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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; 27:2021-2032. [PMID: 39227716 PMCID: PMC11452345 DOI: 10.1038/s41593-024-01742-z] [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: 07/13/2023] [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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Chen XM, Wang ZW, Liang XG, Li FY, Li BB, Wu G, Yi F, Setter TL, Shen S, Zhou SL. Incomplete filling in the basal region of maize endosperm: timing of development of starch synthesis and cell vitality. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39348485 DOI: 10.1111/tpj.17043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/28/2024] [Accepted: 09/04/2024] [Indexed: 10/02/2024]
Abstract
Starch synthesis in maize endosperm adheres to the basipetal sequence from the apex downwards. However, the mechanism underlying nonuniformity among regions of the endosperm in starch accumulation and its significance is poorly understood. Here, we examined the spatiotemporal transcriptomes and starch accumulation dynamics in apical (AE), middle (ME), and basal (BE) regions of endosperm throughout the filling stage. Results demonstrated that the BE had lower levels of gene transcripts and enzymes facilitating starch synthesis, corresponding to incomplete starch storage at maturity, compared with AE and ME. Contrarily, the BE showed abundant gene expression for genetic processing and slow progress in physiological development (quantified by an index calculated from the expression values of development progress marker genes), revealing a sustained cell vitality of the BE. Further analysis demonstrated a significant parabolic correlation between starch synthesis and physiological development. An in-depth examination showed that the BE had more active signaling pathways of IAA and ABA than the AE throughout the filling stage, while ethylene showed the opposite pattern. Besides, SNF1-related protein kinase1 (SnRK1) activity, a regulator for starch synthesis modulated by trehalose-6-phosphate (T6P) signaling, was kept at a lower level in the BE than the AE and ME, corresponding to the distinct gene expression in the T6P pathway in starch synthesis regulation. Collectively, the findings support an improved understanding of the timing of starch synthesis and cell vitality in regions of the endosperm during development, and potential regulation from hormone signaling and T6P/SnRK1 signaling.
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Affiliation(s)
- Xian-Min Chen
- State Key Laboratory of Maize Bio-breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhi-Wei Wang
- State Key Laboratory of Maize Bio-breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiao-Gui Liang
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Agronomy College, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Feng-Yuan Li
- State Key Laboratory of Maize Bio-breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Bin-Bin Li
- State Key Laboratory of Maize Bio-breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Gong Wu
- Agronomy College, Anhui Agricultural University, Hefei, 230036, China
| | - Fei Yi
- State Key Laboratory of Maize Bio-breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Tim L Setter
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
| | - Si Shen
- State Key Laboratory of Maize Bio-breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Innovation Center of Agricultural Technology for Lowland Plain of Hebei, Wuqiao, 061802, China
| | - Shun-Li Zhou
- State Key Laboratory of Maize Bio-breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Innovation Center of Agricultural Technology for Lowland Plain of Hebei, Wuqiao, 061802, China
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3
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Simmonite M, Khammash D, Michon KJ, Hamlin A, Taylor SF, Vesia M, Polk TA. Age and visual cortex inhibition: a TMS-MRS study. Cereb Cortex 2024; 34:bhae352. [PMID: 39227309 DOI: 10.1093/cercor/bhae352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 08/06/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024] Open
Abstract
Paired-pulse transcranial magnetic stimulation is a valuable tool for investigating inhibitory mechanisms in motor cortex. We recently demonstrated its use in measuring cortical inhibition in visual cortex, using an approach in which participants trace the size of phosphenes elicited by stimulation to occipital cortex. Here, we investigate age-related differences in primary visual cortical inhibition and the relationship between primary visual cortical inhibition and local GABA+ in the same region, estimated using magnetic resonance spectroscopy. GABA+ was estimated in 28 young (18 to 28 years) and 47 older adults (65 to 84 years); a subset (19 young, 18 older) also completed a paired-pulse transcranial magnetic stimulation session, which assessed visual cortical inhibition. The paired-pulse transcranial magnetic stimulation measure of inhibition was significantly lower in older adults. Uncorrected GABA+ in primary visual cortex was also significantly lower in older adults, while measures of GABA+ that were corrected for the tissue composition of the magnetic resonance spectroscopy voxel were unchanged with age. Furthermore, paired-pulse transcranial magnetic stimulation-measured inhibition and magnetic resonance spectroscopy-measured tissue-corrected GABA+ were significantly positively correlated. These findings are consistent with an age-related decline in cortical inhibition in visual cortex and suggest paired-pulse transcranial magnetic stimulation effects in visual cortex are driven by GABAergic mechanisms, as has been demonstrated in motor cortex.
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Affiliation(s)
- Molly Simmonite
- Department of Psychiatry, University of Michigan, 4250 Plymouth Road, Ann Arbor, MI 48109, United States
- Department of Psychology, University of Michigan, 530 Church Street, Ann Arbor, MI 48109, United States
| | - Dalia Khammash
- Department of Psychology, University of Michigan, 530 Church Street, Ann Arbor, MI 48109, United States
| | - Katherine J Michon
- Department of Psychology, University of Michigan, 530 Church Street, Ann Arbor, MI 48109, United States
| | - Abbey Hamlin
- Department of Psychology, University of Michigan, 530 Church Street, Ann Arbor, MI 48109, United States
| | - Stephan F Taylor
- Department of Psychiatry, University of Michigan, 4250 Plymouth Road, Ann Arbor, MI 48109, United States
| | - Michael Vesia
- School of Kinesiology, University of Michigan, 830 North University, Ann Arbor, MI 48109, United States
| | - Thad A Polk
- Department of Psychology, University of Michigan, 530 Church Street, Ann Arbor, MI 48109, United States
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Duffy MF, Ding J, Langston RG, Shah SI, Nalls MA, Scholz SW, Whitaker DT, Auluck PK, Marenco S, Gibbs JR, Cookson MR. Divergent patterns of healthy aging across human brain regions at single-cell resolution reveal links to neurodegenerative disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551097. [PMID: 37577533 PMCID: PMC10418086 DOI: 10.1101/2023.07.31.551097] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Age is a major common risk factor underlying neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Previous studies reported that chronological age correlates with differential gene expression across different brain regions. However, prior datasets have not disambiguated whether expression associations with age are due to changes in cell numbers and/or gene expression per cell. In this study, we leveraged single nucleus RNA-sequencing (snRNAseq) to examine changes in cell proportions and transcriptomes in four different brain regions, each from 12 donors aged 20-30 years (young) or 60-85 years (old). We sampled 155,192 nuclei from two cortical regions (entorhinal cortex and middle temporal gyrus) and two subcortical regions (putamen and subventricular zone) relevant to neurodegenerative diseases or the proliferative niche. We found no changes in cellular composition of different brain regions with healthy aging. Surprisingly, we did find that each brain region has a distinct aging signature, with only minor overlap in differentially associated genes across regions. Moreover, each cell type shows distinct age-associated expression changes, including loss of protein synthesis genes in cortical inhibitory neurons, axonogenesis genes in excitatory neurons and oligodendrocyte precursor cells, enhanced gliosis markers in astrocytes and disease-associated markers in microglia, and genes critical for neuron-glia communication. Importantly, we find cell type-specific enrichments of age associations with genes nominated by Alzheimer's disease and Parkinson's disease genome-wide association studies (GWAS), such as apolipoprotein E (APOE), and leucine-rich repeat kinase 2 (LRRK2) in microglia that are independent of overall expression levels across cell types. We present this data as a new resource which highlights, first, region- and cell type-specific transcriptomic changes in healthy aging that may contribute to selective vulnerability and, second, provide context for testing GWAS-nominated disease risk genes in relevant subtypes and developing more targeted therapeutic strategies. The data is readily accessible without requirement for extensive computational support in a public website, https://brainexp-hykyffa56a-uc.a.run.app/.
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Affiliation(s)
- Megan F. Duffy
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Rebekah G. Langston
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Syed I. Shah
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Mike A. Nalls
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - D. Thad Whitaker
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Pavan K. Auluck
- Human Brain Collection Core, Division of Intramural Research, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Stefano Marenco
- Human Brain Collection Core, Division of Intramural Research, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Mark R. Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 20892
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5
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Ardesch DJ, Libedinsky I, Scholtens LH, Wei Y, van den Heuvel MP. Convergence of brain transcriptomic and neuroimaging patterns in schizophrenia, bipolar disorder, autism spectrum disorder and major depression disorder. BIOLOGICAL PSYCHIATRY: COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2023. [DOI: 10.1016/j.bpsc.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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6
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Almeida D, Turecki G. Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection. Methods 2022; 207:3-10. [PMID: 36064002 DOI: 10.1016/j.ymeth.2022.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptome of a cell constitutes an essential piece of cellular identity and contributes to the multifaceted complexity and heterogeneity of cell-types within the mammalian brain. Thus, while a wealth of studies have investigated transcriptomic alterations underlying the pathophysiology of diseases of the brain, their use of bulk-tissue homogenates makes it difficult to tease apart whether observed differences are explained by disease state or cellular composition. Cell-type-specific enrichment strategies are, therefore, crucial in the context of gene expression profiling. Laser capture microdissection (LCM) is one such strategy that allows for the capture of specific cell-types, or regions of interest, under microscopic visualization. In this review, we focus on using LCM for cell-type specific gene expression profiling in post-mortem human brain samples. We begin with a discussion of various LCM systems, followed by a walk-through of each step in the LCM to gene expression profiling workflow and a description of some of the limitations associated with LCM. Throughout the review, we highlight important considerations when using LCM with post-mortem human brain samples. Whenever applicable, commercially available kits that have proven successful in the context of LCM with post-mortem human brain samples are described.
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Affiliation(s)
- Daniel Almeida
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3; Department of Psychiatry, McGill University, Montreal, QC, Canada, H3A 1A1.
