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Wu C, Tu T, Xie M, Wang Y, Yan B, Gong Y, Zhang J, Zhou X, Xie Z. Spatially resolved transcriptome of the aging mouse brain. Aging Cell 2024; 23:e14109. [PMID: 38372175 PMCID: PMC11113349 DOI: 10.1111/acel.14109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Brain aging is associated with cognitive decline, memory loss and many neurodegenerative disorders. The mammalian brain has distinct structural regions that perform specific functions. However, our understanding in gene expression and cell types within the context of the spatial organization of the mammalian aging brain is limited. Here we generated spatial transcriptomic maps of young and old mouse brains. We identified 27 distinguished brain spatial domains, including layer-specific subregions that are difficult to dissect individually. We comprehensively characterized spatial-specific changes in gene expression in the aging brain, particularly for isocortex, the hippocampal formation, brainstem and fiber tracts, and validated some gene expression differences by qPCR and immunohistochemistry. We identified aging-related genes and pathways that vary in a coordinated manner across spatial regions and parsed the spatial features of aging-related signals, providing important clues to understand genes with specific functions in different brain regions during aging. Combined with single-cell transcriptomics data, we characterized the spatial distribution of brain cell types. The proportion of immature neurons decreased in the DG region with aging, indicating that the formation of new neurons is blocked. Finally, we detected changes in information interactions between regions and found specific pathways were deregulated with aging, including classic signaling WNT and layer-specific signaling COLLAGEN. In summary, we established a spatial molecular atlas of the aging mouse brain (http://sysbio.gzzoc.com/Mouse-Brain-Aging/), which provides important resources and novel insights into the molecular mechanism of brain aging.
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Affiliation(s)
- Cheng Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Tianxiang Tu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Mingzhe Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Yiting Wang
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, MOE Innovative Center for New Drug Development of Immune Inflammatory DiseasesInstitutes of Brain Science, Institute for Medical and Engineering Innovation, Department of Ophthalmology, Eye & ENT Hospital, Fudan UniversityShanghaiChina
| | - Biao Yan
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, MOE Innovative Center for New Drug Development of Immune Inflammatory DiseasesInstitutes of Brain Science, Institute for Medical and Engineering Innovation, Department of Ophthalmology, Eye & ENT Hospital, Fudan UniversityShanghaiChina
| | - Yajun Gong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Jiayi Zhang
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, MOE Innovative Center for New Drug Development of Immune Inflammatory DiseasesInstitutes of Brain Science, Institute for Medical and Engineering Innovation, Department of Ophthalmology, Eye & ENT Hospital, Fudan UniversityShanghaiChina
| | - Xiaolai Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
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2
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Weistuch C, Murgas KA, Zhu J, Norton L, Dill KA, Tannenbaum AR, Deasy JO. Functional transcriptional signatures for tumor-type-agnostic phenotype prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.12.536595. [PMID: 37090606 PMCID: PMC10120658 DOI: 10.1101/2023.04.12.536595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Cancer transcriptional patterns exhibit both shared and unique features across diverse cancer types, but whether these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that cancer transcriptional diversity mirrors patterns in normal tissues optimized for distinct functional tasks. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.
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Affiliation(s)
- Corey Weistuch
- Memorial Sloan Kettering Cancer Center, Department of Medical
Physics
| | - Kevin A. Murgas
- Stony Brook University, Department of Biomedical
Informatics
| | - Jiening Zhu
- Stony Brook University, Department of Applied Mathematics and
Statistics
| | - Larry Norton
- Memorial Sloan Kettering Cancer Center, Department of
Medicine
| | - Ken A. Dill
- Stony Brook University, Laufer Center for Physical and
Quantitative Biology
| | - Allen R. Tannenbaum
- Stony Brook University, Department of Applied Mathematics and
Statistics
- Stony Brook University, Department of Computer Science
| | - Joseph O. Deasy
- Memorial Sloan Kettering Cancer Center, Department of Medical
Physics
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3
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van’t Sant LJ, Birkisdóttir MB, Ozinga RA, Gyenis Á, Hoeijmakers JH, Vermeij WP, Jaarsma D. Gene expression changes in cerebellum induced by dietary restriction. Front Mol Neurosci 2023; 16:1185665. [PMID: 37293544 PMCID: PMC10244750 DOI: 10.3389/fnmol.2023.1185665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Background Dietary restriction (DR) is a well-established universal anti-aging intervention, and is neuroprotective in multiple models of nervous system disease, including models with cerebellar pathology. The beneficial effects of DR are associated with a rearrangement of gene expression that modulate metabolic and cytoprotective pathways. However, the effect of DR on the cerebellar transcriptome remained to be fully defined. Results Here we analyzed the effect of a classical 30% DR protocol on the transcriptome of cerebellar cortex of young-adult male mice using RNAseq. We found that about 5% of expressed genes were differentially expressed in DR cerebellum, the far majority of whom showing subtle expression changes. A large proportion of down-regulated genes are implicated in signaling pathways, in particular pathways associated with neuronal signaling. DR up regulated pathways in large part were associated with cytoprotection and DNA repair. Analysis of the expression of cell-specific gene sets, indicated a strong enrichment of DR down genes in Purkinje cells, while genes specifically associated with granule cells did not show such a preferential down-regulation. Conclusion Our data show that DR may have a clear effect on the cerebellar transcriptome inducing a mild shift from physiology towards maintenance and repair, and having cell-type specific effects.
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Affiliation(s)
| | - María B. Birkisdóttir
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Rutger A. Ozinga
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Ákos Gyenis
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, Institute for Genome Stability in Ageing and Disease, University of Cologne, Cologne, Germany
| | - Jan H.J. Hoeijmakers
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, Institute for Genome Stability in Ageing and Disease, University of Cologne, Cologne, Germany
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Dick Jaarsma
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
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4
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Jeanne PV, McLamb F, Feng Z, Griffin L, Gong S, Shea D, Szuch MA, Scott S, Gersberg RM, Bozinovic G. Locomotion and brain gene expression exhibit sex-specific non-monotonic dose-response to HFPO-DA during Drosophila melanogaster lifespan. Neurotoxicology 2023; 96:207-221. [PMID: 37156305 DOI: 10.1016/j.neuro.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Legacy per- and polyfluoroalkyl substances (PFAS), known for their environmental persistence and bio-accumulative properties, have been phased out in the U.S. due to public health concerns. A newer polymerization aid used in the manufacture of some fluoropolymers, hexafluoropropylene oxide-dimer acid (HFPO-DA), has lower reported bioaccumulation and toxicity, but is a potential neurotoxicant implicated in dopaminergic neurodegeneration. OBJECTIVE We investigated HFPO-DA's bio-accumulative potential and sex-specific effects on lifespan, locomotion, and brain gene expression in fruit flies. METHODS We quantified bioaccumulation of HFPO-DA in fruit flies exposed to 8.7×104µg/L of HFPO-DA in the fly media for 14 days via UHPLC-MS. Long-term effect on lifespan was determined by exposing both sexes to 8.7×102 - 8.7×105µg/L of HFPO-DA in media. Locomotion was measured following 3, 7, and 14 days of exposures at 8.7×101 - 8.7×105µg/L of HFPO-DA in media, and high-throughput 3'-end RNA-sequencing was used to quantify gene expression in fly brains across the same time points. RESULTS Bioaccumulation of HFPO-DA in fruit flies was not detected. HFPO-DA-induced effects on lifespan, locomotion, and brain gene expression, and lowest adverse effect level (LOAEL) showed sexually dimorphic patterns. Locomotion scores significantly decreased in at least one dose at all time points for females and only at 3-day exposure for males, while brain gene expression exhibited non-monotonic dose-response. Differentially expressed genes correlated to locomotion scores revealed sex-specific numbers of positively and negatively correlated genes per functional category. CONCLUSION Although HFPO-DA effects on locomotion and survival were significant at doses higher than the US EPA reference dose, the brain transcriptomic profiling reveals sex-specific changes and neurological molecular targets; gene enrichments highlight disproportionately affected categories, including immune response: female-specific co-upregulation suggests potential neuroinflammation. Consistent sex-specific exposure effects necessitate blocking for sex in experimental design during HFPO-DA risk assessment.
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Affiliation(s)
- P Vu Jeanne
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, USA; University of California, San Diego, Division of Extended Studies, La Jolla, CA, USA
| | - Flannery McLamb
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; University of California, San Diego, Division of Extended Studies, La Jolla, CA, USA
| | - Zuying Feng
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, USA
| | - Lindsey Griffin
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; University of California, San Diego, Division of Extended Studies, La Jolla, CA, USA
| | - Sylvia Gong
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, USA; University of California, San Diego, Division of Extended Studies, La Jolla, CA, USA
| | | | - Mary A Szuch
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
| | - Savannah Scott
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
| | - Richard M Gersberg
- San Diego State University, Graduate School of Public Health, San Diego, CA, USA
| | - Goran Bozinovic
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, USA; University of California, San Diego, School of Biological Sciences, La Jolla, CA, USA.
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5
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Foster TC. Animal models for studies of alcohol effects on the trajectory of age-related cognitive decline. Alcohol 2023; 107:4-11. [PMID: 35504438 DOI: 10.1016/j.alcohol.2022.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023]
Abstract
There is growing interest in understanding how ethanol use interacts with advancing age to influence the brain and cognition. Animal models are employed to investigate the cellular and molecular mechanisms of brain aging and age-related neurodegenerative diseases that underlie cognitive decline. However, all too often research on problems and diseases of the elderly are conducted in healthy young animals, providing little clinical relevance. The validity of animal models is discussed, and confounds due to age-related differences in anxiety, sensory-motor function, and procedural learning are highlighted in order to enhance the successful translation of preclinical results into clinical settings. The mechanism of action of ethanol on brain aging will depend on the dose, acute or chronic treatment, or withdrawal from treatment and the age examined. Due to the fact that humans experience alcohol use throughout life, important questions concern the effects of the dose and duration of ethanol treatment on the trajectory of cognitive function. Central to this research will be questions of the specificity of alcohol effects on cognitive functions and related brain regions that decline with age, as well as the interaction of alcohol with mechanisms or biomarkers of brain aging. Alternatively, moderate alcohol use may provide a source of reserve and resilience against brain aging. Longitudinal studies have the advantage of being sensitive to detecting the effects of treatment on the emergence of cognitive impairment in middle age and can minimize effects of stress/anxiety associated with the novelty of alcohol exposure and behavioral testing, which disproportionately influence aged animals. Finally, the effect of alcohol on senescent neurophysiology and biomarkers of brain aging are discussed. In particular, the interaction of age and effects of alcohol on inflammation, oxidative stress, N-methyl-d-aspartate receptor function, and the balance of excitatory and inhibitory synaptic transmission are highlighted.
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Affiliation(s)
- Thomas C Foster
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States.
