciencias Genómicas, UNAM, CP62210, Cuernavaca, México; Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México.
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21
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Kim H, Huh YJ, Kim JH, Jo M, Shin JH, Park SC, Ahn JY, Lee YI, Lee Y. Identification and evaluation of midbrain specific longevity-related genes in exceptionally long-lived but healthy mice. Front Aging Neurosci 2023; 14:1030807. [PMID: 36711211 PMCID: PMC9874112 DOI: 10.3389/fnagi.2022.1030807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Brain aging is a complex biological process that is affected by both genetic background and environment. The transcriptomic analysis of aged human and rodent brains has been applied to identify age-associated molecular and cellular processes for which intervention could possibly restore declining brain functions induced by aging. However, whether these age-associated genetic alterations are indeed involved in the healthy aging of the brain remains unclear. We herein characterized a naturally occurring, extremely long-lived (34 months of age) but healthy mouse group retaining well-preserved motor functions. Strikingly, these long-lived mice maintained tyrosine hydroxylase expression and dopaminergic fiber densities, even in the presence of persistent neuroinflammation and expression of aging markers. Combined with Endeavor gene prioritization, we identified the following midbrain-specific longevity-associated genes in the midbrain of these mice: aimp2, hexb, cacybp, akt2, nrf1, axin1, wwp2, sp2, dnajb9, notch, traf7, and lrp1. A detailed biochemical analysis of the midbrain of these long-lived mice confirmed the increased expression of Nrf1 and the activation of Akt1 and 2. Interestingly, dopaminergic neuroprotective and age-associated E3 ubiquitin ligase parkin expression was retained at high levels in the aforementioned midbrains, possibly supporting the suppression of its toxic substrates AIMP2 and PARIS. In contrast, the 24-month-old mice with dopaminergic neurite deficits failed to maintain parkin expression in the midbrain. AIMP2-induced cytotoxicity, mitochondrial stress, and neurite toxicity can be prevented by overexpression of parkin, Akt1, and Nrf1 in SH-SY5Y and PC12 cells, and basal expression of parkin, Akt1, and Nrf1 is required for maintenance of mitochondrial function and neurite integrity in PC12 cells. Taken together, this longevity-associated pathway could be a potential target of intervention to maintain nigrostriatal dopaminergic fibers and motor ability to ensure healthy longevity.
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Affiliation(s)
- Hyojung Kim
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Yu-Jin Huh
- Division of Biotechnology, Department of Interdisciplinary Studies, Well Aging Research Center, DGIST, Daegu, Republic of Korea,Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Ji Hun Kim
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Minkyung Jo
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Joo-Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Sang Chul Park
- Division of Biotechnology, Department of Interdisciplinary Studies, Well Aging Research Center, DGIST, Daegu, Republic of Korea,The Future Life & Society Research Center, Advanced Institute of Aging Science, Chonnam National University, Gwangju, Republic of Korea
| | - Jee-Yin Ahn
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Yun-Il Lee
- Division of Biotechnology, Department of Interdisciplinary Studies, Well Aging Research Center, DGIST, Daegu, Republic of Korea,*Correspondence: Yun-Il Lee,
| | - Yunjong Lee
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea,Yunjong Lee,
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22
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Huang K, Gong H, Guan J, Zhang L, Hu C, Zhao W, Huang L, Zhang W, Kim P, Zhou X. AgeAnno: a knowledgebase of single-cell annotation of aging in human. Nucleic Acids Res 2023; 51:D805-D815. [PMID: 36200838 PMCID: PMC9825500 DOI: 10.1093/nar/gkac847] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 01/30/2023] Open
Abstract
Aging is a complex process that accompanied by molecular and cellular alterations. The identification of tissue-/cell type-specific biomarkers of aging and elucidation of the detailed biological mechanisms of aging-related genes at the single-cell level can help to understand the heterogeneous aging process and design targeted anti-aging therapeutics. Here, we built AgeAnno (https://relab.xidian.edu.cn/AgeAnno/#/), a knowledgebase of single cell annotation of aging in human, aiming to provide comprehensive characterizations for aging-related genes across diverse tissue-cell types in human by using single-cell RNA and ATAC sequencing data (scRNA and scATAC). The current version of AgeAnno houses 1 678 610 cells from 28 healthy tissue samples with ages ranging from 0 to 110 years. We collected 5580 aging-related genes from previous resources and performed dynamic functional annotations of the cellular context. For the scRNA data, we performed analyses include differential gene expression, gene variation coefficient, cell communication network, transcription factor (TF) regulatory network, and immune cell proportionc. AgeAnno also provides differential chromatin accessibility analysis, motif/TF enrichment and footprint analysis, and co-accessibility peak analysis for scATAC data. AgeAnno will be a unique resource to systematically characterize aging-related genes across diverse tissue-cell types in human, and it could facilitate antiaging and aging-related disease research.
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Affiliation(s)
- Kexin Huang
- West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Med-X Center for Informatics, Sichuan University,Chengdu,Sichuan 610041, P.R. China
| | - Hoaran Gong
- West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Med-X Center for Informatics, Sichuan University,Chengdu,Sichuan 610041, P.R. China
| | - Jingjing Guan
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, P.R. China
| | - Lingxiao Zhang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, P.R. China
| | - Changbao Hu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, P.R. China
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, P.R. China
| | - Wei Zhang
- West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Med-X Center for Informatics, Sichuan University,Chengdu,Sichuan 610041, P.R. China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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23
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Zhang X, An H, Chen Y, Shu N. Neurobiological Mechanisms of Cognitive Decline Correlated with Brain Aging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1419:127-146. [PMID: 37418211 DOI: 10.1007/978-981-99-1627-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Cognitive decline has emerged as one of the greatest health threats of old age. Meanwhile, aging is the primary risk factor for Alzheimer's disease (AD) and other prevalent neurodegenerative disorders. Developing therapeutic interventions for such conditions demands a greater understanding of the processes underlying normal and pathological brain aging. Despite playing an important role in the pathogenesis and incidence of disease, brain aging has not been well understood at a molecular level. Recent advances in the biology of aging in model organisms, together with molecular- and systems-level studies of the brain, are beginning to shed light on these mechanisms and their potential roles in cognitive decline. This chapter seeks to integrate the knowledge about the neurological mechanisms of age-related cognitive changes that underlie aging.
