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Zhang X, Ge R, Wu J, Cai X, Deng G, Lv J, Ma M, Yu N, Yao L, Peng D. Structural characterization and improves cognitive disorder in ageing mice of a glucomannan from Dendrobium huoshanense. Int J Biol Macromol 2024; 269:131995. [PMID: 38692529 DOI: 10.1016/j.ijbiomac.2024.131995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 04/01/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
In the present work, a neutral polysaccharide (DHP-2W) with attenuating cognitive disorder was identified from Dendrobium huoshanense and its structure was clarified. The polysaccharide was successfully purified from D. huoshanense by column chromatography and its activity was evaluated. With a molecular weight of 508.934kDa, this polysaccharide is composed of mannose and glucose at a molar ratio of 75.81: 24.19. Structural characterization revealed that DHP-2W has a backbone consisting of 4)-β-D-Manp-(1 and 4)-β-D-Glcp-(1. In vivo experiments revealed that DHP-2W improved cognitive disorder in D-galactose treated mice and relieved oxidative stress and inflammation. DHP-2W attenuates D-galactose-induced cognitive disorder by inhibiting the BCL2/BAX/CASP3 pathway and activating the AMPK/SIRT pathway, thereby inhibiting apoptosis. Furthermore, DHP-2W had a significant effect on regulating the serum levels of Flavin adenine dinucleotide, Shikimic acid, and Kynurenic acid in aged mice. These, in turn, had a positive impact on AMPK/SIRT1 and BCL2/BAX/CASP3, resulting in protective effects against cognitive disorder.
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Affiliation(s)
- Xiaoqian Zhang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China.
| | - Ruipeng Ge
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China
| | - Jing Wu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China
| | - Xiao Cai
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China
| | - Guanghui Deng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China
| | - Jiahui Lv
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China
| | - Mengzhen Ma
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China
| | - Nianjun Yu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China; MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China; Anhui Province Key Laboratory for Research and Development of Research & Development of Chinese Medicine, Hefei, China.
| | - Liang Yao
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China.
| | - Daiyin Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China; Anhui Academy of Chinese Medicine, Hefei, China; MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China; Anhui Province Key Laboratory for Research and Development of Research & Development of Chinese Medicine, Hefei, China.
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Windener F, Grewing L, Thomas C, Dorion MF, Otteken M, Kular L, Jagodic M, Antel J, Albrecht S, Kuhlmann T. Physiological aging and inflammation-induced cellular senescence may contribute to oligodendroglial dysfunction in MS. Acta Neuropathol 2024; 147:82. [PMID: 38722375 PMCID: PMC11082024 DOI: 10.1007/s00401-024-02733-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024]
Abstract
Aging affects all cell types in the CNS and plays an important role in CNS diseases. However, the underlying molecular mechanisms driving these age-associated changes and their contribution to diseases are only poorly understood. The white matter in the aging brain as well as in diseases, such as Multiple sclerosis is characterized by subtle abnormalities in myelin sheaths and paranodes, suggesting that oligodendrocytes, the myelin-maintaining cells of the CNS, lose the capacity to preserve a proper myelin structure and potentially function in age and certain diseases. Here, we made use of directly converted oligodendrocytes (dchiOL) from young, adult and old human donors to study age-associated changes. dchiOL from all three age groups differentiated in an comparable manner into O4 + immature oligodendrocytes, but the proportion of MBP + mature dchiOL decreased with increasing donor age. This was associated with an increased ROS production and upregulation of cellular senescence markers such as CDKN1A, CDKN2A in old dchiOL. Comparison of the transcriptomic profiles of dchiOL from adult and old donors revealed 1324 differentially regulated genes with limited overlap with transcriptomic profiles of the donors' fibroblasts or published data sets from directly converted human neurons or primary rodent oligodendroglial lineage cells. Methylome analyses of dchiOL and human white matter tissue samples demonstrate that chronological and epigenetic age correlate in CNS white matter as well as in dchiOL and resulted in the identification of an age-specific epigenetic signature. Furthermore, we observed an accelerated epigenetic aging of the myelinated, normal appearing white matter of multiple sclerosis (MS) patients compared to healthy individuals. Impaired differentiation and upregulation of cellular senescence markers could be induced in young dchiOL in vitro using supernatants from pro-inflammatory microglia. In summary, our data suggest that physiological aging as well as inflammation-induced cellular senescence contribute to oligodendroglial pathology in inflammatory demyelinating diseases such as MS.