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6
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Zhang X, An H, Chen Y, Shu N. Neurobiological Mechanisms of Cognitive Decline Correlated with Brain Aging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1419:127-146. [PMID: 37418211 DOI: 10.1007/978-981-99-1627-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Cognitive decline has emerged as one of the greatest health threats of old age. Meanwhile, aging is the primary risk factor for Alzheimer's disease (AD) and other prevalent neurodegenerative disorders. Developing therapeutic interventions for such conditions demands a greater understanding of the processes underlying normal and pathological brain aging. Despite playing an important role in the pathogenesis and incidence of disease, brain aging has not been well understood at a molecular level. Recent advances in the biology of aging in model organisms, together with molecular- and systems-level studies of the brain, are beginning to shed light on these mechanisms and their potential roles in cognitive decline. This chapter seeks to integrate the knowledge about the neurological mechanisms of age-related cognitive changes that underlie aging.
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Affiliation(s)
- Xiaxia Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, Faculty of Psychology, Beijing Normal University, Beijing, China
- Beijing Aging Brain Rejuvenation Initiative (BABRI) Centre, Beijing Normal University, Beijing, China
| | - Haiting An
- Beijing Aging Brain Rejuvenation Initiative (BABRI) Centre, Beijing Normal University, Beijing, China
- Beijing Neurosurgical Institute, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Yuan Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, Faculty of Psychology, Beijing Normal University, Beijing, China
- Beijing Aging Brain Rejuvenation Initiative (BABRI) Centre, Beijing Normal University, Beijing, China
| | - Ni Shu
- State Key Laboratory of Cognitive Neuroscience and Learning, Faculty of Psychology, Beijing Normal University, Beijing, China.
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7
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Bui TA, Jickling GC, Winship IR. Neutrophil dynamics and inflammaging in acute ischemic stroke: A transcriptomic review. Front Aging Neurosci 2022; 14:1041333. [PMID: 36620775 PMCID: PMC9813499 DOI: 10.3389/fnagi.2022.1041333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Stroke is among the leading causes of death and disability worldwide. Restoring blood flow through recanalization is currently the only acute treatment for cerebral ischemia. Unfortunately, many patients that achieve a complete recanalization fail to regain functional independence. Recent studies indicate that activation of peripheral immune cells, particularly neutrophils, may contribute to microcirculatory failure and futile recanalization. Stroke primarily affects the elderly population, and mortality after endovascular therapies is associated with advanced age. Previous analyses of differential gene expression across injury status and age identify ischemic stroke as a complex age-related disease. It also suggests robust interactions between stroke injury, aging, and inflammation on a cellular and molecular level. Understanding such interactions is crucial in developing effective protective treatments. The global stroke burden will continue to increase with a rapidly aging human population. Unfortunately, the mechanisms of age-dependent vulnerability are poorly defined. In this review, we will discuss how neutrophil-specific gene expression patterns may contribute to poor treatment responses in stroke patients. We will also discuss age-related transcriptional changes that may contribute to poor clinical outcomes and greater susceptibility to cerebrovascular diseases.
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Affiliation(s)
- Truong An Bui
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Glen C. Jickling
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada,Department of Medicine, Division of Neurology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ian R. Winship
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada,*Correspondence: Ian R. Winship,
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8
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Lee J, Kim HJ. Normal Aging Induces Changes in the Brain and Neurodegeneration Progress: Review of the Structural, Biochemical, Metabolic, Cellular, and Molecular Changes. Front Aging Neurosci 2022; 14:931536. [PMID: 35847660 PMCID: PMC9281621 DOI: 10.3389/fnagi.2022.931536] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/13/2022] [Indexed: 11/30/2022] Open
Abstract
Aging is accompanied by many changes in brain and contributes to progressive cognitive decline. In contrast to pathological changes in brain, normal aging brain changes have relatively mild but important changes in structural, biochemical and molecular level. Representatively, aging associated brain changes include atrophy of tissues, alteration in neurotransmitters and damage accumulation in cellular environment. These effects have causative link with age associated changes which ultimately results in cognitive decline. Although several evidences were found in normal aging changes of brain, it is not clearly integrated. Figuring out aging related changes in brain is important as aging is the process that everyone goes through, and comprehensive understanding may help to progress further studies. This review clarifies normal aging brain changes in an asymptotic and comprehensive manner, from a gross level to a microscopic and molecular level, and discusses potential approaches to seek the changes with cognitive decline.
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Affiliation(s)
- Jiseon Lee
- Department of Neurology, Hanyang University Hospital, Seoul, South Korea
| | - Hee-Jin Kim
- Department of Neurology, Hanyang University Hospital, Seoul, South Korea
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9
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Kaplow IM, Schäffer DE, Wirthlin ME, Lawler AJ, Brown AR, Kleyman M, Pfenning AR. Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin. BMC Genomics 2022; 23:291. [PMID: 35410163 PMCID: PMC8996547 DOI: 10.1186/s12864-022-08450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Evolutionary conservation is an invaluable tool for inferring functional significance in the genome, including regions that are crucial across many species and those that have undergone convergent evolution. Computational methods to test for sequence conservation are dominated by algorithms that examine the ability of one or more nucleotides to align across large evolutionary distances. While these nucleotide alignment-based approaches have proven powerful for protein-coding genes and some non-coding elements, they fail to capture conservation of many enhancers, distal regulatory elements that control spatial and temporal patterns of gene expression. The function of enhancers is governed by a complex, often tissue- and cell type-specific code that links combinations of transcription factor binding sites and other regulation-related sequence patterns to regulatory activity. Thus, function of orthologous enhancer regions can be conserved across large evolutionary distances, even when nucleotide turnover is high. RESULTS We present a new machine learning-based approach for evaluating enhancer conservation that leverages the combinatorial sequence code of enhancer activity rather than relying on the alignment of individual nucleotides. We first train a convolutional neural network model that can predict tissue-specific open chromatin, a proxy for enhancer activity, across mammals. Next, we apply that model to distinguish instances where the genome sequence would predict conserved function versus a loss of regulatory activity in that tissue. We present criteria for systematically evaluating model performance for this task and use them to demonstrate that our models accurately predict tissue-specific conservation and divergence in open chromatin between primate and rodent species, vastly out-performing leading nucleotide alignment-based approaches. We then apply our models to predict open chromatin at orthologs of brain and liver open chromatin regions across hundreds of mammals and find that brain enhancers associated with neuron activity have a stronger tendency than the general population to have predicted lineage-specific open chromatin. CONCLUSION The framework presented here provides a mechanism to annotate tissue-specific regulatory function across hundreds of genomes and to study enhancer evolution using predicted regulatory differences rather than nucleotide-level conservation measurements.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA. .,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.,Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Michael Kleyman
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA. .,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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10
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Gu J, Chen L, Sun R, Wang JL, Wang J, Lin Y, Lei S, Zhang Y, Lv D, Jiang F, Deng Y, Collman JP, Fu L. Plasmalogens Eliminate Aging-Associated Synaptic Defects and Microglia-Mediated Neuroinflammation in Mice. Front Mol Biosci 2022; 9:815320. [PMID: 35281262 PMCID: PMC8906368 DOI: 10.3389/fmolb.2022.815320] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/02/2022] [Indexed: 12/31/2022] Open
Abstract
Neurodegeneration is a pathological condition in which nervous system or neuron losses its structure, function, or both leading to progressive neural degeneration. Growing evidence strongly suggests that reduction of plasmalogens (Pls), one of the key brain lipids, might be associated with multiple neurodegenerative diseases, including Alzheimer’s disease (AD). Plasmalogens are abundant members of ether-phospholipids. Approximately 1 in 5 phospholipids are plasmalogens in human tissue where they are particularly enriched in brain, heart and immune cells. In this study, we employed a scheme of 2-months Pls intragastric administration to aged female C57BL/6J mice, starting at the age of 16 months old. Noticeably, the aged Pls-fed mice exhibited a better cognitive performance, thicker and glossier body hair in appearance than that of aged control mice. The transmission electron microscopic (TEM) data showed that 2-months Pls supplementations surprisingly alleviate age-associated hippocampal synaptic loss and also promote synaptogenesis and synaptic vesicles formation in aged murine brain. Further RNA-sequencing, immunoblotting and immunofluorescence analyses confirmed that plasmalogens remarkably enhanced both the synaptic plasticity and neurogenesis in aged murine hippocampus. In addition, we have demonstrated that Pls treatment inhibited the age-related microglia activation and attenuated the neuroinflammation in the murine brain. These findings suggest for the first time that Pls administration might be a potential intervention strategy for halting neurodegeneration and promoting neuroregeneration.
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Affiliation(s)
- Jinxin Gu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Lixue Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ran Sun
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Jie-Li Wang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Juntao Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yingjun Lin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shuwen Lei
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Lv
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Faqin Jiang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yuru Deng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - James P. Collman
- Department of Chemistry, Stanford University, Stanford, CA, United States
| | - Lei Fu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou, China
- *Correspondence: Lei Fu,
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11
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Wei Y, de Lange SC, Pijnenburg R, Scholtens LH, Ardesch DJ, Watanabe K, Posthuma D, van den Heuvel MP. Statistical testing in transcriptomic-neuroimaging studies: A how-to and evaluation of methods assessing spatial and gene specificity. Hum Brain Mapp 2021; 43:885-901. [PMID: 34862695 PMCID: PMC8764473 DOI: 10.1002/hbm.25711] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 11/14/2022] Open
Abstract
Multiscale integration of gene transcriptomic and neuroimaging data is becoming a widely used approach for exploring the molecular underpinnings of large‐scale brain organization in health and disease. Proper statistical evaluation of determined associations between imaging‐based phenotypic and transcriptomic data is key in these explorations, in particular to establish whether observed associations exceed “chance level” of random, nonspecific effects. Recent approaches have shown the importance of statistical models that can correct for spatial autocorrelation effects in the data to avoid inflation of reported statistics. Here, we discuss the need for examination of a second category of statistical models in transcriptomic‐neuroimaging analyses, namely those that can provide “gene specificity.” By means of a couple of simple examples of commonly performed transcriptomic‐neuroimaging analyses, we illustrate some of the potentials and challenges of transcriptomic‐imaging analyses, showing that providing gene specificity on observed transcriptomic‐neuroimaging effects is of high importance to avoid reports of nonspecific effects. Through means of simulations we show that the rate of reported nonspecific effects (i.e., effects that cannot be specifically linked to a specific gene or gene‐set) can run as high as 60%, with only less than 5% of transcriptomic‐neuroimaging associations observed through ordinary linear regression analyses showing both spatial and gene specificity. We provide a discussion, a tutorial, and an easy‐to‐use toolbox for the different options of null models in transcriptomic‐neuroimaging analyses.
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Affiliation(s)
- Yongbin Wei
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Siemon C de Lange
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Sleep and Cognition, Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Rory Pijnenburg
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lianne H Scholtens
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dirk Jan Ardesch
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Child and Adolescent Psychiatry and Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Child and Adolescent Psychiatry and Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
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12
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Where the genome meets the connectome: Understanding how genes shape human brain connectivity. Neuroimage 2021; 244:118570. [PMID: 34508898 DOI: 10.1016/j.neuroimage.2021.118570] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/10/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
The integration of modern neuroimaging methods with genetically informative designs and data can shed light on the molecular mechanisms underlying the structural and functional organization of the human connectome. Here, we review studies that have investigated the genetic basis of human brain network structure and function through three complementary frameworks: (1) the quantification of phenotypic heritability through classical twin designs; (2) the identification of specific DNA variants linked to phenotypic variation through association and related studies; and (3) the analysis of correlations between spatial variations in imaging phenotypes and gene expression profiles through the integration of neuroimaging and transcriptional atlas data. We consider the basic foundations, strengths, limitations, and discoveries associated with each approach. We present converging evidence to indicate that anatomical connectivity is under stronger genetic influence than functional connectivity and that genetic influences are not uniformly distributed throughout the brain, with phenotypic variation in certain regions and connections being under stronger genetic control than others. We also consider how the combination of imaging and genetics can be used to understand the ways in which genes may drive brain dysfunction in different clinical disorders.