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7
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Ochi R, Ueno F, Sakuma M, Tani H, Tsugawa S, Graff-Guerrero A, Uchida H, Mimura M, Oshima S, Matsushita S, Nakajima S. Patterns of functional connectivity alterations induced by alcohol reflect somatostatin interneuron expression in the human cerebral cortex. Sci Rep 2022; 12:7896. [PMID: 35550587 PMCID: PMC9098480 DOI: 10.1038/s41598-022-12035-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Acute alcohol administration affects functional connectivity, yet the underlying mechanism is unknown. Previous work suggested that a moderate dose of alcohol reduces the activity of gamma-aminobutyric acidergic (GABAergic) interneurons, thereby leading to a state of pyramidal disinhibition and hyperexcitability. The present study aims to relate alcohol-induced changes in functional connectivity to regional genetic markers of GABAergic interneurons. Healthy young adults (N = 15, 5 males) underwent resting state functional MRI scanning prior to alcohol administration, immediately and 90 min after alcohol administration. Functional connectivity density mapping was performed to quantify alcohol-induced changes in resting brain activity between conditions. Patterns of differences between conditions were related to regional genetic markers that express the primary GABAergic cortical interneuron subtypes (parvalbumin, somatostatin, and 5-hydroxytryptamine receptor 3A) obtained from the Allen Human Brain Atlas. Acute alcohol administration increased local functional connectivity density within the visual cortex, sensorimotor cortex, thalamus, striatum, and cerebellum. Patterns of alcohol-induced changes in local functional connectivity density inversely correlated with somatostatin cortical gene expression. These findings suggest that somatostatin-expressing interneurons modulate alcohol-induced changes in functional connectivity in healthy individuals.
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Affiliation(s)
- Ryo Ochi
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Fumihiko Ueno
- Multimodal Imaging Group, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Mutsuki Sakuma
- National Hospital Organization Kurihama Medical and Addiction Center, Kanagawa, Japan
| | - Hideaki Tani
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Sakiko Tsugawa
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Ariel Graff-Guerrero
- Multimodal Imaging Group, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Hiroyuki Uchida
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Masaru Mimura
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Shunji Oshima
- Sustainable Technology Laboratories, Asahi Quality and Innovations, Ltd., Ibaraki, Japan
| | - Sachio Matsushita
- National Hospital Organization Kurihama Medical and Addiction Center, Kanagawa, Japan
| | - Shinichiro Nakajima
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
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8
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Verkerke M, Hol EM, Middeldorp J. Physiological and Pathological Ageing of Astrocytes in the Human Brain. Neurochem Res 2021; 46:2662-2675. [PMID: 33559106 PMCID: PMC8437874 DOI: 10.1007/s11064-021-03256-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022]
Abstract
Ageing is the greatest risk factor for dementia, although physiological ageing by itself does not lead to cognitive decline. In addition to ageing, APOE ε4 is genetically the strongest risk factor for Alzheimer's disease and is highly expressed in astrocytes. There are indications that human astrocytes change with age and upon expression of APOE4. As these glial cells maintain water and ion homeostasis in the brain and regulate neuronal transmission, it is likely that age- and APOE4-related changes in astrocytes have a major impact on brain functioning and play a role in age-related diseases. In this review, we will discuss the molecular and morphological changes of human astrocytes in ageing and the contribution of APOE4. We conclude this review with a discussion on technical issues, innovations, and future perspectives on how to gain more knowledge on astrocytes in the human ageing brain.
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Affiliation(s)
- Marloes Verkerke
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Elly M Hol
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands.
| | - Jinte Middeldorp
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
- Department of Immunobiology, Biomedical Primate Research Centre (BPRC), P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands
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9
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Micheli L, Creanza TM, Ceccarelli M, D'Andrea G, Giacovazzo G, Ancona N, Coccurello R, Scardigli R, Tirone F. Transcriptome Analysis in a Mouse Model of Premature Aging of Dentate Gyrus: Rescue of Alpha-Synuclein Deficit by Virus-Driven Expression or by Running Restores the Defective Neurogenesis. Front Cell Dev Biol 2021; 9:696684. [PMID: 34485283 PMCID: PMC8415876 DOI: 10.3389/fcell.2021.696684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/21/2021] [Indexed: 02/05/2023] Open
Abstract
The dentate gyrus of the hippocampus and the subventricular zone are neurogenic niches where neural stem and progenitor cells replicate throughout life to generate new neurons. The Btg1 gene maintains the stem cells of the neurogenic niches in quiescence. The deletion of Btg1 leads to an early transient increase of stem/progenitor cells division, followed, however, by a decrease during adulthood of their proliferative capability, accompanied by apoptosis. Since a physiological decrease of neurogenesis occurs during aging, the Btg1 knockout mouse may represent a model of neural aging. We have previously observed that the defective neurogenesis of the Btg1 knockout model is rescued by the powerful neurogenic stimulus of physical exercise (running). To identify genes responsible for stem and progenitor cells maintenance, we sought here to find genes underlying this premature neural aging, and whose deregulated expression could be rescued by running. Through RNA sequencing we analyzed the transcriptomic profiles of the dentate gyrus isolated from Btg1 wild-type or Btg1 knockout adult (2-month-old) mice submitted to physical exercise or sedentary. In Btg1 knockout mice, 545 genes were deregulated, relative to wild-type, while 2081 genes were deregulated by running. We identified 42 genes whose expression was not only down-regulated in the dentate gyrus of Btg1 knockout, but was also counter-regulated to control levels by running in Btg1 knockout mice, vs. sedentary. Among these 42 counter-regulated genes, alpha-synuclein (Snca), Fos, Arc and Npas4 showed significantly greater differential regulation. These genes control neural proliferation, apoptosis, plasticity and memory and are involved in aging. In particular, Snca expression decreases during aging. We tested, therefore, whether an Snca-expressing lentivirus, by rescuing the defective Snca levels in the dentate gyrus of Btg1 knockout mice, could also reverse the aging phenotype, in particular the defective neurogenesis. We found that the exogenous expression of Snca reversed the Btg1 knockout-dependent decrease of stem cell proliferation as well as the increase of progenitor cell apoptosis. This indicates that Snca has a functional role in the process of neural aging observed in this model, and also suggests that Snca acts as a positive regulator of stem cell maintenance.
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Affiliation(s)
- Laura Micheli
- Institute of Biochemistry and Cell Biology, National Research Council, Rome, Italy
| | - Teresa Maria Creanza
- Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, National Research Council, Bari, Italy
| | - Manuela Ceccarelli
- Institute of Biochemistry and Cell Biology, National Research Council, Rome, Italy
| | - Giorgio D'Andrea
- Institute of Biochemistry and Cell Biology, National Research Council, Rome, Italy
| | - Giacomo Giacovazzo
- Preclinical Neuroscience, European Center for Brain Research (CERC)/IRCCS Santa Lucia Foundation, Rome, Italy
| | - Nicola Ancona
- Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, National Research Council, Bari, Italy
| | - Roberto Coccurello
- Preclinical Neuroscience, European Center for Brain Research (CERC)/IRCCS Santa Lucia Foundation, Rome, Italy.,Institute for Complex Systems, National Research Council, Rome, Italy
| | - Raffaella Scardigli
- Institute of Translational Pharmacology, National Research Council, Rome, Italy
| | - Felice Tirone
- Institute of Biochemistry and Cell Biology, National Research Council, Rome, Italy
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10
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Sanfilippo C, Musumeci G, Kazakova M, Mazzone V, Castrogiovanni P, Imbesi R, Di Rosa M. GNG13 Is a Potential Marker of the State of Health of Alzheimer's Disease Patients' Cerebellum. J Mol Neurosci 2020; 71:1046-1060. [PMID: 33057964 DOI: 10.1007/s12031-020-01726-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Brain regions such as the cerebellum (CB) have been neglected for a long time in the study of Alzheimer's disease (AD) pathogenesis. In reference to a new emerging hypothesis according to which there is an altered cerebellar synaptic processing in AD, we verified the possible role played by new biomarkers in the CB of AD patients compared with not-demented healthy control subjects (NDHS). Using a bioinformatics approach, we have collected several microarray datasets and obtained 626 cerebella sample biopsies belonging to subjects who did not die from causes related to neurological diseases and 199 cerebella belonging to AD. The analysis of logical relations between the transcriptome dataset highlighted guanine nucleotide-binding protein (G protein) gamma 13 (GNG13) as a potential new biomarker for Purkinje cells (PCs). We have correlated GNG13 expression levels with already widely existing bibliography of PC marker genes, such as Purkinje cell protein 2 (PCP2), Purkinje cell protein 4 (PCP4), and cerebellin 3 (CBLN3). We showed that expression levels of GNG13 and PCP2, PCP4, and CBLN3 were significantly correlated with each other in NDHS and in AD and significantly reduced in AD patients compared with NDHS subjects. In addition, we highlighted a negative correlation between the expression levels of PC biomarkers and age. From the outcome of our investigation, it is possible to conclude that the identification of GNG13 as a potentially biomarker in PCs represents also a state of health of CB, in association with the expression of PCP2, PCP4, and CBLN3.
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Affiliation(s)
- Cristina Sanfilippo
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124, Messina, Italy
| | - Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Maria Kazakova
- Department of Medical Biology, Medical Faculty, Medical University, Plovdiv, Bulgaria
| | - Venera Mazzone
- Department G.F. Ingrassia, Anatomy, School of Medicine, University of Catania, Catania, Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy.