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Affiliation(s)
- Xiaxia Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, Faculty of Psychology, Beijing Normal University, Beijing, China
- Beijing Aging Brain Rejuvenation Initiative (BABRI) Centre, Beijing Normal University, Beijing, China
| | - Haiting An
- Beijing Aging Brain Rejuvenation Initiative (BABRI) Centre, Beijing Normal University, Beijing, China
- Beijing Neurosurgical Institute, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Yuan Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, Faculty of Psychology, Beijing Normal University, Beijing, China
- Beijing Aging Brain Rejuvenation Initiative (BABRI) Centre, Beijing Normal University, Beijing, China
| | - Ni Shu
- State Key Laboratory of Cognitive Neuroscience and Learning, Faculty of Psychology, Beijing Normal University, Beijing, China.
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24
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Mavrikaki M, Lee JD, Solomon IH, Slack FJ. Severe COVID-19 is associated with molecular signatures of aging in the human brain. NATURE AGING 2022; 2:1130-1137. [PMID: 37118539 DOI: 10.1038/s43587-022-00321-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/25/2022] [Indexed: 04/30/2023]
Abstract
As coronavirus disease 2019 (COVID-19) and aging are both accompanied by cognitive decline, we hypothesized that COVID-19 might lead to molecular signatures similar to aging. We performed whole-transcriptome analysis of the frontal cortex, a critical area for cognitive function, in individuals with COVID-19, age-matched and sex-matched uninfected controls, and uninfected individuals with intensive care unit/ventilator treatment. Our findings indicate that COVID-19 is associated with molecular signatures of brain aging and emphasize the value of neurological follow-up in recovered individuals.
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Affiliation(s)
- Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Jonathan D Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frank J Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA.
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25
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Tonoki A, Nagai S, Yu Z, Yue T, Lyu S, Hou X, Onuki K, Yabana K, Takahashi H, Itoh M. Nitric oxide-soluble guanylyl cyclase pathway as a contributor to age-related memory impairment in Drosophila. Aging Cell 2022; 21:e13691. [PMID: 35963012 PMCID: PMC9470885 DOI: 10.1111/acel.13691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/27/2022] [Indexed: 01/25/2023] Open
Abstract
Age-related changes in the transcriptome lead to memory impairment. Several genes have been identified to cause age-dependent memory impairment (AMI) by changes in their expression, but genetic screens to identify genes critical for AMI have not been performed. The fruit fly is a useful model for studying AMI due to its short lifespan and the availability of consistent techniques and environments to assess its memory ability. We generated a list of candidate genes that act as AMI regulators by performing a comprehensive analysis of RNAsequencing data from young and aged fly heads and genome-wide RNAi screening data to identify memory-regulating genes. A candidate screen using temporal and panneuronal RNAi expression was performed to identify genes critical for AMI. We identified the guanylyl cyclase β-subunit at 100B (gycβ) gene, which encodes a subunit of soluble guanylyl cyclase (sGC), the only intracellular nitric oxide (NO) receptor in fruit flies, as a negative regulator of AMI. RNAi knockdown of gycβ in neurons and NO synthase (NOS) in glia or neurons enhanced the performance of intermediate-term memory (ITM) without apparent effects on memory acquisition. We also showed that pharmacological inhibition of sGC and NOS enhanced ITM in aged individuals, suggesting the possibility that age-related enhancement of the NO-sGC pathway causes memory impairment.
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Affiliation(s)
- Ayako Tonoki
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Saki Nagai
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Zhihua Yu
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Tong Yue
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Sizhe Lyu
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Xue Hou
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Kotomi Onuki
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Kaho Yabana
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | | | - Motoyuki Itoh
- Department of Biochemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
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26
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Kelley CM, Ginsberg SD, Liang WS, Counts SE, Mufson EJ. Posterior cingulate cortex reveals an expression profile of resilience in cognitively intact elders. Brain Commun 2022; 4:fcac162. [PMID: 35813880 PMCID: PMC9263888 DOI: 10.1093/braincomms/fcac162] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/12/2022] [Accepted: 06/17/2022] [Indexed: 12/20/2022] Open
Abstract
The posterior cingulate cortex, a key hub of the default mode network, underlies autobiographical memory retrieval and displays hypometabolic changes early in Alzheimer disease. To obtain an unbiased understanding of the molecular pathobiology of the aged posterior cingulate cortex, we performed RNA sequencing (RNA-seq) on tissue obtained from 26 participants of the Rush Religious Orders Study (11 males/15 females; aged 76-96 years) with a pre-mortem clinical diagnosis of no cognitive impairment and post-mortem neurofibrillary tangle Braak Stages I/II, III, and IV. Transcriptomic data were gathered using next-generation sequencing of RNA extracted from posterior cingulate cortex generating an average of 60 million paired reads per subject. Normalized expression of RNA-seq data was calculated using a global gene annotation and a microRNA profile. Differential expression (DESeq2, edgeR) using Braak staging as the comparison structure isolated genes for dimensional scaling, associative network building and functional clustering. Curated genes were correlated with the Mini-Mental State Examination and semantic, working and episodic memory, visuospatial ability, and a composite Global Cognitive Score. Regulatory mechanisms were determined by co-expression networks with microRNAs and an overlap of transcription factor binding sites. Analysis revealed 750 genes and 12 microRNAs significantly differentially expressed between Braak Stages I/II and III/IV and an associated six groups of transcription factor binding sites. Inputting significantly different gene/network data into a functional annotation clustering model revealed elevated presynaptic, postsynaptic and ATP-related expression in Braak Stages III and IV compared with Stages I/II, suggesting these pathways are integral for cognitive resilience seen in unimpaired elderly subjects. Principal component analysis and Kruskal-Wallis testing did not associate Braak stage with cognitive function. However, Spearman correlations between genes and cognitive test scores followed by network analysis revealed upregulation of classes of synaptic genes positively associated with performance on the visuospatial perceptual orientation domain. Upregulation of key synaptic genes suggests a role for these transcripts and associated synaptic pathways in cognitive resilience seen in elders despite Alzheimer disease pathology and dementia.