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13
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Arnatkeviciute A, Fulcher BD, Bellgrove MA, Fornito A. Imaging Transcriptomics of Brain Disorders. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2021; 2:319-331. [PMID: 36324650 PMCID: PMC9616271 DOI: 10.1016/j.bpsgos.2021.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/05/2023] Open
Abstract
Noninvasive neuroimaging is a powerful tool for quantifying diverse aspects of brain structure and function in vivo, and it has been used extensively to map the neural changes associated with various brain disorders. However, most neuroimaging techniques offer only indirect measures of underlying pathological mechanisms. The recent development of anatomically comprehensive gene expression atlases has opened new opportunities for studying the transcriptional correlates of noninvasively measured neural phenotypes, offering a rich framework for evaluating pathophysiological hypotheses and putative mechanisms. Here, we provide an overview of some fundamental methods in imaging transcriptomics and outline their application to understanding brain disorders of neurodevelopment, adulthood, and neurodegeneration. Converging evidence indicates that spatial variations in gene expression are linked to normative changes in brain structure during age-related maturation and neurodegeneration that are in part associated with cell-specific gene expression markers of gene expression. Transcriptional correlates of disorder-related neuroimaging phenotypes are also linked to transcriptionally dysregulated genes identified in ex vivo analyses of patient brains. Modeling studies demonstrate that spatial patterns of gene expression are involved in regional vulnerability to neurodegeneration and the spread of disease across the brain. This growing body of work supports the utility of transcriptional atlases in testing hypotheses about the molecular mechanism driving disease-related changes in macroscopic neuroimaging phenotypes.
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Affiliation(s)
- Aurina Arnatkeviciute
- Turner Institute for Brain and Mental Health, School of Psychological Science, Monash University, Melbourne, Victoria, Australia
- Address correspondence to Aurina Arnatkeviciute, Ph.D
| | - Ben D. Fulcher
- School of Physics, The University of Sydney, Camperdown, New South Wales, Australia
| | - Mark A. Bellgrove
- Turner Institute for Brain and Mental Health, School of Psychological Science, Monash University, Melbourne, Victoria, Australia
| | - Alex Fornito
- Turner Institute for Brain and Mental Health, School of Psychological Science, Monash University, Melbourne, Victoria, Australia
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14
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Szczurek-Janicka P, Ropka-Molik K, Oczkowicz M, Orczewska-Dudek S, Pietras M, Pieszka M. Expression Profile of Brain Aging and Metabolic Function are Altered by Resveratrol or α-Ketoglutarate Supplementation in Rats Fed a High-Fat Diet. POL J FOOD NUTR SCI 2021. [DOI: 10.31883/pjfns/139081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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15
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Oyefeso FA, Muotri AR, Wilson CG, Pecaut MJ. Brain organoids: A promising model to assess oxidative stress-induced central nervous system damage. Dev Neurobiol 2021; 81:653-670. [PMID: 33942547 DOI: 10.1002/dneu.22828] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/13/2022]
Abstract
Oxidative stress (OS) is one of the most significant propagators of systemic damage with implications for widespread pathologies such as vascular disease, accelerated aging, degenerative disease, inflammation, and traumatic injury. OS can be induced by numerous factors such as environmental conditions, lifestyle choices, disease states, and genetic susceptibility. It is tied to the accumulation of free radicals, mitochondrial dysfunction, and insufficient antioxidant protection, which leads to cell aging and tissue degeneration over time. Unregulated systemic increase in reactive species, which contain harmful free radicals, can lead to diverse tissue-specific OS responses and disease. Studies of OS in the brain, for example, have demonstrated how this state contributes to neurodegeneration and altered neural plasticity. As the worldwide life expectancy has increased over the last few decades, the prevalence of OS-related diseases resulting from age-associated progressive tissue degeneration. Unfortunately, vital translational research studies designed to identify and target disease biomarkers in human patients have been impeded by many factors (e.g., limited access to human brain tissue for research purposes and poor translation of experimental models). In recent years, stem cell-derived three-dimensional tissue cultures known as "brain organoids" have taken the spotlight as a novel model for studying central nervous system (CNS) diseases. In this review, we discuss the potential of brain organoids to model the responses of human neural cells to OS, noting current and prospective limitations. Overall, brain organoids show promise as an innovative translational model to study CNS susceptibility to OS and elucidate the pathophysiology of the aging brain.
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Affiliation(s)
- Foluwasomi A Oyefeso
- Department of Biomedical Engineering Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Alysson R Muotri
- Department of Pediatrics/Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Christopher G Wilson
- Lawrence D. Longo, MD, Center for Perinatal Biology, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Michael J Pecaut
- Department of Biomedical Engineering Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
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16
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Hedderich DM, Menegaux A, Schmitz-Koep B, Nuttall R, Zimmermann J, Schneider SC, Bäuml JG, Daamen M, Boecker H, Wilke M, Zimmer C, Wolke D, Bartmann P, Sorg C, Gaser C. Increased Brain Age Gap Estimate (BrainAGE) in Young Adults After Premature Birth. Front Aging Neurosci 2021; 13:653365. [PMID: 33867970 PMCID: PMC8047054 DOI: 10.3389/fnagi.2021.653365] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
Recent evidence suggests increased metabolic and physiologic aging rates in premature-born adults. While the lasting consequences of premature birth on human brain development are known, its impact on brain aging remains unclear. We addressed the question of whether premature birth impacts brain age gap estimates (BrainAGE) using an accurate and robust machine-learning framework based on structural MRI in a large cohort of young premature-born adults (n = 101) and full-term (FT) controls (n = 111). Study participants are part of a geographically defined population study of premature-born individuals, which have been followed longitudinally from birth until young adulthood. We investigated the association between BrainAGE scores and perinatal variables as well as with outcomes of physical (total intracranial volume, TIV) and cognitive development (full-scale IQ, FS-IQ). We found increased BrainAGE in premature-born adults [median (interquartile range) = 1.4 (-1.3-4.7 years)] compared to full-term controls (p = 0.002, Cohen's d = 0.443), which was associated with low Gestational age (GA), low birth weight (BW), and increased neonatal treatment intensity but not with TIV or FS-IQ. In conclusion, results demonstrate elevated BrainAGE in premature-born adults, suggesting an increased risk for accelerated brain aging in human prematurity.
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Affiliation(s)
- Dennis M. Hedderich
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Aurore Menegaux
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Benita Schmitz-Koep
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Rachel Nuttall
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Anesthesiology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Juliana Zimmermann
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian C. Schneider
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Josef G. Bäuml
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Marcel Daamen
- Functional Neuroimaging Group, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Bonn, Germany
- Department of Neonatology, University Hospital Bonn, Venusberg-Campus, Bonn, Germany
| | - Henning Boecker
- Functional Neuroimaging Group, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Bonn, Germany
| | - Marko Wilke
- Department of Pediatric Neurology and Developmental Medicine and Experimental Pediatric Neuroimaging group, University of Tübingen, Tübingen, Germany
| | - Claus Zimmer
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dieter Wolke
- Department of Psychology, University of Warwick, Coventry, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Peter Bartmann
- Department of Neonatology, University Hospital Bonn, Venusberg-Campus, Bonn, Germany
| | - Christian Sorg
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
- TUM-NIC Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Psychiatry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Gaser
- Department of Psychiatry, University Hospital Jena, Jena, Germany
- Department of Neurology, University Hospital Jena, Jena, Germany
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17
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Wang F, Yang J, Lin H, Li Q, Ye Z, Lu Q, Chen L, Tu Z, Tian G. Improved Human Age Prediction by Using Gene Expression Profiles From Multiple Tissues. Front Genet 2020; 11:1025. [PMID: 33101366 PMCID: PMC7546819 DOI: 10.3389/fgene.2020.01025] [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: 06/25/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022] Open
Abstract
Studying transcriptome chronological change from tissues across the whole body can provide valuable information for understanding aging and longevity. Although there has been research on the effect of single-tissue transcriptomes on human aging or aging in mice across multiple tissues, the study of human body-wide multi-tissue transcriptomes on aging is not yet available. In this study, we propose a quantitative model to predict human age by using gene expression data from 46 tissues generated by the Genotype-Tissue Expression (GTEx) project. Specifically, the biological age of a person is first predicted via the gene expression profile of a single tissue. Then, we combine the gene expression profiles from two tissues and compare the predictive accuracy between single and two tissues. The best performance as measured by the root-mean-square error is 3.92 years for single tissue (pituitary), which deceased to 3.6 years when we combined two tissues (pituitary and muscle) together. Different tissues have different potential in predicting chronological age. The prediction accuracy is improved by combining multiple tissues, supporting that aging is a systemic process involving multiple tissues across the human body.