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11
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Morabito S, Miyoshi E, Michael N, Swarup V. Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer's disease. Hum Mol Genet 2020; 29:2899-2919. [PMID: 32803238 PMCID: PMC7566321 DOI: 10.1093/hmg/ddaa182] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/10/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
Alzheimer's disease (AD) is a devastating neurological disorder characterized by changes in cell-type proportions and consequently marked alterations of the transcriptome. Here we use a data-driven systems biology meta-analytical approach across three human AD cohorts, encompassing six cortical brain regions, and integrate with multi-scale datasets comprising of DNA methylation, histone acetylation, transcriptome- and genome-wide association studies and quantitative trait loci to further characterize the genetic architecture of AD. We perform co-expression network analysis across more than 1200 human brain samples, identifying robust AD-associated dysregulation of the transcriptome, unaltered in normal human aging. We assess the cell-type specificity of AD gene co-expression changes and estimate cell-type proportion changes in human AD by integrating co-expression modules with single-cell transcriptome data generated from 27 321 nuclei from human postmortem prefrontal cortical tissue. We also show that genetic variants of AD are enriched in a microglial AD-associated module and identify key transcription factors regulating co-expressed modules. Additionally, we validate our results in multiple published human AD gene expression datasets, which can be easily accessed using our online resource (https://swaruplab.bio.uci.edu/consensusAD).
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Affiliation(s)
- Samuel Morabito
- Mathematical, Computational and Systems Biology (MCSB) Program, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA 92697, USA
| | - Emily Miyoshi
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA 92697, USA
| | - Neethu Michael
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA 92697, USA
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12
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Kron NS, Schmale MC, Fieber LA. Changes in Metabolism and Proteostasis Drive Aging Phenotype in Aplysia californica Sensory Neurons. Front Aging Neurosci 2020; 12:573764. [PMID: 33101008 PMCID: PMC7522570 DOI: 10.3389/fnagi.2020.573764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022] Open
Abstract
Aging is associated with cognitive declines that originate in impairments of function in the neurons that make up the nervous system. The marine mollusk Aplysia californica (Aplysia) is a premier model for the nervous system uniquely suited to investigation of neuronal aging due to uniquely identifiable neurons and molecular techniques available in this model. This study describes the molecular processes associated with aging in two populations of sensory neurons in Aplysia by applying RNA sequencing technology across the aging process (age 6-12 months). Differentially expressed genes clustered into four to five coherent expression patterns across the aging time series in the two neuron populations. Enrichment analysis of functional annotations in these neuron clusters revealed decreased expression of pathways involved in energy metabolism and neuronal signaling, suggesting that metabolic and signaling pathways are intertwined. Furthermore, increased expression of pathways involved in protein processing and translation suggests that proteostatic stress also occurs in aging. Temporal overlap of enrichment for energy metabolism, proteostasis, and neuronal function suggests that cognitive impairments observed in advanced age result from the ramifications of broad declines in energy metabolism.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
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13
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Saare M, Tserel L, Haljasmägi L, Taalberg E, Peet N, Eimre M, Vetik R, Kingo K, Saks K, Tamm R, Milani L, Kisand K, Peterson P. Monocytes present age-related changes in phospholipid concentration and decreased energy metabolism. Aging Cell 2020; 19:e13127. [PMID: 32107839 PMCID: PMC7189998 DOI: 10.1111/acel.13127] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 01/21/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
Age‐related changes at the cellular level include the dysregulation of metabolic and signaling pathways. Analyses of blood leukocytes have revealed a set of alterations that collectively lower their ability to fight infections and resolve inflammation later in life. We studied the transcriptomic, epigenetic, and metabolomic profiles of monocytes extracted from younger adults and individuals over the age of 65 years to map major age‐dependent changes in their cellular physiology. We found that the monocytes from older persons displayed a decrease in the expression of ribosomal and mitochondrial protein genes and exhibited hypomethylation at the HLA class I locus. Additionally, we found elevated gene expression associated with cell motility, including the CX3CR1 and ARID5B genes, which have been associated with the development of atherosclerosis. Furthermore, the downregulation of two genes, PLA2G4B and ALOX15B, which belong to the arachidonic acid metabolism pathway involved in phosphatidylcholine conversion to anti‐inflammatory lipoxins, correlated with increased phosphatidylcholine content in monocytes from older individuals. We found age‐related changes in monocyte metabolic fitness, including reduced mitochondrial function and increased glycose consumption without the capacity to upregulate it during increased metabolic needs, and signs of increased oxidative stress and DNA damage. In conclusion, our results complement existing findings and elucidate the metabolic alterations that occur in monocytes during aging.
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Affiliation(s)
- Mario Saare
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Liina Tserel
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Liis Haljasmägi
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Egon Taalberg
- Department of Biochemistry Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Nadežda Peet
- Department of Pathophysiology Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Margus Eimre
- Department of Pathophysiology Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Rait Vetik
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Külli Kingo
- Department of Dermatology and Venereology Institute of Clinical Medicine University of Tartu Tartu Estonia
- Clinic of Dermatology Tartu University Hospital Tartu Estonia
| | - Kai Saks
- Department of Internal Medicine Institute of Clinical Medicine University of Tartu Tartu Estonia
| | - Riin Tamm
- Laboratory of Immune Analysis, United Laboratories Tartu University Hospital Tartu Estonia
| | - Lili Milani
- Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia
| | - Kai Kisand
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Pärt Peterson
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
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14
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Zeng L, Yang J, Peng S, Zhu J, Zhang B, Suh Y, Tu Z. Transcriptome analysis reveals the difference between "healthy" and "common" aging and their connection with age-related diseases. Aging Cell 2020; 19:e13121. [PMID: 32077223 PMCID: PMC7059150 DOI: 10.1111/acel.13121] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 01/17/2020] [Accepted: 02/03/2020] [Indexed: 12/16/2022] Open
Abstract
A key goal of aging research was to understand mechanisms underlying healthy aging and develop methods to promote the human healthspan. One approach is to identify gene regulations unique to healthy aging compared with aging in the general population (i.e., "common" aging). Here, we leveraged Genotype-Tissue Expression (GTEx) project data to investigate "healthy" and "common" aging gene expression regulations at a tissue level in humans and their interconnection with diseases. Using GTEx donors' disease annotations, we defined a "healthy" aging cohort for each tissue. We then compared the age-associated genes derived from this cohort with age-associated genes from the "common" aging cohort which included all GTEx donors; we also compared the "healthy" and "common" aging gene expressions with various disease-associated gene expressions to elucidate the relationships among "healthy," "common" aging and disease. Our analyses showed that 1. GTEx "healthy" and "common" aging shared a large number of gene regulations; 2. Despite the substantial commonality, "healthy" and "common" aging genes also showed distinct function enrichment, and "common" aging genes had a higher enrichment for disease genes; 3. Disease-associated gene regulations were overall different from aging gene regulations. However, for genes regulated by both, their regulation directions were largely consistent, implying some aging processes could increase the susceptibility to disease development; and 4. Possible protective mechanisms were associated with some "healthy" aging gene regulations. In summary, our work highlights several unique features of GTEx "healthy" aging program. This new knowledge could potentially be used to develop interventions to promote the human healthspan.
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Affiliation(s)
- Lu Zeng
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Jialiang Yang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Shouneng Peng
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Jun Zhu
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Bin Zhang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Yousin Suh
- Department of GeneticsAlbert Einstein College of MedicineNew YorkNew York
| | - Zhidong Tu
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
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15
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Boczek T, Radzik T, Ferenc B, Zylinska L. The Puzzling Role of Neuron-Specific PMCA Isoforms in the Aging Process. Int J Mol Sci 2019; 20:ijms20246338. [PMID: 31888192 PMCID: PMC6941135 DOI: 10.3390/ijms20246338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 01/02/2023] Open
Abstract
The aging process is a physiological phenomenon associated with progressive changes in metabolism, genes expression, and cellular resistance to stress. In neurons, one of the hallmarks of senescence is a disturbance of calcium homeostasis that may have far-reaching detrimental consequences on neuronal physiology and function. Among several proteins involved in calcium handling, plasma membrane Ca2+-ATPase (PMCA) is the most sensitive calcium detector controlling calcium homeostasis. PMCA exists in four main isoforms and PMCA2 and PMCA3 are highly expressed in the brain. The overall effects of impaired calcium extrusion due to age-dependent decline of PMCA function seem to accumulate with age, increasing the susceptibility to neurotoxic insults. To analyze the PMCA role in neuronal cells, we have developed stable transfected differentiated PC12 lines with down-regulated PMCA2 or PMCA3 isoforms to mimic age-related changes. The resting Ca2+ increased in both PMCA-deficient lines affecting the expression of several Ca2+-associated proteins, i.e., sarco/endoplasmic Ca2+-ATPase (SERCA), calmodulin, calcineurin, GAP43, CCR5, IP3Rs, and certain types of voltage-gated Ca2+ channels (VGCCs). Functional studies also demonstrated profound changes in intracellular pH regulation and mitochondrial metabolism. Moreover, modification of PMCAs membrane composition triggered some adaptive processes to counterbalance calcium overload, but the reduction of PMCA2 appeared to be more detrimental to the cells than PMCA3.
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Affiliation(s)
- Tomasz Boczek
- Department of Molecular Neurochemistry, Medical University, 92-215 Lodz, Poland; (T.B.); (T.R.); (B.F.)
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Tomasz Radzik
- Department of Molecular Neurochemistry, Medical University, 92-215 Lodz, Poland; (T.B.); (T.R.); (B.F.)
| | - Bozena Ferenc
- Department of Molecular Neurochemistry, Medical University, 92-215 Lodz, Poland; (T.B.); (T.R.); (B.F.)
| | - Ludmila Zylinska
- Department of Molecular Neurochemistry, Medical University, 92-215 Lodz, Poland; (T.B.); (T.R.); (B.F.)
- Correspondence: ; Tel.: +48-42-272-5680
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16
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Arnatkevičiūtė A, Fulcher BD, Fornito A. Uncovering the Transcriptional Correlates of Hub Connectivity in Neural Networks. Front Neural Circuits 2019; 13:47. [PMID: 31379515 PMCID: PMC6659348 DOI: 10.3389/fncir.2019.00047] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 07/04/2019] [Indexed: 12/04/2022] Open
Abstract
Connections in nervous systems are disproportionately concentrated on a small subset of neural elements that act as network hubs. Hubs have been found across different species and scales ranging from C. elegans to mouse, rat, cat, macaque, and human, suggesting a role for genetic influences. The recent availability of brain-wide gene expression atlases provides new opportunities for mapping the transcriptional correlates of large-scale network-level phenotypes. Here we review studies that use these atlases to investigate gene expression patterns associated with hub connectivity in neural networks and present evidence that some of these patterns are conserved across species and scales.