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Affiliation(s)
- Christy M Kelley
- Department of Translational Neuroscience, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
- Department of Neurology, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
| | - Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Scott E Counts
- Department of Translational Neuroscience, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
- Department of Family Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
| | - Elliott J Mufson
- Department of Translational Neuroscience, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
- Department of Neurology, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
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27
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Neuroprotective Effects and Therapeutic Potential of the Citrus Flavonoid Hesperetin in Neurodegenerative Diseases. Nutrients 2022; 14:nu14112228. [PMID: 35684025 PMCID: PMC9183194 DOI: 10.3390/nu14112228] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative disorders affect more than fifty million Americans each year and represent serious health threats as the population ages. Neuroinflammation and oxidative stress are critical in the onset, progression, and pathogenesis of neurodegenerative diseases such as Alzheimer’s (AD), Parkinson’s (PD), and amyotrophic lateral sclerosis (ALS). A wide range of natural compounds has been investigated because of their antioxidant, anti-inflammatory, and neuroprotective properties. The citrus flavonoid hesperetin (HPT), an aglycone of hesperidin found in oranges, mandarins, and lemons, has been extensively reported to exert neuroprotective effects in experimental models of neurogenerative diseases. This review has compiled multiple studies on HPT in both in vivo and in vitro models to study neurodegeneration. We focused on the modulatory effects of hesperetin on the release of cellular anti-inflammatory and antioxidative stress mediators. Additionally, this review discusses the hesperetin effect in maintaining the levels of microRNA (miRNA) and modulating autophagy as it relates to hesperetin’s protective mechanisms against neurodegeneration. Moreover, this review is focused on providing experimental data for hesperetin’s potential as a neuroprotective compound and discusses reported evidence that HPT crosses the blood–brain barrier. In summary, this review shows the evidence available in the literature to indicate the efficacy of hesperetin in delaying the onset of neurodegenerative diseases.
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28
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The Neuroprotective Lipocalin Apolipoprotein D Stably Interacts with Specific Subtypes of Detergent-Resistant Membrane Domains in a Basigin-Independent Manner. Mol Neurobiol 2022; 59:4015-4029. [PMID: 35460054 PMCID: PMC9167181 DOI: 10.1007/s12035-022-02829-z] [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: 11/26/2021] [Accepted: 04/02/2022] [Indexed: 11/25/2022]
Abstract
Accumulated evidence points to the lipocalin apolipoprotein D (ApoD), one of the few genes consistently upregulated upon brain ageing and neurodegeneration, as an endogenous controller of the redox state of cellular and extracellular lipid structures. This biochemical function has downstream consequences as apparently varied as control of glycocalyx and myelin compaction, cell viability upon oxidative stress or modulation of signalling pathways. In spite of this knowledge, it is still unclear if ApoD function requires canonical receptor-mediated transductions systems. This work aims to examine ApoD-cell membrane interaction and its dependence on a proposed ApoD receptor, Basigin. Whole and fractionated membrane preparations from the brain, primary astrocytes, glial and neuronal cell lines, reveal ApoD as a very specific component of particular subtypes of detergent-resistant microdomains (DRMs). ApoD interacts in vitro with neuronal membranes and is stably associated with astrocytic membranes. ApoD associates with DRMs with specific buoyancy properties that co-fractionate with plasma or late-endosome-lysosome markers. A mass spectrometry analysis reveals that these Triton X-114 DRMs contain both plasma membrane and endosomal-lysosomal compartment lipid raft proteins. ApoD-DRM association is maintained under metabolic and acute oxidative stress conditions. However, ApoD-membrane interaction, its internalization and its lipid-antioxidant function do not require the presence of Basigin. This work supports a stable association of ApoD with membranes, independent of Basigin, and provides the basis to fully understand ApoD antioxidant neuroprotective mechanism as a mechanism taking place in specific membrane subdomains.
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Induction of Accelerated Aging in a Mouse Model. Cells 2022; 11:cells11091418. [PMID: 35563724 PMCID: PMC9102583 DOI: 10.3390/cells11091418] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
With the global increase of the elderly population, the improvement of the treatment for various aging-related diseases and the extension of a healthy lifespan have become some of the most important current medical issues. In order to understand the developmental mechanisms of aging and aging-related disorders, animal models are essential to conduct relevant studies. Among them, mice have become one of the most prevalently used model animals for aging-related studies due to their high similarity to humans in terms of genetic background and physiological structure, as well as their short lifespan and ease of reproduction. This review will discuss some of the common and emerging mouse models of accelerated aging and related chronic diseases in recent years, with the aim of serving as a reference for future application in fundamental and translational research.
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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.
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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
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Kluever V, Fornasiero EF. Principles of brain aging: Status and challenges of modeling human molecular changes in mice. Ageing Res Rev 2021; 72:101465. [PMID: 34555542 DOI: 10.1016/j.arr.2021.101465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023]
Abstract
Due to the extension of human life expectancy, the prevalence of cognitive impairment is rising in the older portion of society. Developing new strategies to delay or attenuate cognitive decline is vital. For this purpose, it is imperative to understand the cellular and molecular events at the basis of brain aging. While several organs are directly accessible to molecular analysis through biopsies, the brain constitutes a notable exception. Most of the molecular studies are performed on postmortem tissues, where cell death and tissue damage have already occurred. Hence, the study of the molecular aspects of cognitive decline largely relies on animal models and in particular on small mammals such as mice. What have we learned from these models? Do these animals recapitulate the changes observed in humans? What should we expect from future mouse studies? In this review we answer these questions by summarizing the state of the research that has addressed cognitive decline in mice from several perspectives, including genetic manipulation and omics strategies. We conclude that, while extremely valuable, mouse models have limitations that can be addressed by the optimal design of future studies and by ensuring that results are cross-validated in the human context.