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Affiliation(s)
- Fayou Wang
- School of Computer and Data Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, China.,Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institute of Life Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jialiang Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Geneis Beijing Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Huixin Lin
- Geneis Beijing Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Qian Li
- Geneis Beijing Co., Ltd., Beijing, China.,Reproductive Center, Northwest Women and Children's Hospital, Xi'an, China
| | - Zixuan Ye
- Geneis Beijing Co., Ltd., Beijing, China
| | - Qingqing Lu
- Geneis Beijing Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institute of Life Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhidong Tu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Geng Tian
- Geneis Beijing Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
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18
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Handl L, Jalali A, Scherer M, Eggeling R, Pfeifer N. Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data. Bioinformatics 2020; 35:i154-i163. [PMID: 31510704 PMCID: PMC6612879 DOI: 10.1093/bioinformatics/btz338] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION Predictive models are a powerful tool for solving complex problems in computational biology. They are typically designed to predict or classify data coming from the same unknown distribution as the training data. In many real-world settings, however, uncontrolled biological or technical factors can lead to a distribution mismatch between datasets acquired at different times, causing model performance to deteriorate on new data. A common additional obstacle in computational biology is scarce data with many more features than samples. To address these problems, we propose a method for unsupervised domain adaptation that is based on a weighted elastic net. The key idea of our approach is to compare dependencies between inputs in training and test data and to increase the cost of differently behaving features in the elastic net regularization term. In doing so, we encourage the model to assign a higher importance to features that are robust and behave similarly across domains. RESULTS We evaluate our method both on simulated data with varying degrees of distribution mismatch and on real data, considering the problem of age prediction based on DNA methylation data across multiple tissues. Compared with a non-adaptive standard model, our approach substantially reduces errors on samples with a mismatched distribution. On real data, we achieve far lower errors on cerebellum samples, a tissue which is not part of the training data and poorly predicted by standard models. Our results demonstrate that unsupervised domain adaptation is possible for applications in computational biology, even with many more features than samples. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/PfeiferLabTue/wenda. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lisa Handl
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.,Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Biomedical Informatics, University of Tübingen, Tübingen, Germany
| | - Adrin Jalali
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Michael Scherer
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Ralf Eggeling
- Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Biomedical Informatics, University of Tübingen, Tübingen, Germany
| | - Nico Pfeifer
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.,Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Biomedical Informatics, University of Tübingen, Tübingen, Germany
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19
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Liang KJ, Carlson ES. Resistance, vulnerability and resilience: A review of the cognitive cerebellum in aging and neurodegenerative diseases. Neurobiol Learn Mem 2020; 170:106981. [PMID: 30630042 PMCID: PMC6612482 DOI: 10.1016/j.nlm.2019.01.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/14/2018] [Accepted: 01/03/2019] [Indexed: 12/12/2022]
Abstract
In the context of neurodegeneration and aging, the cerebellum is an enigma. Genetic markers of cellular aging in cerebellum accumulate more slowly than in the rest of the brain, and it generates unknown factors that may slow or even reverse neurodegenerative pathology in animal models of Alzheimer's Disease (AD). Cerebellum shows increased activity in early AD and Parkinson's disease (PD), suggesting a compensatory function that may mitigate early symptoms of neurodegenerative pathophysiology. Perhaps most notably, different parts of the brain accumulate neuropathological markers of AD in a recognized progression and generally, cerebellum is the last brain region to do so. Taken together, these data suggest that cerebellum may be resistant to certain neurodegenerative mechanisms. On the other hand, in some contexts of accelerated neurodegeneration, such as that seen in chronic traumatic encephalopathy (CTE) following repeated traumatic brain injury (TBI), the cerebellum appears to be one of the most susceptible brain regions to injury and one of the first to exhibit signs of pathology. Cerebellar pathology in neurodegenerative disorders is strongly associated with cognitive dysfunction. In neurodegenerative or neurological disorders associated with cerebellar pathology, such as spinocerebellar ataxia, cerebellar cortical atrophy, and essential tremor, rates of cognitive dysfunction, dementia and neuropsychiatric symptoms increase. When the cerebellum shows AD pathology, such as in familial AD, it is associated with earlier onset and greater severity of disease. These data suggest that when neurodegenerative processes are active in the cerebellum, it may contribute to pathological behavioral outcomes. The cerebellum is well known for comparing internal representations of information with observed outcomes and providing real-time feedback to cortical regions, a critical function that is disturbed in neuropsychiatric disorders such as intellectual disability, schizophrenia, dementia, and autism, and required for cognitive domains such as working memory. While cerebellum has reciprocal connections with non-motor brain regions and likely plays a role in complex, goal-directed behaviors, it has proven difficult to establish what it does mechanistically to modulate these behaviors. Due to this lack of understanding, it's not surprising to see the cerebellum reflexively dismissed or even ignored in basic and translational neuropsychiatric literature. The overarching goals of this review are to answer the following questions from primary literature: When the cerebellum is affected by pathology, is it associated with decreased cognitive function? When it is intact, does it play a compensatory or protective role in maintaining cognitive function? Are there theoretical frameworks for understanding the role of cerebellum in cognition, and perhaps, illnesses characterized by cognitive dysfunction? Understanding the role of the cognitive cerebellum in neurodegenerative diseases has the potential to offer insight into origins of cognitive deficits in other neuropsychiatric disorders, which are often underappreciated, poorly understood, and not often treated.
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Affiliation(s)
- Katharine J Liang
- University of Washington School of Medicine, Department of Psychiatry and Behavioral Sciences, Seattle, WA, United States
| | - Erik S Carlson
- University of Washington School of Medicine, Seattle, WA, United States.
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20
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Oxidative Stress, Frailty and Cardiovascular Diseases: Current Evidence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1216:65-77. [PMID: 31894548 DOI: 10.1007/978-3-030-33330-0_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The aim of this chapter is to review the results of recent studies analyzing the role of oxidative stress and systemic inflammation as potential contributors to frailty and CVD, and to explain a possible pathogenic relationship between the latter two conditions. Available evidence suggests that frail patients have elevated levels of oxidative stress biomarkers and proinflammatory cytokines, as well as with reduced concentrations of endogenous antioxidants. This implies that oxidative stress and systemic inflammation might play a role in the pathogenesis of frailty, but an underlying mechanism of this relationship is still mostly hypothetical. Oxidative stress and systemic inflammation are also involved in the pathogenesis of CVD. Cardiovascular conditions are established risk factor for frailty and in turn, presence of frailty constitutes an unfavorable prognostic factor in cardiac patients. Finally, some cardiovascular risk factors, such as lack of physical activity, smoking, obesity and inappropriate diet, are also involved in the etiology of oxidative stress, chronic inflammation and frailty. This complex interplay between intrinsic and extrinsic elements should be considered during holistic management of older persons with frailty and/or cardiovascular conditions.
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21
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Li ML, Wu SH, Zhang JJ, Tian HY, Shao Y, Wang ZB, Irwin DM, Li JL, Hu XT, Wu DD. 547 transcriptomes from 44 brain areas reveal features of the aging brain in non-human primates. Genome Biol 2019; 20:258. [PMID: 31779658 PMCID: PMC6883628 DOI: 10.1186/s13059-019-1866-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Brain aging is a complex process that depends on the precise regulation of multiple brain regions; however, the underlying molecular mechanisms behind this process remain to be clarified in non-human primates. RESULTS Here, we explore non-human primate brain aging using 547 transcriptomes originating from 44 brain areas in rhesus macaques (Macaca mulatta). We show that expression connectivity between pairs of cerebral cortex areas as well as expression symmetry between the left and right hemispheres both decrease after aging. Although the aging mechanisms across different brain areas are largely convergent, changes in gene expression and alternative splicing vary at diverse genes, reinforcing the complex multifactorial basis of aging. Through gene co-expression network analysis, we identify nine modules that exhibit gain of connectivity in the aged brain and uncovered a hub gene, PGLS, underlying brain aging. We further confirm the functional significance of PGLS in mice at the gene transcription, molecular, and behavioral levels. CONCLUSIONS Taken together, our study provides comprehensive transcriptomes on multiple brain regions in non-human primates and provides novel insights into the molecular mechanism of healthy brain aging.
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Affiliation(s)
- Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Shi-Hao Wu
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Hang-Yu Tian
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zheng-Bo Wang
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jia-Li Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Xin-Tian Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
- National Research Facility for Phenotypic and Genetic Analysis of Model Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- National Research Facility for Phenotypic and Genetic Analysis of Model Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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22
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Chrzan R, Gleń A, Bryll A, Urbanik A. Computed Tomography Assessment of Brain Atrophy in Centenarians. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16193659. [PMID: 31569457 PMCID: PMC6801833 DOI: 10.3390/ijerph16193659] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/08/2019] [Accepted: 09/20/2019] [Indexed: 11/30/2022]
Abstract
The aim of our study was to compare the degree of brain atrophy in centenarians and in seniors 70–99 years old. The study group consisted of 23 patients aged 100–106 years. The control group consisted of 90 patients, 30 in each age subgroup 90–99, 80–89, 70–79. In all the patients, the brain atrophy linear parameters were measured on computed tomography scans, in relation to both “subcortical atrophy”, evaluated as progressive widening of the ventricular system, and “cortical atrophy”, defined as widening of subarachnoid space. Secondary indices based on the parameters were calculated. Correlations between the above parameters/indices and age were tested. Significantly different values between the centenarians and the control group were found in the brain atrophy parameters: A, B, C, E, FI, ICR, ICL, SW, CFW, F/A ‘frontal horn index’, A/G ‘Evans index’, D/A ‘ventricular index’, H/E ‘cella media Schiersmann index’, A+B ‘Huckman number’. Correlations between parameter/index and age were found for: A, B, C, FI, ICR, ICL, SW, F/A ‘frontal horn index’, A/G ‘Evans index’, D/A ‘ventricular index’, H/E ‘cella media Schiersmann index’, A+B ‘Huckman number’. Brain atrophy associated with aging is a continuously advancing process, affecting centenarians even more than people before the “magic” threshold of 100 years.
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Affiliation(s)
- Robert Chrzan
- Department of Radiology, Jagiellonian University Medical College, Kopernika 19, 31-501 Krakow, Poland.
| | - Agnieszka Gleń
- Department of Radiology, Jagiellonian University Medical College, Kopernika 19, 31-501 Krakow, Poland.
| | - Amira Bryll
- Department of Radiology, Jagiellonian University Medical College, Kopernika 19, 31-501 Krakow, Poland.
| | - Andrzej Urbanik
- Department of Radiology, Jagiellonian University Medical College, Kopernika 19, 31-501 Krakow, Poland.
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Writers and Readers of DNA Methylation/Hydroxymethylation in Physiological Aging and Its Impact on Cognitive Function. Neural Plast 2019; 2019:5982625. [PMID: 31396272 PMCID: PMC6664507 DOI: 10.1155/2019/5982625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/25/2019] [Accepted: 05/26/2019] [Indexed: 12/31/2022] Open
Abstract
The chromatin landscape has acquired deep attention from several fields ranging from cell biology to neurological and psychiatric diseases. The role that DNA modifications have on gene expression regulation has become apparent in several physiological processes, and numerous efforts have been performed to establish a relationship between DNA modifications and physiological conditions, such as cognitive performance and aging. DNA modifications are incorporated by specific sets of enzymes-the writers-and the modified DNA-interacting partners-the readers-are ultimately responsible for maintaining a functional epigenetic landscape. Therefore, understanding how these epigenetic mediators-writers and readers-are modulated in physiological aging will contribute to unraveling how aging-associated neuronal disturbances arise and contribute to the cognitive decline associated with this period of life. In this review, we focused on DNA modifications, writers and readers, highlighting that despite some methodological disparities, the evidence suggests a critical role for epigenetic mediators in the aging-associated neuronal dysfunction.
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Thubron EB, Rosa HS, Hodges A, Sivaprasad S, Francis PT, Pienaar IS, Malik AN. Regional mitochondrial DNA and cell-type changes in post-mortem brains of non-diabetic Alzheimer's disease are not present in diabetic Alzheimer's disease. Sci Rep 2019; 9:11386. [PMID: 31388037 PMCID: PMC6684616 DOI: 10.1038/s41598-019-47783-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/09/2019] [Indexed: 12/26/2022] Open
Abstract
Diabetes increases the risk of Alzheimer's disease (AD), and mitochondrial dysfunction is implicated in both diseases, however the impact of both diabetes and AD on brain mitochondria is not known. We measured mitochondrial DNA (mtDNA), an indicator of mitochondrial function, in frontal, parietal, and cerebellar regions of post-mortem human brains (n = 74) from non-cognitively impaired controls (NCI), mild-cognitively impaired (MCI) and AD cases. In a subset of parietal cortices, we measured mRNAs corresponding to cell types and mitochondrial function and semi-automated stereological assessment was performed on immune-staining of parietal cortex sections. mtDNA showed significant regional variation, highest in parietal cortex, and lowest in cerebellum. Irrespective of cognitive status, all brain regions had significantly higher mtDNA in diabetic cases. In the absence of diabetes, AD parietal cortices had decreased mtDNA, reduced MAP2 (neuronal) and increased GFAP (astrocyte) mRNA, relative to NCI. However, in the presence of diabetes, we did not observe these AD-related changes, suggesting that the pathology observed in diabetic AD may be different to that seen in non-diabetic AD. The lack of clear functional changes in mitochondrial parameters in diabetic AD suggest different cellular mechanisms contributing to cognitive impairment in diabetes which remain to be fully understood.