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Affiliation(s)
- Aurina Arnatkevičiūtė
- Monash Biomedical Imaging, School of Psychological Sciences, Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC, Australia
| | - Ben D. Fulcher
- Monash Biomedical Imaging, School of Psychological Sciences, Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC, Australia
- School of Physics, The University of Sydney, Sydney, NSW, Australia
| | - Alex Fornito
- Monash Biomedical Imaging, School of Psychological Sciences, Turner Institute for Brain and Mental Health, Monash University, Clayton, VIC, Australia
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17
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Lupo G, Gaetani S, Cacci E, Biagioni S, Negri R. Molecular Signatures of the Aging Brain: Finding the Links Between Genes and Phenotypes. Neurotherapeutics 2019; 16:543-553. [PMID: 31161490 PMCID: PMC6694319 DOI: 10.1007/s13311-019-00743-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aging is associated with cognitive decline and increased vulnerability to neurodegenerative diseases. The progressive extension of the average human lifespan is bound to lead to a corresponding increase in the fraction of cognitively impaired elderly individuals among the human population, with an enormous societal and economic burden. At the cellular and tissue levels, cognitive decline is linked to a reduction in specific neuronal subpopulations, a widespread decrease in synaptic plasticity and an increase in neuroinflammation due to an enhanced activation of astrocytes and microglia, but the molecular mechanisms underlying these functional changes during normal aging and in neuropathological conditions remain poorly understood. In this review, we summarize very recent and outstanding progress in elucidating the molecular changes associated with cognitive decline through the genome-wide profiling of aging brain cells at different molecular levels (genomic, epigenomic, transcriptomic, proteomic). We discuss how the correlation of different molecular and phenotypic traits driven by mathematical and computational analyses of large datasets has led to the prediction of key molecular nodes of neurodegenerative pathways, and provide a few examples of candidate regulators of cognitive decline identified with these approaches. Furthermore, we highlight the dysregulation of the synaptic transcriptome in neuronal cells and of the inflammatory transcriptome in glial cells as some of the key events during normal and neuropathological human brain aging.
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Affiliation(s)
- Giuseppe Lupo
- Department of Chemistry, Sapienza University of Rome, Piazzale A. Moro, 00185, Rome, Italy.
| | - Silvana Gaetani
- Department of Physiology and Farmacology "V. Erspamer", Sapienza University of Rome, Piazzale A. Moro, 00185, Rome, Italy
| | - Emanuele Cacci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro, 00185, Rome, Italy
| | - Stefano Biagioni
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro, 00185, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro, 00185, Rome, Italy
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18
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Calcium Dyshomeostasis Alters CCL5 Signaling in Differentiated PC12 Cells. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9616248. [PMID: 31032369 PMCID: PMC6457283 DOI: 10.1155/2019/9616248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/04/2019] [Indexed: 11/22/2022]
Abstract
Background Plasma membrane Ca2+-ATPase (PMCA) is the most sensitive cellular calcium detector. It exists in four main isoforms (PMCA1-4), among which PMCA2 and PMCA3 are considered as fast-acting neuron-specific forms. In the brain, PMCA function declines progressively during aging; thereby impaired calcium homeostasis may contribute to some neurodegenerative diseases. These destructive processes can be propagated by proinflammatory chemokines, including chemokine CCL5, which causes phospholipase C-mediated liberation of Ca2+ from endoplasmic reticulum by IP3-gated channels. Methods To mimic the changes in aged neurons we used stable transfected differentiated PC12 cells with downregulated PMCA2 or PMCA3 and analyzed the effect of CCL5 on calcium transients with Fluo-4 reagent. Chemokine receptors were evaluated using Western blot, and IP3 receptors expression level was assessed using qRT-PCR and Western blot. Results In PMCA-reduced cell lines, CCL5 released more Ca2+ by IP3-sensitive receptors, and the time required for Ca2+ clearance was significantly longer. Also, in these lines we detected altered expression level of CCR5 and IP3 receptors. Conclusion Although modification of PMCAs composition could provide some protection against calcium overload, reduction of PMCA2 appeared to be more detrimental to the cells than deficiency of PMCA3. Under pathological conditions, including inflammatory CCL5 action and long-lasting Ca2+ dyshomeostasis, insufficient cell protection may result in progressive degeneration and death of neurons.
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19
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Mukherjee S, Klaus C, Pricop-Jeckstadt M, Miller JA, Struebing FL. A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks. Front Neurosci 2019; 13:2. [PMID: 30733664 PMCID: PMC6353788 DOI: 10.3389/fnins.2019.00002] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/03/2019] [Indexed: 01/06/2023] Open
Abstract
Aging is regarded as a major risk factor for neurodegenerative diseases. Thus, a better understanding of the similarities between the aging process and neurodegenerative diseases at the cellular and molecular level may reveal better understanding of this detrimental relationship. In the present study, we mined publicly available gene expression datasets from healthy individuals and patients affected by neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, and Huntington's disease) across a broad age spectrum and compared those with mouse aging and mouse cell-type specific gene expression profiles. We performed weighted gene co-expression network analysis (WGCNA) and found a gene network strongly related with both aging and neurodegenerative diseases. This network was significantly enriched with a microglial signature as imputed from cell type-specific sequencing data. Since mouse models are extensively used for the study of human diseases, we further compared these human gene regulatory networks with age-specific mouse brain transcriptomes. We discovered significantly preserved networks with both human aging and human disease and identified 17 shared genes in the top-ranked immune/microglia module, among which we found five human hub genes TYROBP, FCER1G, ITGB2, MYO1F, PTPRC, and two mouse hub genes Trem2 and C1qa. Taken together, these results support the hypothesis that microglia are key players involved in human aging and neurodegenerative diseases, and suggest that mouse models should be appropriate for studying these microglial changes in human.
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Affiliation(s)
- Shradha Mukherjee
- Health Informatics Advanced Science Masters Program, Arizona State University, Tempe, AZ, United States
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Christine Klaus
- Neural Regeneration Group, Institute of Reconstructive Neurobiology, University of Bonn, Bonn, Germany
| | - Mihaela Pricop-Jeckstadt
- Institute for Medical Informatics and Biometry, Faculty of Medicine “Carl Gustav Carus”, TU Dresden, Dresden, Germany
| | | | - Felix L. Struebing
- Department of Translational Brain Research, German Center for Neurodegenerative Diseases, Munich, Germany
- Center for Neuropathology and Prion Research, Ludwig Maximilian University of Munich, Munich, Germany
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
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20
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Arnatkeviciute A, Fulcher BD, Fornito A. A practical guide to linking brain-wide gene expression and neuroimaging data. Neuroimage 2019; 189:353-367. [PMID: 30648605 DOI: 10.1016/j.neuroimage.2019.01.011] [Citation(s) in RCA: 347] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/03/2019] [Accepted: 01/05/2019] [Indexed: 12/19/2022] Open
Abstract
The recent availability of comprehensive, brain-wide gene expression atlases such as the Allen Human Brain Atlas (AHBA) has opened new opportunities for understanding how spatial variations on molecular scale relate to the macroscopic neuroimaging phenotypes. A rapidly growing body of literature is demonstrating relationships between gene expression and diverse properties of brain structure and function, but approaches for combining expression atlas data with neuroimaging are highly inconsistent, with substantial variations in how the expression data are processed. The degree to which these methodological variations affect findings is unclear. Here, we outline a seven-step analysis pipeline for relating brain-wide transcriptomic and neuroimaging data and compare how different processing choices influence the resulting data. We suggest that studies using the AHBA should work towards a unified data processing pipeline to ensure consistent and reproducible results in this burgeoning field.
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Affiliation(s)
- Aurina Arnatkeviciute
- Brain and Mental Health Research Hub, Monash Institute of Cognitive and Clinical Neurosciences, School of Psychological Sciences, Monash University, 770 Blackburn Rd, Clayton, 3168, VIC, Australia.
| | - Ben D Fulcher
- Brain and Mental Health Research Hub, Monash Institute of Cognitive and Clinical Neurosciences, School of Psychological Sciences, Monash University, 770 Blackburn Rd, Clayton, 3168, VIC, Australia; School of Physics, Sydney University, Sydney, 2006, NSW, Australia
| | - Alex Fornito
- Brain and Mental Health Research Hub, Monash Institute of Cognitive and Clinical Neurosciences, School of Psychological Sciences, Monash University, 770 Blackburn Rd, Clayton, 3168, VIC, Australia
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21
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Abstract
Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing. These encompass widely reported features of ageing such as increased senescence and inflammation, reduced electron transport chain activity and reduced ribosome synthesis, but also reveal a surprising lack of gene expression responses to known age-linked cellular stresses. We discuss how the existence of conserved transcriptomic hallmarks relates to genome-wide epigenetic differences underlying ageing clocks, and how the changing transcriptome results in proteomic alterations where data is available and to variations in cell physiology characteristic of ageing. Identification of gene expression events that occur during ageing across distant organisms should be informative as to conserved underlying mechanisms of ageing, and provide additional biomarkers to assess the effects of diet and other environmental factors on the rate of ageing.