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Vinexin contributes to autophagic decline in brain ageing across species. Cell Death Differ 2021; 29:1055-1070. [PMID: 34848853 PMCID: PMC9090768 DOI: 10.1038/s41418-021-00903-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 01/29/2023] Open
Abstract
Autophagic decline is considered a hallmark of ageing. The activity of this intracytoplasmic degradation pathway decreases with age in many tissues and autophagy induction ameliorates ageing in many organisms, including mice. Autophagy is a critical protective pathway in neurons and ageing is the primary risk factor for common neurodegenerative diseases. Here, we describe that autophagosome biogenesis declines with age in mouse brains and that this correlates with increased expression of the SORBS3 gene (encoding vinexin) in older mouse and human brain tissue. We characterise vinexin as a negative regulator of autophagy. SORBS3 knockdown increases F-actin structures, which compete with YAP/TAZ for binding to their negative regulators, angiomotins, in the cytosol. This promotes YAP/TAZ translocation into the nucleus, thereby increasing YAP/TAZ transcriptional activity and autophagy. Our data therefore suggest brain autophagy decreases with age in mammals and that this is likely, in part, mediated by increasing levels of vinexin.
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Mavrikaki M, Lee JD, Solomon IH, Slack FJ. Severe COVID-19 induces molecular signatures of aging in the human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.24.21266779. [PMID: 34845457 PMCID: PMC8629201 DOI: 10.1101/2021.11.24.21266779] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is predominantly an acute respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and remains a significant threat to public health. COVID-19 is accompanied by neurological symptoms and cognitive decline, but the molecular mechanisms underlying this effect remain unclear. As aging induces distinct molecular signatures in the brain associated with cognitive decline in healthy populations, we hypothesized that COVID-19 may induce molecular signatures of aging. Here, we performed whole transcriptomic analysis of human frontal cortex, a critical area for cognitive function, in 12 COVID-19 cases and age- and sex-matched uninfected controls. COVID-19 induces profound changes in gene expression, despite the absence of detectable virus in brain tissue. Pathway analysis shows downregulation of genes involved in synaptic function and cognition and upregulation of genes involved in immune processes. Comparison with five independent transcriptomic datasets of aging human frontal cortex reveals striking similarities between aged individuals and severe COVID-19 patients. Critically, individuals below 65 years of age exhibit profound transcriptomic changes not observed among older individuals in our patient cohort. Our data indicate that severe COVID-19 induces molecular signatures of aging in the human brain and emphasize the value of neurological follow-up in recovered individuals.
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Affiliation(s)
- Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally: Maria Mavrikaki and Jonathan D. Lee
- Correspondence to M.M. and F.J.S.: ;
| | - Jonathan D. Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally: Maria Mavrikaki and Jonathan D. Lee
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Frank J. Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02215, USA
- Correspondence to M.M. and F.J.S.: ;
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Shively CA, Lacreuse A, Frye BM, Rothwell ES, Moro M. Nonhuman primates at the intersection of aging biology, chronic disease, and health: An introduction to the American Journal of Primatology Special Issue on aging, cognitive decline, and neuropathology in nonhuman primates. Am J Primatol 2021; 83:e23309. [PMID: 34403529 PMCID: PMC8935964 DOI: 10.1002/ajp.23309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/05/2021] [Indexed: 11/06/2022]
Abstract
Aging across the Primate Order is poorly understood because ages of individuals are often unknown, there is a dearth of aged animals available for study, and because aging is best characterized by longitudinal studies which are difficult to carry out in long-lived species. The human population is aging rapidly, and advanced age is a primary risk factor for several chronic diseases and conditions that impact healthspan. As lifespan has increased, diseases and disorders of the central nervous system (CNS) have become more prevalent, and Alzheimer's disease and related dementias have become epidemic. Nonhuman primate (NHP) models are key to understanding the aging primate CNS. This Special Issue presents a review of current knowledge about NHP CNS aging across the Primate Order. Similarities and differences to human aging, and their implications for the validity of NHP models of aging are considered. Topics include aging-related brain structure and function, neuropathologies, cognitive performance, social behavior and social network characteristics, and physical, sensory, and motor function. Challenges to primate CNS aging research are discussed. Together, this collection of articles demonstrates the value of studying aging in a breadth of NHP models to advance our understanding of human and nonhuman primate aging and healthspan.
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Affiliation(s)
- Carol A. Shively
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston Salem, North Carolina, USA
- Alzheimer’s Disease Research Center, Wake Forest School of Medicine, Winston Salem, North Carolina, USA
| | - Agnès Lacreuse
- Department of Psychological and Brain Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Brett M. Frye
- Department of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston Salem, North Carolina, USA
| | - Emily S. Rothwell
- Department of Psychological and Brain Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Manuel Moro
- Division of Aging Biology, National Institute on Aging, National Institutes of Health, Maryland, USA
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Sanchez D, Ganfornina MD. The Lipocalin Apolipoprotein D Functional Portrait: A Systematic Review. Front Physiol 2021; 12:738991. [PMID: 34690812 PMCID: PMC8530192 DOI: 10.3389/fphys.2021.738991] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022] Open
Abstract
Apolipoprotein D is a chordate gene early originated in the Lipocalin protein family. Among other features, regulation of its expression in a wide variety of disease conditions in humans, as apparently unrelated as neurodegeneration or breast cancer, have called for attention on this gene. Also, its presence in different tissues, from blood to brain, and different subcellular locations, from HDL lipoparticles to the interior of lysosomes or the surface of extracellular vesicles, poses an interesting challenge in deciphering its physiological function: Is ApoD a moonlighting protein, serving different roles in different cellular compartments, tissues, or organisms? Or does it have a unique biochemical mechanism of action that accounts for such apparently diverse roles in different physiological situations? To answer these questions, we have performed a systematic review of all primary publications where ApoD properties have been investigated in chordates. We conclude that ApoD ligand binding in the Lipocalin pocket, combined with an antioxidant activity performed at the rim of the pocket are properties sufficient to explain ApoD association with different lipid-based structures, where its physiological function is better described as lipid-management than by long-range lipid-transport. Controlling the redox state of these lipid structures in particular subcellular locations or extracellular structures, ApoD is able to modulate an enormous array of apparently diverse processes in the organism, both in health and disease. The new picture emerging from these data should help to put the physiological role of ApoD in new contexts and to inspire well-focused future research.