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Affiliation(s)
- Elisabeth B Thubron
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Hannah S Rosa
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Angela Hodges
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Paul T Francis
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Ilse S Pienaar
- School of Life Sciences, University of Sussex, Falmer, BN1 9PH, UK
| | - Afshan N Malik
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.
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Lubec J, Smidak R, Malikovic J, Feyissa DD, Korz V, Höger H, Lubec G. Dentate Gyrus Peroxiredoxin 6 Levels Discriminate Aged Unimpaired From Impaired Rats in a Spatial Memory Task. Front Aging Neurosci 2019; 11:198. [PMID: 31417400 PMCID: PMC6684764 DOI: 10.3389/fnagi.2019.00198] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/16/2019] [Indexed: 12/29/2022] Open
Abstract
Similar to humans, the normal aged rat population is not homogeneous in terms of cognitive function. Two distinct subpopulations of aged Sprague-Dawley rats can be identified on the basis of spatial memory performance in the hole-board paradigm. It was the aim of the study to reveal protein changes relevant to aging and spatial memory performance. Aged impaired (AI) and unimpaired (AU) male rats, 22-24 months old were selected from a large cohort of 160 animals; young animals served as control. Enriched synaptosomal fractions from dentate gyrus from behaviorally characterized old animals were used for isobaric tags labeling based quantitative proteomic analysis. As differences in peroxiredoxin 6 (PRDX6) levels were a pronounced finding, PRDX6 levels were also quantified by immunoblotting. AI showed impaired spatial memory abilities while AU performed comparably to young animals. Our study demonstrates substantial quantitative alteration of proteins involved in energy metabolism, inflammation and synaptic plasticity during aging. Moreover, we identified protein changes specifically coupled to memory performance of aged rats. PRDX6 levels clearly differentiated AI from AU and levels in AU were comparable to those of young animals. In addition, it was observed that stochasticity in protein levels increased with age and discriminate between AI and AU groups. Moreover, there was a significantly higher variability of protein levels in AI. PRDX6 is a member of the PRDX family and well-defined as a cystein-1 PRDX that reduces and detoxifies hydroxyperoxides. It is well-known and documented that the aging brain shows increased active oxygen species but so far no study proposed a potential target with antioxidant activity that would discriminate between impaired and unimpaired memory performers. Current data, representing so far the largest proteomics data set in aging dentate gyrus (DG), provide the first evidence for a probable role of PRDX6 in memory performance.
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Affiliation(s)
- Jana Lubec
- Department of Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
| | - Roman Smidak
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Jovana Malikovic
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Himberg, Austria
| | - Daniel Daba Feyissa
- Department of Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
| | - Volker Korz
- Department of Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
| | - Harald Höger
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Himberg, Austria
| | - Gert Lubec
- Department of Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
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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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Cui B, Huang X, Li S, Hao K, Chang BH, Tu X, Pang B, Zhang Z. Quercetin Affects the Growth and Development of the Grasshopper Oedaleus asiaticus (Orthoptera: Acrididae). JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:1175-1182. [PMID: 30916750 DOI: 10.1093/jee/toz050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Indexed: 06/09/2023]
Abstract
Flavonoids are secondary metabolites that help plants resist insect attack, but pest insects have evolved enzymes that reduce the toxicity of these secondary metabolites. We studied the response of the grasshopper Oedaleus asiaticus Bey-Bienko fed different concentrations of quercetin, a representative flavonoid. Oedaleus asiaticus growth (survival rate and growth rate) was significantly reduced at high quercetin concentrations. Reactive oxygen species (ROS) increased significantly in response to the diet stress associated with high quercetin concentrations. Gene expression and protein phosphorylation level of the IGF→FOXO cascade related to the stress response in the O. asiaticus insulin-like signaling pathway (ILP) were also reduced. Multiple protective enzyme activities were regulated by FOXO. Mixed-function oxidase (MFO), superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were all significantly increased with exposure to high quercetin concentrations. Quercetin negatively regulated the ILP pathway, and was detrimental to O. asiaticus growth and survival, as more energy was required for detoxification. This study showed how flavonoids impact on O. asiaticus biochemical pathways, physiology, and development. Flavonoids offer a new option for the development of biological pesticides for application to grasshopper biological control.
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Affiliation(s)
- Boyang Cui
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in XilinGol Rangeland, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Xilinhot, China
- Research Center for Grassland Entomology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xunbing Huang
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Shuang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in XilinGol Rangeland, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Xilinhot, China
| | - Kun Hao
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in XilinGol Rangeland, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Xilinhot, China
| | - Babar Hussain Chang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in XilinGol Rangeland, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Xilinhot, China
| | - Xiongbing Tu
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in XilinGol Rangeland, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Xilinhot, China
| | - Baoping Pang
- Research Center for Grassland Entomology, Inner Mongolia Agricultural University, Hohhot, China
| | - Zehua Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in XilinGol Rangeland, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Xilinhot, China
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Chang BH, Cui B, Ullah H, Li S, Hao K, Tu X, Wang G, Nong X, McNeill MR, Huang X, Zhang Z. Role of PTP/PTK trans activated insulin-like signalling pathway in regulation of grasshopper (Oedaleus asiaticus) development. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:8312-8324. [PMID: 30706274 DOI: 10.1007/s11356-019-04212-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Protein tyrosine phosphatase (PTPs) and protein tyrosine kinase (PTKs) genes are responsible for the regulation of insect insulin-like pathway (ILP), cells growth, metabolism initiation, gene transcription and observing immune response. Signal transduction in insect cell is also associated with PTPs and PTKs. The grasshopper (Oedaleus asiaticus) 'Bey-Bienko' were treated with dsRNA of protein tyrosine non-receptor type 4 (PTPN4) and protein tyrosine kinase 5 (PTK5) along with control (water). Applying dsPTK5 treatments in 5th instar of Oedaleus asiaticus, significant reduction was recorded in body dry mass, growth rate and overall performance except survival rate. Whereas with PTPN4, no such significant impact on all of these growth parameters was recorded. Expression of genes in ILP 5th instar of Oedaleus asiaticus by the application of dsPTPN4 and dsPTK5 revealed that PTK, INSR (insulin receptor), IRS (insulin receptor substrate), PI3K (phosphoinositide 3-kinase), PDK (3-phosphoinositide-dependent protein kinase), Akt (protein kinase B) and FOXO (forkhead transcription factor) significantly expressed with downregulation except PTPN4, which remained non-significant. On the other hand, the phosphorylation level of ILP four proteins in O. asiaticus with the treatment of dsPTPN4 and dsPTK5 significantly affected P-IRS and P-FOXO, while P-INSR and P-AKT remained stable at the probability level of 5%. This indicated that the stress response in the O. asiaticus insulin-like signalling pathway (ILP) reduced. Regarding association of protective enzymatic activities, ROS (relative oxygen species), CAT (catalase) and PO (phenol oxidase) increased significantly with exposure to dsPTK5 as compared to dsPTPN4 and control, while exposure of 5th instar of O. asiaticus to dsPTPN4 treatment slightly raised CAT and PO activities with but significant contribution. No such significant effect on MFO and POD was seen using dsPTPN4 and dsPTK5. This showed that in the ILP of O. asiaticus, PTK5 was detrimental to growth, body mass and overall performance, which ultimately benefited insect detoxification with high-energy cost.
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Affiliation(s)
- Babar Hussain Chang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | - Boyang Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | - Hidayat Ullah
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | - Shuang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | - Kun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | - Xiongbing Tu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | - Guangjun Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | - Xiangqun Nong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | | | - Xunbing Huang
- College of Agriculture and Forestry Science, Linyi University, Linyi, China.
| | - Zehua Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China.
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China.
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29
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Chen J, Zou Q, Lv D, Raza MA, Wang X, Li P, Chen Y, Xi X, Wen A, Zhu L, Tang G, Li M, Li X, Jiang Y. Comprehensive transcriptional profiling of porcine brain aging. Gene 2019; 693:1-9. [PMID: 30695714 DOI: 10.1016/j.gene.2019.01.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/27/2018] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
Abstract
The brain as an important organ can be affected largely by aging, and the comprehensive transcriptional underpinnings of brain aging remain poorly understood. Here, we performed a high throughput RNA sequencing to evaluate the expression profiles of messenger RNA (mRNA), long non-coding RNAs (lncRNAs), micro RNAs (miRNAs), and circular RNAs (circRNAs) in porcine brain. We have identified 714 mRNAs, 38lncRNAs, 41miRNAs, and 148circRNAs were age-related genes in the porcine cerebral cortex. The lncRNAs, miRNAs and circRNAs have effect on the age of porcine brain due to the much changes of expression level as noncoding RNAs. The up-regulated genes were significantly enriched for stress response, reproductive regulatory process, immune response and metabolic process, and the down-regulated genes were related to neurologic function, stress response and signaling pathway. The synaptic transmission pathway may be the key role in aging of porcine brain that it was co-enriched for in both differentially expressed mRNAs and lncRNAs. Moreover, some lncRNAs and their target genes were also differentially expressed during brain aging. We further assessed the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks during brain aging. We also selected 2 mRNAs, 2 lncRNAs, 2 miRNAs, and 1 circRNAs to perform the q-PCR, and the expression patterns were highly consistent between the two methods confirming the high reproducibility and reliability of the gene expression profiling in our study. In conclusion, our findings will contribute to understand the transcriptional underpinnings of brain aging and provide a foundation for future studies on the molecular mechanisms underlying brain aging.
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Affiliation(s)
- Jianning Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Daojun Lv
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd., Chengdu, Sichuan 611130, China
| | - Muhammad Ali Raza
- Department of Crop Cultivation and Farming System, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xue Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Peilin Li
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd., Chengdu, Sichuan 611130, China
| | - Yan Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xiaoyu Xi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Anxiang Wen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China.
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30
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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: 323] [Impact Index Per Article: 64.6] [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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Zhang H, Lin S, Chen X, Gu L, Zhu X, Zhang Y, Reyes K, Wang B, Jin K. The effect of age, sex and strains on the performance and outcome in animal models of stroke. Neurochem Int 2018; 127:2-11. [PMID: 30291954 DOI: 10.1016/j.neuint.2018.10.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/26/2022]
Abstract
Stroke is one of the leading causes of death worldwide, and the majority of cerebral stroke is caused by occlusion of cerebral circulation, which eventually leads to brain infarction. Although stroke occurs mainly in the aged population, most animal models for experimental stroke in vivo almost universally rely on young-adult rodents for the evaluation of neuropathological, neurological, or behavioral outcomes after stroke due to their greater availability, lower cost, and fewer health problems. However, it is well established that aged animals differ from young animals in terms of physiology, neurochemistry, and behavior. Stroke-induced changes are more pronounced with advancing age. Therefore, the overlooked role of age in animal models of stroke could have an impact on data quality and hinder the translation of rodent models to humans. In addition to aging, other factors also influence functional performance after ischemic stroke. In this article, we summarize the differences between young and aged animals, the impact of age, sex and animal strains on performance and outcome in animal models of stroke and emphasize age as a key factor in preclinical stroke studies.