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Affiliation(s)
- Stephen Frenk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
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22
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Bortell N, Basova L, Najera JA, Morsey B, Fox HS, Marcondes MCG. Sirtuin 1-Chromatin-Binding Dynamics Points to a Common Mechanism Regulating Inflammatory Targets in SIV Infection and in the Aging Brain. J Neuroimmune Pharmacol 2017; 13:163-178. [PMID: 29280055 DOI: 10.1007/s11481-017-9772-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/20/2017] [Indexed: 12/20/2022]
Abstract
Microglia and macrophages are the main non-neuronal subsets of myeloid origin in the brain, and are critical regulators in neurodegenerative disorders, where inflammation is a key factor. Since HIV infection results in neurological perturbations that are similar to those in aging, we examined microglial and infiltrating myeloid subsets in the search for changes that might resemble the ones in aging. For that, we used the SIV infection in rhesus macaques to model neuroAIDS. We found that Sirt-1, a molecule that impacts survival and health in many models, was decreased in cell preparations containing a majority of microglia and myeloid cells from the brain of infected macaques. The role of Sirt-1 in neuroAIDS is unknown. We hypothesized that Sirt-1 silencing functions are affected by SIV. Mapping of Sirt-1 binding patterns to chromatin revealed that the number of Sirt-1-bound genes was 29.6% increased in myeloid cells from infected animals with mild or no detectable neuropathology, but 51% was decreased in severe neuropathology, compared to controls. Importantly, Sirt-1-bound genes in controls largely participate in neuroinflammation. Promoters of type I IFN pathway genes IRF7, IRF1, IFIT1, and AIF1, showed Sirt-1 binding in controls, which was consistently lost after infection, together with higher transcription. Loss of Sirt-1 binding was also found in brains from old uninfected animals, suggesting a common regulation. The role of Sirt-1 in regulating these inflammatory markers was confirmed in two different in vitro models, where Sirt-1 blockage modulated IRF7, IRF1 and AIF1 levels both in human macrophage cell lines and in human blood-derived monocytes from various normal donors, stimulated with a TLR9 agonist. Our data suggests that Sirt-1-inflammatory gene silencing is disturbed by SIV infection, resembling aging in brains. These findings may impact our knowledge on the contribution of myeloid subsets to the neurological consequences of HIV infection, aggravated and overlapping with the aging process.
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Affiliation(s)
- Nikki Bortell
- Molecular and Cellular Neurosciences Department, The Scripps Research Institute, La Jolla, CA, USA
| | - Liana Basova
- Molecular and Cellular Neurosciences Department, The Scripps Research Institute, La Jolla, CA, USA.,San Diego Biomedical Research Institute, 10865 Road to Cure, Suite 100, San Diego, CA, 92121, USA
| | - Julia A Najera
- Molecular and Cellular Neurosciences Department, The Scripps Research Institute, La Jolla, CA, USA
| | - Brenda Morsey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5800, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5800, USA
| | - Maria Cecilia Garibaldi Marcondes
- Molecular and Cellular Neurosciences Department, The Scripps Research Institute, La Jolla, CA, USA. .,San Diego Biomedical Research Institute, 10865 Road to Cure, Suite 100, San Diego, CA, 92121, USA.
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Transcriptomic profiling of the human brain reveals that altered synaptic gene expression is associated with chronological aging. Sci Rep 2017; 7:16890. [PMID: 29203886 PMCID: PMC5715102 DOI: 10.1038/s41598-017-17322-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/22/2017] [Indexed: 11/23/2022] Open
Abstract
Aging is a biologically universal event, and yet the key events that drive aging are still poorly understood. One approach to generate new hypotheses about aging is to use unbiased methods to look at change across lifespan. Here, we have examined gene expression in the human dorsolateral frontal cortex using RNA- Seq to populate a whole gene co-expression network analysis. We show that modules of co-expressed genes enriched for those encoding synaptic proteins are liable to change with age. We extensively validate these age-dependent changes in gene expression across several datasets including the publically available GTEx resource which demonstrated that gene expression associations with aging vary between brain regions. We also estimated the extent to which changes in cellular composition account for age associations and find that there are independent signals for cellularity and aging. Overall, these results demonstrate that there are robust age-related alterations in gene expression in the human brain and that genes encoding for neuronal synaptic function may be particularly sensitive to the aging process.
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24
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Soreq L, Rose J, Soreq E, Hardy J, Trabzuni D, Cookson MR, Smith C, Ryten M, Patani R, Ule J. Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging. Cell Rep 2017; 18:557-570. [PMID: 28076797 PMCID: PMC5263238 DOI: 10.1016/j.celrep.2016.12.011] [Citation(s) in RCA: 269] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/04/2016] [Accepted: 12/02/2016] [Indexed: 02/06/2023] Open
Abstract
Gene expression studies suggest that aging of the human brain is determined by a complex interplay of molecular events, although both its region- and cell-type-specific consequences remain poorly understood. Here, we extensively characterized aging-altered gene expression changes across ten human brain regions from 480 individuals ranging in age from 16 to 106 years. We show that astrocyte- and oligodendrocyte-specific genes, but not neuron-specific genes, shift their regional expression patterns upon aging, particularly in the hippocampus and substantia nigra, while the expression of microglia- and endothelial-specific genes increase in all brain regions. In line with these changes, high-resolution immunohistochemistry demonstrated decreased numbers of oligodendrocytes and of neuronal subpopulations in the aging brain cortex. Finally, glial-specific genes predict age with greater precision than neuron-specific genes, thus highlighting the need for greater mechanistic understanding of neuron-glia interactions in aging and late-life diseases.
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Affiliation(s)
- Lilach Soreq
- Institute of Neurology, University College London, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | | | - Jamie Rose
- MRC Edinburgh Brain Bank, Academic Neuropathology, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Eyal Soreq
- The Computational, Cognitive and Clinical NeuroImaging Laboratory, Division of Brain Sciences, Imperial College, London SW7 2AZ, UK
| | - John Hardy
- Institute of Neurology, University College London, London WC1N 3BG, UK; Reta Lila Weston Institute of Neurological Studies, UCL ION, 1 Wakefield Street, London WC1N 1PJ, UK
| | - Daniah Trabzuni
- Institute of Neurology, University College London, London WC1N 3BG, UK; Departments of Genetics, King Faisal Specialist Hospital and Research Centre. Riyadh 12713, Saudi Arabia
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Colin Smith
- MRC Edinburgh Brain Bank, Academic Neuropathology, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Mina Ryten
- Institute of Neurology, University College London, London WC1N 3BG, UK; Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Rickie Patani
- Institute of Neurology, University College London, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Reta Lila Weston Institute of Neurological Studies, UCL ION, 1 Wakefield Street, London WC1N 1PJ, UK; Euan MacDonald Centre for MND, University of Edinburgh, Edinburgh EH8 9YL, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK.
| | - Jernej Ule
- Institute of Neurology, University College London, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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25
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Identification of a T cell gene expression clock obtained by exploiting a MZ twin design. Sci Rep 2017; 7:6005. [PMID: 28729616 PMCID: PMC5519672 DOI: 10.1038/s41598-017-05694-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/01/2017] [Indexed: 02/02/2023] Open
Abstract
Many studies investigated age-related changes in gene expression of different tissues, with scarce agreement due to the high number of affecting factors. Similarly, no consensus has been reached on which genes change expression as a function of age and not because of environment. In this study we analysed gene expression of T lymphocytes from 27 healthy monozygotic twin couples, with ages ranging over whole adult lifespan (22 to 98 years). This unique experimental design allowed us to identify genes involved in normative aging, which expression changes independently from environmental factors. We obtained a transcriptomic signature with 125 genes, from which chronological age can be estimated. This signature has been tested in two datasets of same cell type hybridized over two different platforms, showing a significantly better performance compared to random signatures. Moreover, the same signature was applied on a dataset from a different cell type (human muscle). A lower performance was obtained, indicating the possibility that the signature is T cell-specific. As a whole our results suggest that this approach can be useful to identify age-modulated genes.