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Affiliation(s)
- Diego Sanchez
- Instituto de Biologia y Genetica Molecular, Unidad de Excelencia, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas, Valladolid, Spain
| | - Maria D Ganfornina
- Instituto de Biologia y Genetica Molecular, Unidad de Excelencia, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas, Valladolid, Spain
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Gao Y, Webster MA, Jiang F. Changes of tuning but not dynamics of contrast adaptation with age. Vision Res 2021; 187:129-136. [PMID: 34252728 PMCID: PMC8363565 DOI: 10.1016/j.visres.2021.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/24/2021] [Accepted: 03/29/2021] [Indexed: 10/20/2022]
Abstract
Normal aging results in pronounced optical and neural changes in the visual system. Processes of adaptation are thought to help compensate for many of these changes in order to maintain perceptual constancy, but it is uncertain how stable adaptation itself remains with aging. We compared the dynamics of adaptation in young (aged 19-24 years) and older (aged 66-74) adults. Contrast thresholds for Gabor patterns were tracked during and after 300 s adaptation to vertical and horizontal Gabor patches. The time course of contrast adaptation and asymptotic adaptation magnitude were similar between older and young adults when normalized for their respective baseline thresholds. Older adults showed stronger transfer of adaptation to the orthogonal orientation and there was an asymmetry between the transfer of adaptation between the horizontal and vertical orientations for both groups. These results suggest age-related changes in orientation tuning while the processes of cortical contrast adaptation remain largely intact with aging.
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Affiliation(s)
- Yi Gao
- University of Nevada, Reno, United States.
| | | | - Fang Jiang
- University of Nevada, Reno, United States
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Marcos-Pérez D, Saenz-Antoñanzas A, Matheu A. Centenarians as models of healthy aging: Example of REST. Ageing Res Rev 2021; 70:101392. [PMID: 34139339 DOI: 10.1016/j.arr.2021.101392] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023]
Abstract
Centenarians are a group of individuals exhibiting extreme longevity, who are characterized by a remarkable compression of morbidity. Therefore, centenarians have been postulated as a model of healthy aging. Different approaches have been used to decipher the biology and genetics of centenarians in order to identify key anti-aging pathways. The majority of studies have taken advantage of blood samples to perform their analysis. Besides, a recent study in human brain samples deciphered the transcription factor REST (Repressor Element-1 Silencing Transcription Factor) as an important player of extreme longevity and cognitive activity. This study goes from human to animal models and revealed that REST acts as an epigenetic regulator of neuronal homeostasis, to control aging and longevity. The aim of this view point is to summarize recent literature describing genetic and epigenetic factors, as well as molecular pathways associated with centenarians and the biology of aging. We will pay particular attention to the impact of REST in centenarians and longevity.
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Affiliation(s)
- Diego Marcos-Pérez
- Biodonostia Health Research Institute, Group of Cellular Oncology, San Sebastián, Spain
| | | | - Ander Matheu
- Biodonostia Health Research Institute, Group of Cellular Oncology, San Sebastián, Spain; CIBER of Frailty and Healthy Aging (CIBERfes), Carlos III Institute, Madrid, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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Webb JL, Moe SM, Bolstad AK, McNeill EM. Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive. PLoS One 2021; 16:e0255085. [PMID: 34379632 PMCID: PMC8357136 DOI: 10.1371/journal.pone.0255085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 07/09/2021] [Indexed: 11/19/2022] Open
Abstract
Aging is universal, yet characterizing the molecular changes that occur in aging which lead to an increased risk for neurological disease remains a challenging problem. Aging affects the prefrontal cortex (PFC), which governs executive function, learning, and memory. Previous sequencing studies have demonstrated that aging alters gene expression in the PFC, however the extent to which these changes are conserved across species and are meaningful in neurodegeneration is unknown. Identifying conserved, age-related genetic and morphological changes in the brain allows application of the wealth of tools available to study underlying mechanisms in model organisms such as Drosophila melanogaster. RNA sequencing data from human PFC and fly heads were analyzed to determine conserved transcriptome signatures of age. Our analysis revealed that expression of 50 conserved genes can accurately determine age in Drosophila (R2 = 0.85) and humans (R2 = 0.46). These transcriptome signatures were also able to classify Drosophila into three age groups with a mean accuracy of 88% and classify human samples with a mean accuracy of 69%. Overall, this work identifies 50 highly conserved aging-associated genetic changes in the brain that can be further studied in model organisms and demonstrates a novel approach to uncovering genetic changes conserved across species from multi-study public databases.
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Affiliation(s)
- Joe L. Webb
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
| | - Simon M. Moe
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
| | - Andrew K. Bolstad
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States of America
| | - Elizabeth M. McNeill
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
- Neuroscience Interdepartmental Graduate program, Iowa State University, Ames, IA, United States of America
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Inotsuka R, Udono M, Yamatsu A, Kim M, Katakura Y. Exosome-Mediated Activation of Neuronal Cells Triggered by γ-Aminobutyric Acid (GABA). Nutrients 2021; 13:nu13082544. [PMID: 34444704 PMCID: PMC8399553 DOI: 10.3390/nu13082544] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/08/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
γ-Aminobutyric acid (GABA) is a potent bioactive amino acid, and several studies have shown that oral administration of GABA induces relaxation, improves sleep, and reduces psychological stress and fatigue. In a recent study, we reported that exosomes derived from GABA-treated intestinal cells serve as signal transducers that mediate brain–gut interactions. Therefore, the purpose of this study was to verify the functionality of GABA-derived exosomes and to examine the possibility of improving memory function following GABA administration. The results showed that exosomes derived from GABA-treated intestinal cells (Caco-2) activated neuronal cells (SH-SY5Y) by regulating genes related to neuronal cell functions. Furthermore, we found that exosomes derived from the serum of GABA-treated mice also activated SH-SY5Y cells, indicating that exosomes, which are capable of activating neuronal cells, circulate in the blood of mice orally administered GABA. Finally, we performed a microarray analysis of mRNA isolated from the hippocampus of mice that were orally administered GABA. The results revealed changes in the expression of genes related to brain function. Gene Set Enrichment Analysis (GSEA) showed that oral administration of GABA affected the expression of genes related to memory function in the hippocampus.