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Affiliation(s)
- Hongxia Zhang
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Siyang Lin
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Xudong Chen
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Lei Gu
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Xiaohong Zhu
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yinuo Zhang
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Kassandra Reyes
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Brian Wang
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Kunlin Jin
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
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32
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Chappell S, Patel T, Guetta-Baranes T, Sang F, Francis PT, Morgan K, Brookes KJ. Observations of extensive gene expression differences in the cerebellum and potential relevance to Alzheimer's disease. BMC Res Notes 2018; 11:646. [PMID: 30180886 PMCID: PMC6123947 DOI: 10.1186/s13104-018-3732-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/24/2018] [Indexed: 12/15/2022] Open
Abstract
Objectives In order to determine how gene expression is altered in disease it is of fundamental importance that the global distribution of gene expression levels across the disease-free brain are understood and how differences between tissue types might inform tissue choice for investigation of altered expression in disease state. The aim of this pilot project was to use RNA-sequencing to investigate gene expression differences between five general areas of post-mortem human brain (frontal, temporal, occipital, parietal and cerebellum), and in particular changes in gene expression in the cerebellum compared to cortex regions for genes relevant to Alzheimer’s disease, as the cerebellum is largely preserved from disease pathology and could be an area of interest for neuroprotective pathways. Results General gene expression profiles were found to be similar between cortical regions of the brain, however the cerebellum presented a distinct expression profile. Focused exploration of gene expression for genes associated with Alzheimer’s disease suggest that those involved in the immunity pathway show little expression in the brain. Furthermore some Alzheimer’s disease associated genes display significantly different expression in the cerebellum compared with other brain regions, which might indicate potential neuroprotective measures.
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Affiliation(s)
- Sally Chappell
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Tulsi Patel
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Tamar Guetta-Baranes
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Fei Sang
- DeepSeq Facility, University of Nottingham, Nottingham, UK
| | - Paul T Francis
- Wolfson Centre for Age Related Diseases, King's College London, London, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Keeley J Brookes
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK.
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Kelley KW, Nakao-Inoue H, Molofsky AV, Oldham MC. Variation among intact tissue samples reveals the core transcriptional features of human CNS cell classes. Nat Neurosci 2018; 21:1171-1184. [PMID: 30154505 PMCID: PMC6192711 DOI: 10.1038/s41593-018-0216-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/10/2018] [Indexed: 02/08/2023]
Abstract
It is widely assumed that cells must be physically isolated to study their molecular profiles. However, intact tissue samples naturally exhibit variation in cellular composition, which drives covariation of cell-class-specific molecular features. By analyzing transcriptional covariation in 7,221 intact CNS samples from 840 neurotypical individuals, representing billions of cells, we reveal the core transcriptional identities of major CNS cell classes in humans. By modeling intact CNS transcriptomes as a function of variation in cellular composition, we identify cell-class-specific transcriptional differences in Alzheimer's disease, among brain regions, and between species. Among these, we show that PMP2 is expressed by human but not mouse astrocytes and significantly increases mouse astrocyte size upon ectopic expression in vivo, causing them to more closely resemble their human counterparts. Our work is available as an online resource ( http://oldhamlab.ctec.ucsf.edu/ ) and provides a generalizable strategy for determining the core molecular features of cellular identity in intact biological systems.
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Affiliation(s)
- Kevin W Kelley
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California at San Francisco, San Francisco, CA, USA
| | - Hiromi Nakao-Inoue
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
| | - Anna V Molofsky
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
| | - Michael C Oldham
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.
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Li X, Li W, Xu Y. Human Age Prediction Based on DNA Methylation Using a Gradient Boosting Regressor. Genes (Basel) 2018; 9:genes9090424. [PMID: 30134623 PMCID: PMC6162650 DOI: 10.3390/genes9090424] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 01/12/2023] Open
Abstract
All tissues of organisms will become old as time goes on. In recent years, epigenetic investigations have found that there is a close correlation between DNA methylation and aging. With the development of DNA methylation research, a quantitative statistical relationship between DNA methylation and different ages was established based on the change rule of methylation with age, it is then possible to predict the age of individuals. All the data in this work were retrieved from the Illumina HumanMethylation BeadChip platform (27K or 450K). We analyzed 16 sets of healthy samples and 9 sets of diseased samples. The healthy samples included a total of 1899 publicly available blood samples (0–103 years old) and the diseased samples included 2395 blood samples. Six age-related CpG sites were selected through calculating Pearson correlation coefficients between age and DNA methylation values. We built a gradient boosting regressor model for these age-related CpG sites. 70% of the data was randomly selected as training data and the other 30% as independent data in each dataset for 25 runs in total. In the training dataset, the healthy samples showed that the correlation between predicted age and DNA methylation was 0.97, and the mean absolute deviation (MAD) was 2.72 years. In the independent dataset, the MAD was 4.06 years. The proposed model was further tested using the diseased samples. The MAD was 5.44 years for the training dataset and 7.08 years for the independent dataset. Furthermore, our model worked well when it was applied to saliva samples. These results illustrated that the age prediction based on six DNA methylation markers is very effective using the gradient boosting regressor.
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Affiliation(s)
- Xingyan Li
- Department of Information and Computer Science, University of Science and Technology Beijing, Beijing 100083, China.
| | - Weidong Li
- Department of Information and Computer Science, University of Science and Technology Beijing, Beijing 100083, China.
| | - Yan Xu
- Department of Information and Computer Science, University of Science and Technology Beijing, Beijing 100083, China.
- Beijing Key Laboratory for Magneto-photoelectrical Composites and Interface Science, University of Science and Technology Beijing, Beijing 100083, China.
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Age-related gene expression in luminal epithelial cells is driven by a microenvironment made from myoepithelial cells. Aging (Albany NY) 2018; 9:2026-2051. [PMID: 29016359 PMCID: PMC5680554 DOI: 10.18632/aging.101298] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/28/2017] [Indexed: 12/24/2022]
Abstract
Luminal epithelial cells in the breast gradually alter gene and protein expression with age, appearing to lose lineage-specificity by acquiring myoepithelial-like characteristics. We hypothesize that the luminal lineage is particularly sensitive to microenvironment changes, and age-related microenvironment changes cause altered luminal cell phenotypes. To evaluate the effects of different microenvironments on the fidelity of epigenetically regulated luminal and myoepithelial gene expression, we generated a set of lineage-specific probes for genes that are controlled through DNA methylation. Culturing primary luminal cells under conditions that favor myoepithelial propogation led to their reprogramming at the level of gene methylation, and to a more myoepithelial-like expression profile. Primary luminal cells' lineage-specific gene expression could be maintained when they were cultured as bilayers with primary myoepithelial cells. Isogenic stromal fibroblast co-cultures were unable to maintain the luminal phenotype. Mixed-age luminal-myoepithelial bilayers revealed that luminal cells adopt transcription and methylation patterns consistent with the chronological age of the myoepithelial cells. We provide evidence that the luminal epithelial phenotype is exquisitely sensitive to microenvironment conditions, and that states of aging are cell non-autonomously communicated through microenvironment cues over at least one cell diameter.
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Azpurua J, Mahoney RE, Eaton BA. Transcriptomics of aged Drosophila motor neurons reveals a matrix metalloproteinase that impairs motor function. Aging Cell 2018; 17. [PMID: 29411505 PMCID: PMC5847883 DOI: 10.1111/acel.12729] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2017] [Indexed: 12/12/2022] Open
Abstract
The neuromuscular junction (NMJ) is responsible for transforming nervous system signals into motor behavior and locomotion. In the fruit fly Drosophila melanogaster, an age‐dependent decline in motor function occurs, analogous to the decline experienced in mice, humans, and other mammals. The molecular and cellular underpinnings of this decline are still poorly understood. By specifically profiling the transcriptome of Drosophila motor neurons across age using custom microarrays, we found that the expression of the matrix metalloproteinase 1 (dMMP1) gene reproducibly increased in motor neurons in an age‐dependent manner. Modulation of physiological aging also altered the rate of dMMP1 expression, validating dMMP1 expression as a bona fide aging biomarker for motor neurons. Temporally controlled overexpression of dMMP1 specifically in motor neurons was sufficient to induce deficits in climbing behavior and cause a decrease in neurotransmitter release at neuromuscular synapses. These deficits were reversible if the dMMP1 expression was shut off again immediately after the onset of motor dysfunction. Additionally, repression of dMMP1 enzymatic activity via overexpression of a tissue inhibitor of metalloproteinases delayed the onset of age‐dependent motor dysfunction. MMPs are required for proper tissue architecture during development. Our results support the idea that matrix metalloproteinase 1 is acting as a downstream effector of antagonistic pleiotropy in motor neurons and is necessary for proper development, but deleterious when reactivated at an advanced age.
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Affiliation(s)
- Jorge Azpurua
- Department of Anesthesiology; Stony Brook University School of Medicine; Stony Brook NY USA
| | - Rebekah E. Mahoney
- Department of Cellular and Integrative Physiology; UTHSCSA; San Antonio TX USA
- Barshop Institute for Longevity and Aging Studies; UTHSCSA; San Antonio TX USA
| | - Benjamin A. Eaton
- Department of Cellular and Integrative Physiology; UTHSCSA; San Antonio TX USA
- Barshop Institute for Longevity and Aging Studies; UTHSCSA; San Antonio TX USA
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37
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Popa-Wagner A, Sandu RE, Cristin C, Uzoni A, Welle KA, Hryhorenko JR, Ghaemmaghami S. Increased Degradation Rates in the Components of the Mitochondrial Oxidative Phosphorylation Chain in the Cerebellum of Old Mice. Front Aging Neurosci 2018; 10:32. [PMID: 29503614 PMCID: PMC5820363 DOI: 10.3389/fnagi.2018.00032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/26/2018] [Indexed: 12/11/2022] Open
Abstract
Brain structures differ in the magnitude of age-related neuron loss with the cerebellum being more affected. An underlying cause could be an age-related decline in mitochondrial bioenergetics. Successful aging of mitochondria reflects a balanced turnover of proteins involved in mitochondrial biogenesis and mitophagy. Thus, an imbalance in mitochondrial turnover can contribute to the diminution of cellular function seen during aging. Mitochondrial biogenesis and mitophagy are mediated by a set of proteins including MFN1, MFN2, OPA1, DRP1, FIS1 as well as DMN1l and DNM1, all of which are required for mitochondrial fission. Using N15 labeling, we report that the turnover rates for DMN1l and FIS1 go in opposite directions in the cerebellum of 22-month-old C57BL6j mice as compared to 3-month-old mice. Previous studies have reported decreased turnover rates for the mitochondrial respiratory complexes of aged rodents. In contrast, we found increased turnover rates for mitochondrial proteins of the oxidative phosphorylation chain in the aged mice as compared to young mice. Furthermore, the turnover rate of the components that are most affected by aging –complex III components (ubiquinol cytochrome C oxidoreductase) and complex IV components (cytochrome C oxidase)– was significantly increased in the senescent cerebellum. However, the turnover rates of proteins involved in mitophagy (i.e., the proteasomal and lysosomal degradation of damaged mitochondria) were not significantly altered with age. Overall, our results suggest that an age-related imbalance in the turnover rates of proteins involved in mitochondrial biogenesis and mitophagy (DMN1l, FIS1) in conjunction with an age-related imbalance in the turnover rates of proteins of the complexes III and IV of the electron transfer chain, might impair cerebellar mitochondrial bioenergetics in old mice.