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26
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Brouwer RM, Panizzon MS, Glahn DC, Hibar DP, Hua X, Jahanshad N, Abramovic L, de Zubicaray GI, Franz CE, Hansell NK, Hickie IB, Koenis MMG, Martin NG, Mather KA, McMahon KL, Schnack HG, Strike LT, Swagerman SC, Thalamuthu A, Wen W, Gilmore JH, Gogtay N, Kahn RS, Sachdev PS, Wright MJ, Boomsma DI, Kremen WS, Thompson PM, Hulshoff Pol HE. Genetic influences on individual differences in longitudinal changes in global and subcortical brain volumes: Results of the ENIGMA plasticity working group. Hum Brain Mapp 2017; 38:4444-4458. [PMID: 28580697 DOI: 10.1002/hbm.23672] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 12/12/2022] Open
Abstract
Structural brain changes that occur during development and ageing are related to mental health and general cognitive functioning. Individuals differ in the extent to which their brain volumes change over time, but whether these differences can be attributed to differences in their genotypes has not been widely studied. Here we estimate heritability (h2 ) of changes in global and subcortical brain volumes in five longitudinal twin cohorts from across the world and in different stages of the lifespan (N = 861). Heritability estimates of brain changes were significant and ranged from 16% (caudate) to 42% (cerebellar gray matter) for all global and most subcortical volumes (with the exception of thalamus and pallidum). Heritability estimates of change rates were generally higher in adults than in children suggesting an increasing influence of genetic factors explaining individual differences in brain structural changes with age. In children, environmental influences in part explained individual differences in developmental changes in brain structure. Multivariate genetic modeling showed that genetic influences of change rates and baseline volume significantly overlapped for many structures. The genetic influences explaining individual differences in the change rate for cerebellum, cerebellar gray matter and lateral ventricles were independent of the genetic influences explaining differences in their baseline volumes. These results imply the existence of genetic variants that are specific for brain plasticity, rather than brain volume itself. Identifying these genes may increase our understanding of brain development and ageing and possibly have implications for diseases that are characterized by deviant developmental trajectories of brain structure. Hum Brain Mapp 38:4444-4458, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Rachel M Brouwer
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Matthew S Panizzon
- Department of Psychiatry, University of California, San Diego, California
| | - David C Glahn
- Department of Psychiatry, Yale University of Medicine, New Haven, Connecticut
| | - Derrek P Hibar
- Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, California
| | - Xue Hua
- Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, California
| | - Neda Jahanshad
- Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, California
| | - Lucija Abramovic
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Greig I de Zubicaray
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia
| | - Carol E Franz
- Department of Psychiatry, University of California, San Diego, California
| | - Narelle K Hansell
- Queensland Brain Institute, University of Queensland, St. Lucia, QLD, Australia
| | - Ian B Hickie
- Clinical Research Unit, Brain & Mind Research Institute, University of Sydney, NSW, Australia
| | - Marinka M G Koenis
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Karen A Mather
- Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales, Sydney, Australia
| | - Katie L McMahon
- Centre for Advanced Imaging, University of Queensland, St. Lucia, QLD, Australia
| | - Hugo G Schnack
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lachlan T Strike
- Queensland Brain Institute, University of Queensland, St. Lucia, QLD, Australia
| | - Suzanne C Swagerman
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales, Sydney, Australia
| | - Wei Wen
- Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales, Sydney, Australia
| | - John H Gilmore
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina
| | - Nitin Gogtay
- National Institute of Mental Health, Bethesda, Maryland
| | - René S Kahn
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales, Sydney, Australia
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, St. Lucia, QLD, Australia.,Centre for Advanced Imaging, University of Queensland, St. Lucia, QLD, Australia
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - William S Kremen
- Department of Psychiatry, University of California, San Diego, California
| | - Paul M Thompson
- Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, California
| | - Hilleke E Hulshoff Pol
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
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27
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French L, Ma T, Oh H, Tseng GC, Sibille E. Age-Related Gene Expression in the Frontal Cortex Suggests Synaptic Function Changes in Specific Inhibitory Neuron Subtypes. Front Aging Neurosci 2017; 9:162. [PMID: 28611654 PMCID: PMC5446995 DOI: 10.3389/fnagi.2017.00162] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/09/2017] [Indexed: 12/22/2022] Open
Abstract
Genome-wide expression profiling of the human brain has revealed genes that are differentially expressed across the lifespan. Characterizing these genes adds to our understanding of both normal functions and pathological conditions. Additionally, the specific cell-types that contribute to the motor, sensory and cognitive declines during aging are unclear. Here we test if age-related genes show higher expression in specific neural cell types. Our study leverages data from two sources of murine single-cell expression data and two sources of age-associations from large gene expression studies of postmortem human brain. We used nonparametric gene set analysis to test for age-related enrichment of genes associated with specific cell-types; we also restricted our analyses to specific gene ontology groups. Our analyses focused on a primary pair of single-cell expression data from the mouse visual cortex and age-related human post-mortem gene expression information from the orbitofrontal cortex. Additional pairings that used data from the hippocampus, prefrontal cortex, somatosensory cortex and blood were used to validate and test specificity of our findings. We found robust age-related up-regulation of genes that are highly expressed in oligodendrocytes and astrocytes, while genes highly expressed in layer 2/3 glutamatergic neurons were down-regulated across age. Genes not specific to any neural cell type were also down-regulated, possibly due to the bulk tissue source of the age-related genes. A gene ontology-driven dissection of the cell-type enriched genes highlighted the strong down-regulation of genes involved in synaptic transmission and cell-cell signaling in the Somatostatin (Sst) neuron subtype that expresses the cyclin dependent kinase 6 (Cdk6) and in the vasoactive intestinal peptide (Vip) neuron subtype expressing myosin binding protein C, slow type (Mybpc1). These findings provide new insights into cell specific susceptibility to normal aging, and suggest age-related synaptic changes in specific inhibitory neuron subtypes.
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Affiliation(s)
- Leon French
- Neurobiology of Depression and Aging Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research InstituteToronto, ON, Canada.,Department of Psychiatry, University of TorontoToronto, ON, Canada.,Institute of Medical Science, University of TorontoToronto, ON, Canada
| | - TianZhou Ma
- Department of Biostatistics, University of PittsburghPittsburgh, PA, United States
| | - Hyunjung Oh
- Neurobiology of Depression and Aging Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research InstituteToronto, ON, Canada
| | - George C Tseng
- Department of Biostatistics, University of PittsburghPittsburgh, PA, United States
| | - Etienne Sibille
- Neurobiology of Depression and Aging Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research InstituteToronto, ON, Canada.,Department of Psychiatry, University of TorontoToronto, ON, Canada.,Department of Pharmacology and Toxicology, University of TorontoToronto, ON, Canada
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28
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Chen BJ, Ueberham U, Mills JD, Kirazov L, Kirazov E, Knobloch M, Bochmann J, Jendrek R, Takenaka K, Bliim N, Arendt T, Janitz M. RNA sequencing reveals pronounced changes in the noncoding transcriptome of aging synaptosomes. Neurobiol Aging 2017; 56:67-77. [PMID: 28499146 DOI: 10.1016/j.neurobiolaging.2017.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/31/2017] [Accepted: 04/08/2017] [Indexed: 12/12/2022]
Abstract
Normal aging is associated with impairments in cognitive functions. These alterations are caused by diminutive changes in the biology of synapses, and ineffective neurotransmission, rather than loss of neurons. Hitherto, only a few studies, exploring molecular mechanisms of healthy brain aging in higher vertebrates, utilized synaptosomal fractions to survey local changes in aging-related transcriptome dynamics. Here we present, for the first time, a comparative analysis of the synaptosomes transcriptome in the aging mouse brain using RNA sequencing. Our results show changes in the expression of genes contributing to biological pathways related to neurite guidance, synaptosomal physiology, and RNA splicing. More intriguingly, we also discovered alterations in the expression of thousands of novel, unannotated lincRNAs during aging. Further, detailed characterization of the cleavage and polyadenylation factor I subunit 1 (Clp1) mRNA and protein expression indicates its increased expression in neuronal processes of hippocampal stratum radiatum in aging mice. Together, our study uncovers a new layer of transcriptional regulation which is targeted by aging within the local environment of interconnecting neuronal cells.
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Affiliation(s)
- Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Uwe Ueberham
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - James D Mills
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ludmil Kirazov
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany; Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Evgeni Kirazov
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany; Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Mara Knobloch
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Jana Bochmann
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Renate Jendrek
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicola Bliim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Thomas Arendt
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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29
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Waller R, Woodroofe MN, Wharton SB, Ince PG, Francese S, Heath PR, Cudzich-Madry A, Thomas RH, Rounding N, Sharrack B, Simpson JE. Gene expression profiling of the astrocyte transcriptome in multiple sclerosis normal appearing white matter reveals a neuroprotective role. J Neuroimmunol 2016; 299:139-146. [DOI: 10.1016/j.jneuroim.2016.09.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 01/03/2023]
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30
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Strisovsky K. Rhomboid protease inhibitors: Emerging tools and future therapeutics. Semin Cell Dev Biol 2016; 60:52-62. [PMID: 27567709 DOI: 10.1016/j.semcdb.2016.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/16/2016] [Accepted: 08/24/2016] [Indexed: 02/01/2023]
Abstract
Rhomboid-family intramembrane serine proteases are evolutionarily widespread. Their functions in different organisms are gradually being uncovered and already suggest medical relevance for infectious diseases and cancer. In contrast to these advances, selective inhibitors that could serve as efficient tools for investigation of physiological functions of rhomboids, validation of their disease relevance or as templates for drug development are lacking. In this review I extract what is known about rhomboid protease mechanism and specificity, examine the currently used inhibitors, their mechanism of action and limitations, and conclude by proposing routes for future development of rhomboid protease inhibitors.
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Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic.
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31
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Substrates and physiological functions of secretase rhomboid proteases. Semin Cell Dev Biol 2016; 60:10-18. [PMID: 27497690 DOI: 10.1016/j.semcdb.2016.07.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/26/2016] [Accepted: 07/31/2016] [Indexed: 02/01/2023]
Abstract
Rhomboids are conserved intramembrane serine proteases with widespread functions. They were the earliest discovered members of the wider rhomboid-like superfamily of proteases and pseudoproteases. The secretase class of rhomboid proteases, distributed through the secretory pathway, are the most numerous in eukaryotes, but our knowledge of them is limited. Here we aim to summarise all that has been published on secretase rhomboids in a concise encyclopaedia of the enzymes, their substrates, and their biological roles. We also discuss emerging themes of how these important enzymes are regulated.
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32
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Biswal S, Sharma D, Kumar K, Nag TC, Barhwal K, Hota SK, Kumar B. Global hypoxia induced impairment in learning and spatial memory is associated with precocious hippocampal aging. Neurobiol Learn Mem 2016; 133:157-170. [PMID: 27246251 DOI: 10.1016/j.nlm.2016.05.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/09/2016] [Accepted: 05/27/2016] [Indexed: 01/10/2023]
Abstract
Both chronological aging and chronic hypoxia stress have been reported to cause degeneration of hippocampal CA3 neurons and spatial memory impairment through independent pathways. However, the possible occurrence of precocious biological aging on exposure to single episode of global hypoxia resulting in impairment of learning and memory remains to be established. The present study thus aimed at bridging this gap in existing literature on hypoxia induced biological aging. Male Sprague Dawley rats were exposed to simulated hypobaric hypoxia (25,000ft) for different durations and were compared with aged rats. Behavioral studies in Morris Water Maze showed decline in learning abilities of both chronologically aged as well as hypoxic rats as evident from increased latency and pathlength to reach target platform. These behavioral changes in rats exposed to global hypoxia were associated with deposition of lipofuscin and ultrastructural changes in the mitochondria of hippocampal neurons that serve as hallmarks of aging. A single episode of chronic hypobaric hypoxia exposure also resulted in the up-regulation of pro-aging protein, S100A9 and down regulation of Tau, SNAP25, APOE and Sod2 in the hippocampus similar to that in aged rats indicating hypoxia induced accelerated aging. The present study therefore provides evidence for role of biological aging of hippocampal neurons in hypoxia induced impairment of learning and memory.