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Affiliation(s)
- Ryo Inotsuka
- Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan;
| | - Miyako Udono
- Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan;
| | - Atsushi Yamatsu
- International GABA Research Center, Kyoto 615-8245, Japan;
- Pharma Foods International Co., Ltd., Kyoto 615-8245, Japan;
| | - Mujo Kim
- Pharma Foods International Co., Ltd., Kyoto 615-8245, Japan;
| | - Yoshinori Katakura
- Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan;
- Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan;
- Correspondence:
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Abbasi DA, Nguyen TTA, Hall DA, Robertson-Dick E, Berry-Kravis E, Cologna SM. Characterization of the Cerebrospinal Fluid Proteome in Patients with Fragile X-Associated Tremor/Ataxia Syndrome. THE CEREBELLUM 2021; 21:86-98. [PMID: 34046842 DOI: 10.1007/s12311-021-01262-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/16/2021] [Indexed: 01/11/2023]
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS), first described in 2001, is a neurodegenerative and movement disorder, caused by a premutation in the fragile X mental retardation 1 (FMR1) gene. To date, the biological mechanisms causing this condition are still not well understood, as not all premutation carriers develop FXTAS. To further understand this syndrome, we quantitatively compared the cerebrospinal fluid (CSF) proteome of FXTAS patients with age-matched controls using mass spectrometry. We identified 415 proteins of which 97 were altered in FXTAS patients. These proteins suggest changes in acute phase response signaling, liver X receptor/ retinoid X receptor (LXR/RXR) activation, and farnesoid X receptor (FXR)/RXR activation, which are the main pathways found to be affected. Additionally, we detected changes in many other proteins including amyloid-like protein 2, contactin-1, afamin, cell adhesion molecule 4, NPC intracellular cholesterol transporter 2, and cathepsin B, that had been previously noted to hold important roles in other movement disorders. Specific to RXR pathways, several apolipoproteins (APOA1, APOA2, APOA4, APOC2, and APOD) showed significant changes in the CSF of FXTAS patients. Lastly, CSF parameters were analyzed to investigate abnormalities in blood brain barrier function. Correlations were observed between patient albumin quotient values, a measure of permeability, and CGG repeat length as well as FXTAS rating scale scores.
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Affiliation(s)
- Diana A Abbasi
- Department of Pediatrics and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Thu T A Nguyen
- Department of Chemistry, University of Illinois At Chicago, Chicago, IL, USA
| | - Deborah A Hall
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Erin Robertson-Dick
- Department of Communication Sciences and Disorders, Northwestern University, Chicago, IL, USA
| | - Elizabeth Berry-Kravis
- Department of Pediatrics and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois At Chicago, Chicago, IL, USA.
- Laboratory of Integrated Neuroscience, University of Illinois At Chicago, 845 W Taylor Street, Room 4500, Chicago, IL, 60607, USA.
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Su H, Liu D, Shao J, Li Y, Wang X, Gao Q. Aging Liver: Can Exercise be a Better Way to Delay the Process than Nutritional and Pharmacological Intervention? Focus on Lipid Metabolism. Curr Pharm Des 2021; 26:4982-4991. [PMID: 32503400 DOI: 10.2174/1381612826666200605111232] [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: 03/05/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Nowadays, the world is facing a common problem that the population aging process is accelerating. How to delay metabolic disorders in middle-aged and elderly people, has become a hot scientific and social issue worthy of attention. The liver plays an important role in lipid metabolism, and abnormal lipid metabolism may lead to liver diseases. Exercise is an easily controlled and implemented intervention, which has attracted extensive attention in improving the health of liver lipid metabolism in the elderly. This article reviewed the body aging process, changes of lipid metabolism in the aging liver, and the mechanism and effects of different interventions on lipid metabolism in the aging liver, especially focusing on exercise intervention. METHODS A literature search was performed using PubMed-NCBI, EBSCO Host and Web of Science, and also a report from WHO. In total, 143 studies were included from 1986 to 15 February 2020. CONCLUSION Nutritional and pharmacological interventions can improve liver disorders, and nutritional interventions are less risky relatively. Exercise intervention can prevent and improve age-related liver disease, especially the best high-intensity interval training intensity and duration is expected to be one of the research directions in the future.
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Affiliation(s)
- Hao Su
- The School of Sport Science, Beijing Sport University, Beijing, China
| | - Dongsen Liu
- The School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Jia Shao
- The Graduate School, Beijing Sport University, Beijing, China
| | - Yinuo Li
- The Graduate School, Beijing Sport University, Beijing, China
| | - Xiaoxia Wang
- The School of Physical Education and Art Education, Beijing Technology and Business University, Beijing, China
| | - Qi Gao
- The School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
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42
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Xia L, Chen H, Dong J, Luo S, Feng L. Decline of Orientation and Direction Sensitivity in the Aging Population. Front Neurosci 2021; 15:643414. [PMID: 33897356 PMCID: PMC8064032 DOI: 10.3389/fnins.2021.643414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/02/2021] [Indexed: 11/24/2022] Open
Abstract
While the aging population is growing, our knowledge regarding age-related deterioration of visual perception remains limited. In the present study, we investigated the effects of aging on orientation and direction sensitivity in a healthy population using a weighted up–down adaptive method to improve the efficiency and reliability of the task. A total of 57 healthy participants aged 22–72 years were included and divided into old and young groups. Raw experimental data were processed using a psychometric method to determine the differences between the two groups. In the orientation task, the threshold of the discrimination angle and bias (i.e., the difference between the perceived midpoint from the logistic function and the reference point) was increased, while the lapsing rate (i.e., 1—the maximum logistic function) did not significantly change in the old group compared with the young group. In the motion direction task, the threshold, bias, and lapsing rate were significantly increased in the old group compared with the young group. These results suggest that the decreased ability of old participants in discrimination of stimulus orientation and motion direction could be related to the impaired function of visual cortex.