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Affiliation(s)
- Aurel Popa-Wagner
- Department of Neurology, Chair of Vascular Neurology and Dementia, Essen University Hospital, Essen, Germany.,Neurobiology of Aging Group, University of Medicine and Pharmacy Craiova, Craiova, Romania.,School of Medicine, Griffith University, Southport, QLD, Australia
| | - Raluca E Sandu
- Neurobiology of Aging Group, University of Medicine and Pharmacy Craiova, Craiova, Romania
| | - Coman Cristin
- Institutul Naţional de Cercetare şi Dezvoltare pentru Microbiologie şi Imunologie (Cantacuzino), Bucharest, Romania
| | - Adriana Uzoni
- Department of Psychiatry, University of Medicine Rostock, Rostock, Germany
| | - Kevin A Welle
- Department of Biology, University of Rochester, Rochester, NY, United States
| | | | - Sina Ghaemmaghami
- Department of Biology, University of Rochester, Rochester, NY, United States
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38
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Identification of human age-associated gene co-expressions in functional modules using liquid association. Oncotarget 2017; 9:1063-1074. [PMID: 29416677 PMCID: PMC5787419 DOI: 10.18632/oncotarget.23148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/17/2017] [Indexed: 01/10/2023] Open
Abstract
Aging is a major risk factor for age-related diseases such as certain cancers. In this study, we developed Age Associated Gene Co-expression Identifier (AAGCI), a liquid association based method to infer age-associated gene co-expressions at thousands of biological processes and pathways across 9 human tissues. Several hundred to thousands of gene pairs were inferred to be age co-expressed across different tissues, the genes involved in which are significantly enriched in functions like immunity, ATP binding, DNA damage, and many cancer pathways. The age co-expressed genes are significantly overlapped with aging genes curated in the GenAge database across all 9 tissues, suggesting a tissue-wide correlation between age-associated genes and co-expressions. Interestingly, age-associated gene co-expressions are significantly different from gene co-expressions identified through correlation analysis, indicating that aging might only contribute to a small portion of gene co-expressions. Moreover, the key driver analysis identified biologically meaningful genes in important function modules. For example, IGF1, ERBB2, TP53 and STAT5A were inferred to be key genes driving age co-expressed genes in the network module associated with function “T cell proliferation”. Finally, we prioritized a few anti-aging drugs such as metformin based on an enrichment analysis between age co-expressed genes and drug signatures from a recent study. The predicted drugs were partially validated by literature mining and can be readily used to generate hypothesis for further experimental validations.
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39
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Ianov L, De Both M, Chawla MK, Rani A, Kennedy AJ, Piras I, Day JJ, Siniard A, Kumar A, Sweatt JD, Barnes CA, Huentelman MJ, Foster TC. Hippocampal Transcriptomic Profiles: Subfield Vulnerability to Age and Cognitive Impairment. Front Aging Neurosci 2017; 9:383. [PMID: 29276487 PMCID: PMC5727020 DOI: 10.3389/fnagi.2017.00383] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/07/2017] [Indexed: 01/11/2023] Open
Abstract
The current study employed next-generation RNA sequencing to examine gene expression differences related to brain aging, cognitive decline, and hippocampal subfields. Young and aged rats were trained on a spatial episodic memory task. Hippocampal regions CA1, CA3, and the dentate gyrus were isolated. Poly-A mRNA was examined using two different sequencing platforms, Illumina, and Ion Proton. The Illumina platform was used to generate seed lists of genes that were statistically differentially expressed across regions, ages, or in association with cognitive function. The gene lists were then retested using the data from the Ion Proton platform. The results indicate hippocampal subfield differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response-related genes, particularly in the dentate gyrus. For the memory task, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1. Finally, we provide a transcriptomic characterization of the three subfields regardless of age or cognitive status, highlighting and confirming a correspondence between cytoarchitectural boundaries and molecular profiling.
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Affiliation(s)
- Lara Ianov
- Departments of Neuroscience and Genetics and Genomics Program, Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, United States.,Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Matt De Both
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Monica K Chawla
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
| | - Asha Rani
- Departments of Neuroscience and Genetics and Genomics Program, Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Andrew J Kennedy
- Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, AL, United States
| | - Ignazio Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Jeremy J Day
- Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, AL, United States
| | - Ashley Siniard
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ashok Kumar
- Departments of Neuroscience and Genetics and Genomics Program, Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - J David Sweatt
- Evelyn F. McKnight Brain Institute, University of Alabama, Birmingham, AL, United States.,Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Carol A Barnes
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States.,Departments of Psychology, Neurology and Neuroscience, University of Arizona, Tucson, AZ, United States
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States.,Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
| | - Thomas C Foster
- Departments of Neuroscience and Genetics and Genomics Program, Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, United States
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40
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Ashapkin VV, Kutueva LI, Vanyushin BF. Aging as an Epigenetic Phenomenon. Curr Genomics 2017; 18:385-407. [PMID: 29081695 PMCID: PMC5635645 DOI: 10.2174/1389202918666170412112130] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 01/17/2016] [Accepted: 02/09/2016] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Hypermethylation of genes associated with promoter CpG islands, and hypomethylation of CpG poor genes, repeat sequences, transposable elements and intergenic genome sections occur during aging in mammals. Methylation levels of certain CpG sites display strict correlation to age and could be used as "epigenetic clock" to predict biological age. Multi-substrate deacetylases SIRT1 and SIRT6 affect aging via locus-specific modulations of chromatin structure and activity of multiple regulatory proteins involved in aging. Random errors in DNA methylation and other epigenetic marks during aging increase the transcriptional noise, and thus lead to enhanced phenotypic variation between cells of the same tissue. Such variation could cause progressive organ dysfunction observed in aged individuals. Multiple experimental data show that induction of NF-κB regulated gene sets occurs in various tissues of aged mammals. Upregulation of multiple miRNAs occurs at mid age leading to downregulation of enzymes and regulatory proteins involved in basic cellular functions, such as DNA repair, oxidative phosphorylation, intermediate metabolism, and others. CONCLUSION Strong evidence shows that all epigenetic systems contribute to the lifespan control in various organisms. Similar to other cell systems, epigenome is prone to gradual degradation due to the genome damage, stressful agents, and other aging factors. But unlike mutations and other kinds of the genome damage, age-related epigenetic changes could be fully or partially reversed to a "young" state.
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Affiliation(s)
- Vasily V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Lyudmila I Kutueva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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41
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Balivada S, Ganta CK, Zhang Y, Pawar HN, Ortiz RJ, Becker KG, Khan AM, Kenney MJ. Microarray analysis of aging-associated immune system alterations in the rostral ventrolateral medulla of F344 rats. Physiol Genomics 2017; 49:400-415. [PMID: 28626023 PMCID: PMC5582943 DOI: 10.1152/physiolgenomics.00131.2016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/12/2017] [Accepted: 06/12/2017] [Indexed: 11/22/2022] Open
Abstract
The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats were analyzed with Agilent's whole rat genome microarray. The RVLM gene expression profile varied with age, and an association between chronological age and specific RVLM gene expression patterns was observed [P < 0.05, false discovery rate (FDR) < 0.3]. Functional analysis of RVLM microarray data via gene ontology profiling and pathway analysis identified upregulation of genes associated with immune- and stress-related responses and downregulation of genes associated with lipid biosynthesis and neurotransmission in aged compared with middle-aged and young rats. Differentially expressed genes associated with the complement system and microglial cells were further validated by quantitative PCR with separate RVLM samples (P < 0.05, FDR < 0.1). The present results have identified age-related changes in the transcriptomic profile of the RVLM, modifications that may provide the molecular backdrop for understanding age-dependent changes in physiological regulation.
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Affiliation(s)
- Sivasai Balivada
- Department of Biological Sciences, College of Science, University of Texas at El Paso, El Paso, Texas;
| | - Chanran K Ganta
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas; and
| | - Yongqing Zhang
- Gene Expression and Genomics Unit, National Institute on Aging, Baltimore, Maryland
| | - Hitesh N Pawar
- Department of Biological Sciences, College of Science, University of Texas at El Paso, El Paso, Texas
| | - Richard J Ortiz
- Department of Biological Sciences, College of Science, University of Texas at El Paso, El Paso, Texas
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging, Baltimore, Maryland
| | - Arshad M Khan
- Department of Biological Sciences, College of Science, University of Texas at El Paso, El Paso, Texas
| | - Michael J Kenney
- Department of Biological Sciences, College of Science, University of Texas at El Paso, El Paso, Texas
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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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43
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Jones MK, Lu B, Girman S, Wang S. Cell-based therapeutic strategies for replacement and preservation in retinal degenerative diseases. Prog Retin Eye Res 2017; 58:1-27. [PMID: 28111323 PMCID: PMC5441967 DOI: 10.1016/j.preteyeres.2017.01.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/08/2017] [Accepted: 01/17/2017] [Indexed: 12/13/2022]
Abstract
Cell-based therapeutics offer diverse options for treating retinal degenerative diseases, such as age-related macular degeneration (AMD) and retinitis pigmentosa (RP). AMD is characterized by both genetic and environmental risks factors, whereas RP is mainly a monogenic disorder. Though treatments exist for some patients with neovascular AMD, a majority of retinal degenerative patients have no effective therapeutics, thus indicating a need for universal therapies to target diverse patient populations. Two main cell-based mechanistic approaches are being tested in clinical trials. Replacement therapies utilize cell-derived retinal pigment epithelial (RPE) cells to supplant lost or defective host RPE cells. These cells are similar in morphology and function to native RPE cells and can potentially supplant the responsibilities of RPE in vivo. Preservation therapies utilize supportive cells to aid in visual function and photoreceptor preservation partially by neurotrophic mechanisms. The goal of preservation strategies is to halt or slow the progression of disease and maintain remaining visual function. A number of clinical trials are testing the safety of replacement and preservation cell therapies in patients; however, measures of efficacy will need to be further evaluated. In addition, a number of prevailing concerns with regards to the immune-related response, longevity, and functionality of the grafted cells will need to be addressed in future trials. This review will summarize the current status of cell-based preclinical and clinical studies with a focus on replacement and preservation strategies and the obstacles that remain regarding these types of treatments.