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Affiliation(s)
- Suryanarayan Biswal
- Defence Institute of High Altitude Research, C/o 56 APO, Leh-Ladakh, Jammu & Kashmir 901205, India
| | - Deepti Sharma
- Defence Institute of High Altitude Research, C/o 56 APO, Leh-Ladakh, Jammu & Kashmir 901205, India
| | - Kushal Kumar
- Defence Institute of High Altitude Research, C/o 56 APO, Leh-Ladakh, Jammu & Kashmir 901205, India
| | - Tapas Chandra Nag
- Department of Anatomy, All India Institute of Medical Science, New Delhi, India
| | - Kalpana Barhwal
- Defence Institute of High Altitude Research, C/o 56 APO, Leh-Ladakh, Jammu & Kashmir 901205, India
| | - Sunil Kumar Hota
- Defence Institute of High Altitude Research, C/o 56 APO, Leh-Ladakh, Jammu & Kashmir 901205, India.
| | - Bhuvnesh Kumar
- Defence Institute of High Altitude Research, C/o 56 APO, Leh-Ladakh, Jammu & Kashmir 901205, India
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33
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Abstract
PURPOSE OF REVIEW The review aims to provide a summary of recent developments in the study of gene expression in the aging human brain. RECENT FINDINGS Profiling differentially expressed genes or 'transcripts' in the human brain over the course of normal aging has provided valuable insights into the biological pathways that appear activated or suppressed in late life. Genes mediating neuroinflammation and immune system activation in particular, show significant age-related upregulation creating a state of vulnerability to neurodegenerative and neuropsychiatric disease in the aging brain. Cellular ionic dyshomeostasis and age-related decline in a host of molecular influences on synaptic efficacy may underlie neurocognitive decline in later life. Critically, these investigations have also shed light on the mobilization of protective genetic responses within the aging human brain that help determine health and disease trajectories in older age. There is growing interest in the study of pre and posttranscriptional regulators of gene expression, and the role of noncoding RNAs in particular, as mediators of the phenotypic diversity that characterizes human brain aging. SUMMARY Gene expression studies in healthy brain aging offer an opportunity to unravel the intricately regulated cellular underpinnings of neurocognitive aging as well as disease risk and resiliency in late life. In doing so, new avenues for early intervention in age-related neurodegenerative disease could be investigated with potentially significant implications for the development of disease-modifying therapies.
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34
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Saura CA, Parra-Damas A, Enriquez-Barreto L. Gene expression parallels synaptic excitability and plasticity changes in Alzheimer's disease. Front Cell Neurosci 2015; 9:318. [PMID: 26379494 PMCID: PMC4548151 DOI: 10.3389/fncel.2015.00318] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/03/2015] [Indexed: 11/14/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by abnormal accumulation of β-amyloid and tau and synapse dysfunction in memory-related neural circuits. Pathological and functional changes in the medial temporal lobe, a region essential for explicit memory encoding, contribute to cognitive decline in AD. Surprisingly, functional imaging studies show increased activity of the hippocampus and associated cortical regions during memory tasks in presymptomatic and early AD stages, whereas brain activity declines as the disease progresses. These findings suggest an emerging scenario where early pathogenic events might increase neuronal excitability leading to enhanced brain activity before clinical manifestations of the disease, a stage that is followed by decreased brain activity as neurodegeneration progresses. The mechanisms linking pathology with synaptic excitability and plasticity changes leading to memory loss in AD remain largely unclear. Recent studies suggest that increased brain activity parallels enhanced expression of genes involved in synaptic transmission and plasticity in preclinical stages, whereas expression of synaptic and activity-dependent genes are reduced by the onset of pathological and cognitive symptoms. Here, we review recent evidences indicating a relationship between transcriptional deregulation of synaptic genes and neuronal activity and memory loss in AD and mouse models. These findings provide the basis for potential clinical applications of memory-related transcriptional programs and their regulatory mechanisms as novel biomarkers and therapeutic targets to restore brain function in AD and other cognitive disorders.
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Affiliation(s)
- Carlos A. Saura
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de BarcelonaBarcelona, Spain
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35
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Enrichment of single neurons and defined brain regions from human brain tissue samples for subsequent proteome analysis. J Neural Transm (Vienna) 2015; 122:993-1005. [PMID: 26123835 DOI: 10.1007/s00702-015-1414-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 06/11/2015] [Indexed: 12/11/2022]
Abstract
Brain function in normal aging and neurological diseases has long been a subject of interest. With current technology, it is possible to go beyond descriptive analyses to characterize brain cell populations at the molecular level. However, the brain comprises over 100 billion highly specialized cells, and it is a challenge to discriminate different cell groups for analyses. Isolating intact neurons is not feasible with traditional methods, such as tissue homogenization techniques. The advent of laser microdissection techniques promises to overcome previous limitations in the isolation of specific cells. Here, we provide a detailed protocol for isolating and analyzing neurons from postmortem human brain tissue samples. We describe a workflow for successfully freezing, sectioning and staining tissue for laser microdissection. This protocol was validated by mass spectrometric analysis. Isolated neurons can also be employed for western blotting or PCR. This protocol will enable further examinations of brain cell-specific molecular pathways and aid in elucidating distinct brain functions.
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36
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Reynolds LM, Ding J, Taylor JR, Lohman K, Soranzo N, de la Fuente A, Liu TF, Johnson C, Barr RG, Register TC, Donohue KM, Talor MV, Cihakova D, Gu C, Divers J, Siscovick D, Burke G, Post W, Shea S, Jacobs DR, Hoeschele I, McCall CE, Kritchevsky SB, Herrington D, Tracy RP, Liu Y. Transcriptomic profiles of aging in purified human immune cells. BMC Genomics 2015; 16:333. [PMID: 25898983 PMCID: PMC4417516 DOI: 10.1186/s12864-015-1522-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/10/2015] [Indexed: 01/08/2023] Open
Abstract
Background Transcriptomic studies hold great potential towards understanding the human aging process. Previous transcriptomic studies have identified many genes with age-associated expression levels; however, small samples sizes and mixed cell types often make these results difficult to interpret. Results Using transcriptomic profiles in CD14+ monocytes from 1,264 participants of the Multi-Ethnic Study of Atherosclerosis (aged 55–94 years), we identified 2,704 genes differentially expressed with chronological age (false discovery rate, FDR ≤ 0.001). We further identified six networks of co-expressed genes that included prominent genes from three pathways: protein synthesis (particularly mitochondrial ribosomal genes), oxidative phosphorylation, and autophagy, with expression patterns suggesting these pathways decline with age. Expression of several chromatin remodeler and transcriptional modifier genes strongly correlated with expression of oxidative phosphorylation and ribosomal protein synthesis genes. 17% of genes with age-associated expression harbored CpG sites whose degree of methylation significantly mediated the relationship between age and gene expression (p < 0.05). Lastly, 15 genes with age-associated expression were also associated (FDR ≤ 0.01) with pulse pressure independent of chronological age. Comparing transcriptomic profiles of CD14+ monocytes to CD4+ T cells from a subset (n = 423) of the population, we identified 30 age-associated (FDR < 0.01) genes in common, while larger sets of differentially expressed genes were unique to either T cells (188 genes) or monocytes (383 genes). At the pathway level, a decline in ribosomal protein synthesis machinery gene expression with age was detectable in both cell types. Conclusions An overall decline in expression of ribosomal protein synthesis genes with age was detected in CD14+ monocytes and CD4+ T cells, demonstrating that some patterns of aging are likely shared between different cell types. Our findings also support cell-specific effects of age on gene expression, illustrating the importance of using purified cell samples for future transcriptomic studies. Longitudinal work is required to establish the relationship between identified age-associated genes/pathways and aging-related diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1522-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lindsay M Reynolds
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - Jingzhong Ding
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - Jackson R Taylor
- Department of Gerontology and Geriatric Medicine, J. Paul Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - Kurt Lohman
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | | | - Alberto de la Fuente
- FBN, Leibniz Institute for Farm Animal Biology, Genetics and Biometry, Mecklenburg-Vorpommern, Germany.
| | - Tie Fu Liu
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - Craig Johnson
- Departments of Medicine and Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, 98115, USA.
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University, New York, New York, 10032, USA.
| | - Thomas C Register
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - Kathleen M Donohue
- Departments of Medicine and Epidemiology, Columbia University, New York, New York, 10032, USA.
| | - Monica V Talor
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, 21205, USA.
| | - Daniela Cihakova
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, 21205, USA.
| | - Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA.
| | - Jasmin Divers
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - David Siscovick
- New York Academy of Medicine, New York, New York, 10029, USA.
| | - Gregory Burke
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - Wendy Post
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, 21205, USA.
| | - Steven Shea
- Departments of Medicine and Epidemiology, Columbia University, New York, New York, 10032, USA.
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, 55454, USA.
| | - Ina Hoeschele
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Charles E McCall
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA. .,Department of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - Stephen B Kritchevsky
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA. .,Department of Gerontology and Geriatric Medicine, J. Paul Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - David Herrington
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
| | - Russell P Tracy
- Department of Pathology, University of Vermont, Colchester, Vermont, 05446, USA.
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, USA.