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Affiliation(s)
- Lin Xia
- Department of Ophthalmology, First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Branch of National Clinical Research Center for Ocular Diseases, Hefei, China
| | - He Chen
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jiong Dong
- Department of Ophthalmology, First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Branch of National Clinical Research Center for Ocular Diseases, Hefei, China
| | - Sha Luo
- Department of Ophthalmology, First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Branch of National Clinical Research Center for Ocular Diseases, Hefei, China
| | - Lixia Feng
- Department of Ophthalmology, First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Branch of National Clinical Research Center for Ocular Diseases, Hefei, China
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Koch SC, Nelson A, Hartenstein V. Structural aspects of the aging invertebrate brain. Cell Tissue Res 2021; 383:931-947. [PMID: 33409654 PMCID: PMC7965346 DOI: 10.1007/s00441-020-03314-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/28/2020] [Indexed: 11/26/2022]
Abstract
Aging is characterized by a decline in neuronal function in all animal species investigated so far. Functional changes are accompanied by and may be in part caused by, structurally visible degenerative changes in neurons. In the mammalian brain, normal aging shows abnormalities in dendrites and axons, as well as ultrastructural changes in synapses, rather than global neuron loss. The analysis of the structural features of aging neurons, as well as their causal link to molecular mechanisms on the one hand, and the functional decline on the other hand is crucial in order to understand the aging process in the brain. Invertebrate model organisms like Drosophila and C. elegans offer the opportunity to apply a forward genetic approach to the analysis of aging. In the present review, we aim to summarize findings concerning abnormalities in morphology and ultrastructure in invertebrate brains during normal aging and compare them to what is known for the mammalian brain. It becomes clear that despite of their considerably shorter life span, invertebrates display several age-related changes very similar to the mammalian condition, including the retraction of dendritic and axonal branches at specific locations, changes in synaptic density and increased accumulation of presynaptic protein complexes. We anticipate that continued research efforts in invertebrate systems will significantly contribute to reveal (and possibly manipulate) the molecular/cellular pathways leading to neuronal aging in the mammalian brain.
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Affiliation(s)
- Sandra C Koch
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Annie Nelson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA.
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Bahadur Patel A, Veeraiah P, Shameem M, Mahesh Kumar J, Saba K. Impaired GABAergic and glutamatergic neurometabolic activity in aged mice brain as measured by 1 H-[ 13 C]-NMR spectroscopy. FASEB J 2021; 35:e21321. [PMID: 33543543 DOI: 10.1096/fj.202001704rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023]
Abstract
Healthy aging is associated with a decline in cognitive function, and is a major risk factor for many neurodegenerative diseases. Although, there are several evidence that brain mitochondrial function is altered with aging its significance at the cellular level is elusive. In this study, we have investigated mitochondrial TCA cycle and neurotransmitter cycle fluxes associated with glutamatergic, GABAergic neurons and astroglia in the cerebral cortex and hippocampus of young (6 months) and aged (24 months) C57BL6 mice by using 1 H-[13 C]-NMR spectroscopy together with timed infusion of 13 C-labeled glucose and acetate. The ratio VCyc /VTCA was determined from a steady-state [2-13 C]acetate experiment. Metabolic fluxes were obtained by fitting a three-compartment metabolic model to 13 C turnover of amino acids from glucose. Levels of glutamate, aspartate and taurine were reduced in the cerebral cortex, while glutamine and choline were elevated in the hippocampus of aged mice. Interestingly, the rate of acetate oxidation increased in the cerebral cortex, while the flux of mitochondrial TCA cycle of glutamatergic neurons decreased in the cerebral cortex (P < .0001) and hippocampus (P = .025) of aged mice. The glutamate-glutamine neurotransmitter cycle flux was reduced in the cerebral cortex (P < .0001). The GABAergic TCA cycle flux was reduced in the cerebral cortex (P = .0008), while GABA-glutamine neurotransmitter cycling flux was also reduced in the cerebral cortex (P = .011) and hippocampus (P = .042) of aged brain. In conclusion, the reduction in excitatory and inhibitory neurotransmitter activity of glutamatergic and GABAergic neurons in the cerebral cortex and hippocampus correlates qualitatively with declined cognitive function in aged mice.
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Affiliation(s)
- Anant Bahadur Patel
- NMR Microimaging and Spectroscopy, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pandichelvam Veeraiah
- NMR Microimaging and Spectroscopy, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Mohammad Shameem
- NMR Microimaging and Spectroscopy, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Jerald Mahesh Kumar
- NMR Microimaging and Spectroscopy, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Kamal Saba
- NMR Microimaging and Spectroscopy, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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45
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Pembroke WG, Hartl CL, Geschwind DH. Evolutionary conservation and divergence of the human brain transcriptome. Genome Biol 2021; 22:52. [PMID: 33514394 PMCID: PMC7844938 DOI: 10.1186/s13059-020-02257-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022] Open
Abstract
Background Mouse models have allowed for the direct interrogation of genetic effects on molecular, physiological, and behavioral brain phenotypes. However, it is unknown to what extent neurological or psychiatric traits may be human- or primate-specific and therefore which components can be faithfully recapitulated in mouse models. Results We compare conservation of co-expression in 116 independent data sets derived from human, mouse, and non-human primate representing more than 15,000 total samples. We observe greater changes occurring on the human lineage than mouse, and substantial regional variation that highlights cerebral cortex as the most diverged region. Glia, notably microglia, astrocytes, and oligodendrocytes are the most divergent cell type, three times more on average than neurons. We show that cis-regulatory sequence divergence explains a significant fraction of co-expression divergence. Moreover, protein coding sequence constraint parallels co-expression conservation, such that genes with loss of function intolerance are enriched in neuronal, rather than glial modules. We identify dozens of human neuropsychiatric and neurodegenerative disease risk genes, such as COMT, PSEN-1, LRRK2, SHANK3, and SNCA, with highly divergent co-expression between mouse and human and show that 3D human brain organoids recapitulate in vivo co-expression modules representing several human cell types. Conclusions We identify robust co-expression modules reflecting whole-brain and regional patterns of gene expression. Compared with those that represent basic metabolic processes, cell-type-specific modules, most prominently glial modules, are the most divergent between species. These data and analyses serve as a foundational resource to guide human disease modeling and its interpretation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-020-02257-z.