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Affiliation(s)
- Melissa K Jones
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048, USA
| | - Bin Lu
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048, USA
| | - Sergey Girman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048, USA
| | - Shaomei Wang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA 90048, USA; David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave., Los Angeles, CA 90095, USA.
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Nuclear but not mitochondrial-encoded oxidative phosphorylation genes are altered in aging, mild cognitive impairment, and Alzheimer's disease. Alzheimers Dement 2016; 13:510-519. [PMID: 27793643 DOI: 10.1016/j.jalz.2016.09.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/30/2016] [Accepted: 09/12/2016] [Indexed: 01/01/2023]
Abstract
INTRODUCTION We have comprehensively described the expression profiles of mitochondrial DNA and nuclear DNA genes that encode subunits of the respiratory oxidative phosphorylation (OXPHOS) complexes (I-V) in the hippocampus from young controls, age matched, mild cognitively impaired (MCI), and Alzheimer's disease (AD) subjects. METHODS Hippocampal tissues from 44 non-AD controls (NC), 10 amnestic MCI, and 18 AD cases were analyzed on Affymetrix Hg-U133 plus 2.0 arrays. RESULTS The microarray data revealed significant down regulation in OXPHOS genes in AD, particularly those encoded in the nucleus. In contrast, there was up regulation of the same gene(s) in MCI subjects compared to AD and ND cases. No significant differences were observed in mtDNA genes identified in the array between AD, ND, and MCI subjects except one mt-ND6. DISCUSSION Our findings suggest that restoration of the expression of nuclear-encoded OXPHOS genes in aging could be a viable strategy for blunting AD progression.
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45
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Huh CJ, Zhang B, Victor MB, Dahiya S, Batista LF, Horvath S, Yoo AS. Maintenance of age in human neurons generated by microRNA-based neuronal conversion of fibroblasts. eLife 2016; 5. [PMID: 27644593 PMCID: PMC5067114 DOI: 10.7554/elife.18648] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/15/2016] [Indexed: 12/19/2022] Open
Abstract
Aging is a major risk factor in many forms of late-onset neurodegenerative disorders. The ability to recapitulate age-related characteristics of human neurons in culture will offer unprecedented opportunities to study the biological processes underlying neuronal aging. Here, we show that using a recently demonstrated microRNA-based cellular reprogramming approach, human fibroblasts from postnatal to near centenarian donors can be efficiently converted into neurons that maintain multiple age-associated signatures. Application of an epigenetic biomarker of aging (referred to as epigenetic clock) to DNA methylation data revealed that the epigenetic ages of fibroblasts were highly correlated with corresponding age estimates of reprogrammed neurons. Transcriptome and microRNA profiles reveal genes differentially expressed between young and old neurons. Further analyses of oxidative stress, DNA damage and telomere length exhibit the retention of age-associated cellular properties in converted neurons from corresponding fibroblasts. Our results collectively demonstrate the maintenance of age after neuronal conversion.
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Affiliation(s)
- Christine J Huh
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States.,Program in Molecular and Cellular Biology, Washington University School of Medicine, St. Louis, United States
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
| | - Matheus B Victor
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States.,Program in Neuroscience, Washington University School of Medicine, St. Louis, United States
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
| | - Luis Fz Batista
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States.,Department of Medicine, Washington University School of Medicine, St. Louis, United States
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, United States
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
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Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ. Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Front Aging Neurosci 2016; 8:183. [PMID: 27536236 PMCID: PMC4971101 DOI: 10.3389/fnagi.2016.00183] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/15/2016] [Indexed: 11/13/2022] Open
Abstract
Human aging is associated with cognitive decline and an increased risk of neurodegenerative disease. Our objective for this study was to evaluate potential relationships between age and variation in gene expression across different regions of the brain. We analyzed the Genotype-Tissue Expression (GTEx) data from 54 to 101 tissue samples across 13 brain regions in post-mortem donors of European descent aged between 20 and 70 years at death. After accounting for the effects of covariates and hidden confounding factors, we identified 1446 protein-coding genes whose expression in one or more brain regions is correlated with chronological age at a false discovery rate of 5%. These genes are involved in various biological processes including apoptosis, mRNA splicing, amino acid biosynthesis, and neurotransmitter transport. The distribution of these genes among brain regions is uneven, suggesting variable regional responses to aging. We also found that the aging response of many genes, e.g., TP37 and C1QA, depends on individuals' genotypic backgrounds. Finally, using dispersion-specific analysis, we identified genes such as IL7R, MS4A4E, and TERF1/TERF2 whose expressions are differentially dispersed by aging, i.e., variances differ between age groups. Our results demonstrate that age-related gene expression is brain region-specific, genotype-dependent, and associated with both mean and dispersion changes. Our findings provide a foundation for more sophisticated gene expression modeling in the studies of age-related neurodegenerative diseases.
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Affiliation(s)
| | - Jinting Guan
- Department of Automation, Xiamen UniversityXiamen, China
| | - Guoli Ji
- Department of Automation, Xiamen UniversityXiamen, China
- Innovation Center for Cell Signaling Network, Xiamen UniversityXiamen, China
| | - James J. Cai
- Department of Veterinary Integrative Biosciences, Texas A&M UniversityCollege Station, TX, USA
- Interdisciplinary Program in Genetics, Texas A&M UniversityCollege Station, TX, USA
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Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds. BMC Genomics 2016; 17:410. [PMID: 27230888 PMCID: PMC4882810 DOI: 10.1186/s12864-016-2714-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/07/2016] [Indexed: 01/08/2023] Open
Abstract
Background Kiwi represent the most basal extant avian lineage (paleognaths) and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan. Despite intense interest in their evolution and their threatened status, genomic resources for kiwi were virtually non-existent until the recent publication of a single genome. Here we present the most comprehensive kiwi transcriptomes to date, obtained via Illumina sequencing of whole blood and de novo assembly of mRNA sequences of eight individuals from each of the two rarest kiwi species, little spotted kiwi (LSK; Apteryx owenii) and rowi (A. rowi). Results Sequences obtained were orthologous with a wide diversity of functional genes despite the sequencing of a single tissue type. Individual and composite assemblies contain more than 7900 unique protein coding transcripts in each of LSK and rowi that show strong homology with chicken (Gallus gallus), including those associated with growth, development, disease resistance, reproduction and behavior. The assemblies also contain 66,909 SNPs that distinguish between LSK and rowi, 12,384 SNPs among LSK (associated with 3088 genes), and 29,313 SNPs among rowi (associated with 4953 genes). We found 3084 transcripts differentially expressed between LSK and rowi and 150 transcripts differentially expressed between the sexes. Of the latter, 83 could be mapped to chicken chromosomes with 95% syntenic with chromosome Z. Conclusions Our study has simultaneously sequenced multiple species, sexes, and individual kiwi at thousands of genes, and thus represents a significant leap forward in genomic resources available for kiwi. The expression pattern we observed among chromosome Z related genes in kiwi is similar to that observed in ostriches and emu, suggesting a common and ancestral pattern of sex chromosome homomorphy, recombination, and gene dosage among living paleognaths. The transcriptome assemblies described here will provide a rich resource for polymorphic marker development and studies of adaptation of these highly unusual and endangered birds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2714-2) contains supplementary material, which is available to authorized users.
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48
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Ianov L, Rani A, Beas BS, Kumar A, Foster TC. Transcription Profile of Aging and Cognition-Related Genes in the Medial Prefrontal Cortex. Front Aging Neurosci 2016; 8:113. [PMID: 27242522 PMCID: PMC4868850 DOI: 10.3389/fnagi.2016.00113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/29/2016] [Indexed: 12/22/2022] Open
Abstract
Cognitive function depends on transcription; however, there is little information linking altered gene expression to impaired prefrontal cortex function during aging. Young and aged F344 rats were characterized on attentional set shift and spatial memory tasks. Transcriptional differences associated with age and cognition were examined using RNA sequencing to construct transcriptomic profiles for the medial prefrontal cortex (mPFC), white matter, and region CA1 of the hippocampus. The results indicate regional differences in vulnerability to aging. Age-related gene expression in the mPFC was similar to, though less robust than, changes in the dorsolateral PFC of aging humans suggesting that aging processes may be similar. Importantly, the pattern of transcription associated with aging did not predict cognitive decline. Rather, increased mPFC expression of genes involved in regulation of transcription, including transcription factors that regulate the strength of excitatory and inhibitory inputs, and neural activity-related immediate-early genes was observed in aged animals that exhibit delayed set shift behavior. The specificity of impairment on a mPFC-dependent task, associated with a particular mPFC transcriptional profile indicates that impaired executive function involves altered transcriptional regulation and neural activity/plasticity processes that are distinct from that described for impaired hippocampal function.
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Affiliation(s)
- Lara Ianov
- Department of Neuroscience, McKnight Brain Institute, University of FloridaGainesville, FL, USA
- Genetics and Genomics Program, Genetics Institute, University of FloridaGainesville, FL, USA
| | - Asha Rani
- Department of Neuroscience, McKnight Brain Institute, University of FloridaGainesville, FL, USA
| | - Blanca S. Beas
- Department of Neuroscience, McKnight Brain Institute, University of FloridaGainesville, FL, USA
| | - Ashok Kumar
- Department of Neuroscience, McKnight Brain Institute, University of FloridaGainesville, FL, USA
| | - Thomas C. Foster
- Department of Neuroscience, McKnight Brain Institute, University of FloridaGainesville, FL, USA
- Genetics and Genomics Program, Genetics Institute, University of FloridaGainesville, FL, USA
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Hullinger R, Puglielli L. Molecular and cellular aspects of age-related cognitive decline and Alzheimer's disease. Behav Brain Res 2016; 322:191-205. [PMID: 27163751 DOI: 10.1016/j.bbr.2016.05.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/19/2016] [Accepted: 05/03/2016] [Indexed: 01/14/2023]
Abstract
As the population of people aged 60 or older continues to rise, it has become increasingly important to understand the molecular basis underlying age-related cognitive decline. In fact, a better understanding of aging biology will help us identify ways to maintain high levels of cognitive functioning throughout the aging process. Many cellular and molecular aspects of brain aging are shared with other organ systems; however, certain age-related changes are unique to the nervous system due to its structural, cellular and molecular complexity. Importantly, the brain appears to show differential changes throughout the aging process, with certain regions (e.g. frontal and temporal regions) being more vulnerable than others (e.g. brain stem). Within the medial temporal lobe, the hippocampus is especially susceptible to age-related changes. The important role of the hippocampus in age-related cognitive decline and in vulnerability to disease processes such as Alzheimer's disease has prompted this review, which will focus on the complexity of changes that characterize aging, and on the molecular connections that exist between normal aging and Alzheimer's disease. Finally, it will discuss behavioral interventions and emerging insights for promoting healthy cognitive aging.
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Affiliation(s)
- Rikki Hullinger
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA; Wisconsin Alzheimer's Disease Research Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Geriatric Research Education Clinical Center, VA Medical Center, Madison, WI 53705, USA.
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Cornejo F, von Bernhardi R. Age-Dependent Changes in the Activation and Regulation of Microglia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 949:205-226. [DOI: 10.1007/978-3-319-40764-7_10] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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