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Li Q, Zhang N, Zhang L, Ma H. Differential evolution of members of the rhomboid gene family with conservative and divergent patterns. THE NEW PHYTOLOGIST 2015; 206:368-380. [PMID: 25417867 DOI: 10.1111/nph.13174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 10/16/2014] [Indexed: 05/29/2023]
Abstract
Rhomboid proteins are intramembrane serine proteases that are involved in a plethora of biological functions, but the evolutionary history of the rhomboid gene family is not clear. We performed a comprehensive molecular evolutionary analysis of the rhomboid gene family and also investigated the organization and sequence features of plant rhomboids in different subfamilies. Our results showed that eukaryotic rhomboids could be divided into five subfamilies (RhoA-RhoD and PARL). Most orthology groups appeared to be conserved only as single or low-copy genes in all lineages in RhoB-RhoD and PARL, whereas RhoA genes underwent several duplication events, resulting in multiple gene copies. These duplication events were due to whole genome duplications in plants and animals and the duplicates might have experienced functional divergence. We also identified a novel group of plant rhomboid (RhoB1) that might have lost their enzymatic activity; their existence suggests that they might have evolved new mechanisms. Plant and animal rhomboids have similar evolutionary patterns. In addition, there are mutations affecting key active sites in RBL8, RBL9 and one of the Brassicaceae PARL duplicates. This study delineates a possible evolutionary scheme for intramembrane proteins and illustrates distinct fates and a mechanism of evolution of gene duplicates.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Plant Biology Center for Evolutionary Biology, Fudan University, Shanghai, 200433, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China
| | - Ning Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Plant Biology Center for Evolutionary Biology, Fudan University, Shanghai, 200433, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China
| | - Liangsheng Zhang
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Advanced Institute of Translational Medicine, Tongji University, Shanghai, 200092, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Plant Biology Center for Evolutionary Biology, Fudan University, Shanghai, 200433, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China
- Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
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Glaab E, Schneider R. Comparative pathway and network analysis of brain transcriptome changes during adult aging and in Parkinson's disease. Neurobiol Dis 2014; 74:1-13. [PMID: 25447234 DOI: 10.1016/j.nbd.2014.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/23/2014] [Accepted: 11/03/2014] [Indexed: 01/19/2023] Open
Abstract
Aging is considered as one of the main factors promoting the risk for Parkinson's disease (PD), and common mechanisms of dopamine neuron degeneration in aging and PD have been proposed in recent years. Here, we use a statistical meta-analysis of human brain transcriptomics data to investigate potential mechanistic relationships between adult brain aging and PD pathogenesis at the pathway and network level. The analyses identify statistically significant shared pathway and network alterations in aging and PD and an enrichment in PD-associated sequence variants from genome-wide association studies among the jointly deregulated genes. We find robust discriminative patterns for groups of functionally related genes with potential applications as combined risk biomarkers to detect aging- and PD-linked oxidative stress, e.g., a consistent over-expression of metallothioneins matching with findings in previous independent studies. Interestingly, analyzing the regulatory network and mouse knockout expression data for NR4A2, a transcription factor previously associated with rare mutations in PD and here found as the most significantly under-expressed gene in PD among the jointly altered genes, suggests that aging-related NR4A2 expression changes may increase PD risk via downstream effects similar to disease-linked mutations and to expression changes in sporadic PD. Overall, the analyses suggest mechanistic explanations for the age-dependence of PD risk and reveal significant and robust shared process alterations with potential applications in biomarker development for pre-symptomatic risk assessment or early stage diagnosis.
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Affiliation(s)
- Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg.
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
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Trabzuni D, Thomson PC. Analysis of gene expression data using a linear mixed model/finite mixture model approach: application to regional differences in the human brain. ACTA ACUST UNITED AC 2014; 30:1555-61. [PMID: 24519379 DOI: 10.1093/bioinformatics/btu088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Gene expression data exhibit common information over the genome. This article shows how data can be analysed from an efficient whole-genome perspective. Further, the methods have been developed so that users with limited expertise in bioinformatics and statistical computing techniques could use and modify this procedure to their own needs. The method outlined first uses a large-scale linear mixed model for the expression data genome-wide, and then uses finite mixture models to separate differentially expressed (DE) from non-DE transcripts. These methods are illustrated through application to an exceptional UK Brain Expression Consortium involving 12 human frozen post-mortem brain regions. RESULTS Fitting linear mixed models has allowed variation in gene expression between different biological states (e.g. brain regions, gender, age) to be investigated. The model can be extended to allow for differing levels of variation between different biological states. Predicted values of the random effects show the effects of each transcript in a particular biological state. Using the UK Brain Expression Consortium data, this approach yielded striking patterns of co-regional gene expression. Fitting the finite mixture model to the effects within each state provides a convenient method to filter transcripts that are DE: these DE transcripts can then be extracted for advanced functional analysis. AVAILABILITY The data for all regions except HYPO and SPCO are available at the Gene Expression Omnibus (GEO) site, accession number GSE46706. R code for the analysis is available in the Supplementary file.
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Affiliation(s)
- Daniah Trabzuni
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK, Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia and ReproGen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, NSW 2570, AustraliaDepartment of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK, Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia and ReproGen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, NSW 2570, Australia
| | | | - Peter C Thomson
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK, Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia and ReproGen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, NSW 2570, Australia
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Sharma S, Eghbali M. Influence of sex differences on microRNA gene regulation in disease. Biol Sex Differ 2014; 5:3. [PMID: 24484532 PMCID: PMC3912347 DOI: 10.1186/2042-6410-5-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 12/30/2013] [Indexed: 12/21/2022] Open
Abstract
Sexual dimorphism is observed in most human diseases. The difference in the physiology and genetics between sexes can contribute tremendously to the disease prevalence, severity, and outcome. Both hormonal and genetic differences between males and females can lead to differences in gene expression patterns that can influence disease risk and course. MicroRNAs have emerged as potential regulatory molecules in all organisms. They can have a broad effect on every aspect of physiology, including embryogenesis, metabolism, and growth and development. Numerous microRNAs have been identified and elucidated to play a key role in cardiovascular diseases, as well as in neurological and autoimmune disorders. This is especially important as microRNA-based tools can be exploited as beneficial therapies for disease treatment and prevention. Sex steroid hormones as well as X-linked genes can have a considerable influence on the regulation of microRNAs. However, there are very few studies highlighting the role of microRNAs in sex biased diseases. This review attempts to summarize differentially regulated microRNAs in males versus females in different diseases and calls for more attention in this underexplored area that should set the basis for more effective therapeutic strategies for sexually dimorphic diseases.
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Affiliation(s)
| | - Mansoureh Eghbali
- Department of Anesthesiology, Division of Molecular Medicine, and Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, BH-160CHS, Los Angeles, CA 90095-7115, USA.
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Rao YS, Mott NN, Wang Y, Chung WCJ, Pak TR. MicroRNAs in the aging female brain: a putative mechanism for age-specific estrogen effects. Endocrinology 2013; 154:2795-806. [PMID: 23720423 PMCID: PMC3713211 DOI: 10.1210/en.2013-1230] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/21/2013] [Indexed: 11/19/2022]
Abstract
Menopause is characterized by the rapid age-related decline of circulating 17β-estradiol (E(2)) levels in women, which can sometimes result in cognitive disorders such as impaired memory and increased anxiety. Hormone therapy (HT) is a widely used treatment for the adverse effects associated with menopause; however, evidence suggests that HT administered to postmenopausal women age 65 years and over can lead to increased risks for cognitive disorders. We hypothesized that these age-related changes in E(2) action are due to posttranscriptional gene regulation by microRNAs (miRNAs). miRNAs are a class of small noncoding RNAs that regulate gene expression by binding to the 3'-untranslated region of target mRNAs and subsequently target these transcripts for degradation. In the present study, 3- and 18-month-old female rats were oophorectomized (OVX) and treated 1 week after surgery with 2.5 μg E(2) once per day for 3 days. Total RNA was isolated from the ventral and dorsal hippocampus, central amygdala, and paraventricular nucleus. Our results showed that E(2) differentially altered miRNA levels in an age- and brain region-dependent manner. Multiple miRNA target prediction algorithms revealed putative target genes that are important for memory and stress regulation, such as BDNF, glucocorticoid receptor, and SIRT-1. Indeed, quantitative RT-PCR analyses of some of the predicted targets, such as SIRT1, showed that the mRNA expression levels were the inverse of the targeting miRNA, thereby confirming the prediction algorithms. Taken together, these data show that E(2) regulates miRNA expression in an age- and E(2)-dependent manner, which we hypothesize results in differential gene expression and consequently altered neuronal function.
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Affiliation(s)
- Yathindar S Rao
- Department of Cell and Molecular Physiology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, USA
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Guintivano J, Aryee MJ, Kaminsky ZA. A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics 2013; 8:290-302. [PMID: 23426267 PMCID: PMC3669121 DOI: 10.4161/epi.23924] [Citation(s) in RCA: 281] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Brain cellular heterogeneity may bias cell type specific DNA methylation patterns, influencing findings in psychiatric epigenetic studies. We performed fluorescence activated cell sorting (FACS) of neuronal nuclei and Illumina HM450 DNA methylation profiling in post mortem frontal cortex of 29 major depression and 29 matched controls. We identify genomic features and ontologies enriched for cell type specific epigenetic variation. Using the top cell epigenotype specific (CETS) marks, we generated a publically available R package, “CETS,” capable of quantifying neuronal proportions and generating in silico neuronal profiles from DNA methylation data. We demonstrate a significant overlap in major depression DNA methylation associations between FACS separated and CETS model generated neuronal profiles relative to bulk profiles. CETS derived neuronal proportions correlated significantly with age in the frontal cortex and cerebellum and accounted for epigenetic variation between brain regions. CETS based control of cellular heterogeneity will enable more robust hypothesis testing in the brain.
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Affiliation(s)
- Jerry Guintivano
- The Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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An emerging role for microRNAs in sexually dimorphic neurobiological systems. Pflugers Arch 2013; 465:655-67. [PMID: 23397171 DOI: 10.1007/s00424-013-1227-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 01/28/2013] [Indexed: 10/27/2022]
Abstract
Over the past 20 years, our understanding of the basic mechanisms of gene regulation has vastly expanded due to the unexpected roles of small regulatory RNAs, in particular microRNAs (miRNAs). miRNAs add another layer of complexity to the regulation of effector molecules for nearly every physiological process, making them excellent candidate molecules as therapeutic targets, biomarkers, and disease predictors. Hormonal contributions to mature miRNA expression, biosynthetic processing, and downstream functions have only just begun to be investigated. Elucidating the physiological consequences of miRNA sexual dimorphism, and their associated regulatory processes, may be key toward understanding both normal and pathological processes in the brain. This short review provides a basic overview of miRNA biosynthesis, their role in normal brain development, and potential links to neurological diseases. We conclude with a brief discussion of the current knowledge of sex-specific miRNA processes in both the brain and the heart to conceptually integrate the relevance of miRNAs with the overarching theme ("sex differences in health and disease: brain and heart connections") of this special topics issue.
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