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Affiliation(s)
- William G Pembroke
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Christopher L Hartl
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA. .,Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA. .,Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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Frazier HN, Ghoweri AO, Sudkamp E, Johnson ES, Anderson KL, Fox G, Vatthanaphone K, Xia M, Lin RL, Hargis-Staggs KE, Porter NM, Pauly JR, Blalock EM, Thibault O. Long-Term Intranasal Insulin Aspart: A Profile of Gene Expression, Memory, and Insulin Receptors in Aged F344 Rats. J Gerontol A Biol Sci Med Sci 2021; 75:1021-1030. [PMID: 31180116 DOI: 10.1093/gerona/glz105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Indexed: 02/06/2023] Open
Abstract
Intranasal insulin is a safe and effective method for ameliorating memory deficits associated with pathological brain aging. However, the impact of different formulations and the duration of treatment on insulin's efficacy and the cellular processes targeted by the treatment remain unclear. Here, we tested whether intranasal insulin aspart, a short-acting insulin formulation, could alleviate memory decline associated with aging and whether long-term treatment affected regulation of insulin receptors and other potential targets. Outcome variables included measures of spatial learning and memory, autoradiography and immunohistochemistry of the insulin receptor, and hippocampal microarray analyses. Aged Fischer 344 rats receiving long-term (3 months) intranasal insulin did not show significant memory enhancement on the Morris water maze task. Autoradiography results showed that long-term treatment reduced insulin binding in the thalamus but not the hippocampus. Results from hippocampal immunofluorescence revealed age-related decreases in insulin immunoreactivity that were partially offset by intranasal administration. Microarray analyses highlighted numerous insulin-sensitive genes, suggesting insulin aspart was able to enter the brain and alter hippocampal RNA expression patterns including those associated with tumor suppression. Our work provides insights into potential mechanisms of intranasal insulin and insulin resistance, and highlights the importance of treatment duration and the brain regions targeted.
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Affiliation(s)
| | | | - Emily Sudkamp
- The College of Pharmacy, University of Kentucky, Lexington, Kentucky
| | | | | | - Grant Fox
- Department of Pharmacology and Nutritional Sciences
| | | | - Mengfan Xia
- Department of Pharmacology and Nutritional Sciences
| | | | | | | | - James R Pauly
- The College of Pharmacy, University of Kentucky, Lexington, Kentucky
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The aging mouse brain: cognition, connectivity and calcium. Cell Calcium 2021; 94:102358. [PMID: 33517250 DOI: 10.1016/j.ceca.2021.102358] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/16/2021] [Accepted: 01/18/2021] [Indexed: 02/08/2023]
Abstract
Aging is a complex process that differentially impacts multiple cognitive, sensory, neuronal and molecular processes. Technological innovations now allow for parallel investigation of neuronal circuit function, structure and molecular composition in the brain of awake behaving adult mice. Thus, mice have become a critical tool to better understand how aging impacts the brain. However, a more granular systems-based approach, which considers the impact of age on key features relating to neural processing, is required. Here, we review evidence probing the impact of age on the mouse brain. We focus on a range of processes relating to neuronal function, including cognitive abilities, sensory systems, synaptic plasticity and calcium regulation. Across many systems, we find evidence for prominent age-related dysregulation even before 12 months of age, suggesting that emerging age-related alterations can manifest by late adulthood. However, we also find reports suggesting that some processes are remarkably resilient to aging. The evidence suggests that aging does not drive a parallel, linear dysregulation of all systems, but instead impacts some processes earlier, and more severely, than others. We propose that capturing the more fine-scale emerging features of age-related vulnerability and resilience may provide better opportunities for the rejuvenation of the aged brain.
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Altered GABA-mediated information processing and cognitive dysfunctions in depression and other brain disorders. Mol Psychiatry 2021; 26:151-167. [PMID: 32346158 DOI: 10.1038/s41380-020-0727-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/13/2020] [Accepted: 04/01/2020] [Indexed: 12/18/2022]
Abstract
Cognitive dysfunctions, including impaired attention, learning, memory, planning and problem solving, occur in depressive episodes, often persist during remission, predict relapse, worsen with recurrent episodes, and are not treated by current antidepressants or other medications. Cognitive symptoms are also present in other psychiatric disorders, are a hallmark of aging, and define several late-life disorders, including Alzheimer's disease. This pervasive occurrence suggests either a non-specific outcome of a diseased brain, or a shared underlying pathology contributing to this symptom dimension. Recent findings suggest a role for altered GABAergic inhibition in cognitive symptoms. Cellular, molecular and biochemical studies in human subjects report changes affecting the gamma-amino butyric acid (GABA) system, specifically somatostatin-expressing (SST+) GABAergic interneurons, across brain disorders and during aging. SST+ neurons gate excitatory input onto pyramidal neurons within cortical microcircuits. Experimentally reducing the function of these neurons affects excitatory signal-to-noise ratio, reduces synchronized cellular and neural activity, and leads to cognitive dysfunctions. Conversely, augmenting SST+ cell post-synaptic α5-GABA-A receptor activity has pro-cognitive efficacy in stress and aging models. Together, this suggests that reduced signaling of the SST+ neuron/α5-GABA-A receptor pathway contributes to cognitive dysfunctions, and that it represents a novel therapeutic target for remediating mood and cognitive symptoms in depression, other psychiatric disorders and during aging.
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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: 21] [Impact Index Per Article: 5.3] [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.
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Advances in transcriptome analysis of human brain aging. Exp Mol Med 2020; 52:1787-1797. [PMID: 33244150 PMCID: PMC8080664 DOI: 10.1038/s12276-020-00522-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Aging is associated with gradual deterioration of physiological and biochemical functions, including cognitive decline. Transcriptome profiling of brain samples from individuals of varying ages has identified the whole-transcriptome changes that underlie age-associated cognitive declines. In this review, we discuss transcriptome-based research on human brain aging performed by using microarray and RNA sequencing analyses. Overall, decreased synaptic function and increased immune function are prevalent in most regions of the aged brain. Age-associated gene expression changes are also cell dependent and region dependent and are affected by genotype. In addition, the transcriptome changes that occur during brain aging include different splicing events, intersample heterogeneity, and altered levels of various types of noncoding RNAs. Establishing transcriptome-based hallmarks of human brain aging will improve the understanding of cognitive aging and neurodegenerative diseases and eventually lead to interventions that delay or prevent brain aging.
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