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Affiliation(s)
- Farina Windener
- Institute of Neuropathology, University Hospital Münster, 48149, Münster, Germany
| | - Laureen Grewing
- Institute of Neuropathology, University Hospital Münster, 48149, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, 48149, Münster, Germany
| | - Marie-France Dorion
- Neuroimmunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Marie Otteken
- Institute of Neuropathology, University Hospital Münster, 48149, Münster, Germany
| | - Lara Kular
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jack Antel
- Neuroimmunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Stefanie Albrecht
- Institute of Neuropathology, University Hospital Münster, 48149, Münster, Germany
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital Münster, 48149, Münster, Germany.
- Neuroimmunology Unit, Montreal Neurological Institute and Department of Neurology and Neurosurgery, McGill University, Montreal, Canada.
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Castro CFG, Nardiello C, Hadzic S, Kojonazarov B, Kraut S, Gierhardt M, Schäffer J, Bednorz M, Quanz K, Heger J, Korfei M, Wilhelm J, Hecker M, Bartkuhn M, Arnhold S, Guenther A, Seeger W, Schulz R, Weissmann N, Sommer N, Pak O. The Role of the Redox Enzyme p66Shc in Biological Aging of the Lung. Aging Dis 2024; 15:911-926. [PMID: 37548932 PMCID: PMC10917546 DOI: 10.14336/ad.2023.0715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/15/2023] [Indexed: 08/08/2023] Open
Abstract
The mitochondrial adaptor protein p66Shc has been suggested to control life span in mice via the release of hydrogen peroxide. However, the role of p66Shc in lung aging remains unsolved. Thus, we investigated the effects of p66Shc-/- on the aging of the lung and pulmonary circulation. In vivo lung and cardiac characteristics were investigated in p66Shc-/- and wild type (WT) mice at 3, 12, and 24 months of age by lung function measurements, micro-computed tomography (µCT), and echocardiography. Alveolar number and muscularization of small pulmonary arteries were measured by stereology and vascular morphometry, respectively. Protein and mRNA levels of senescent markers were measured by western blot and PCR, respectively. Lung function declined similarly in WT and p66Shc-/- mice during aging. However, µCT analyses and stereology showed slightly enhanced signs of aging-related parameters in p66Shc-/- mice, such as a decline of alveolar density. Accordingly, p66Shc-/- mice showed higher protein expression of the senescence marker p21 in lung homogenate compared to WT mice of the corresponding age. Pulmonary vascular remodeling was increased during aging, but aged p66Shc-/- mice showed similar muscularization of pulmonary vessels and hemodynamics like WT mice. In the heart, p66Shc-/- prevented the deterioration of right ventricular (RV) function but promoted the decline of left ventricular (LV) function during aging. p66Shc-/- affects the aging process of the lung and the heart differently. While p66Shc-/- slightly accelerates lung aging and deteriorates LV function in aged mice, it seems to exert protective effects on RV function during aging.
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Affiliation(s)
- Claudia F. Garcia Castro
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Claudio Nardiello
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Stefan Hadzic
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Baktybek Kojonazarov
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
| | - Simone Kraut
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Mareike Gierhardt
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
| | - Julia Schäffer
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Mariola Bednorz
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Karin Quanz
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Jacqueline Heger
- Institute of Physiology, Justus-Liebig University of Giessen, Giessen, Germany.
| | - Martina Korfei
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Jochen Wilhelm
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
| | - Matthias Hecker
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Marek Bartkuhn
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
| | - Stefan Arnhold
- Institute of Veterinary Anatomy, Histology and Embryology, Justus-Liebig University of Giessen, Giessen, Germany.
| | - Andreas Guenther
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- European IPF Registry & Biobank (eurIPFreg), Giessen, Germany.
- Agaplesion Evangelisches Krankenhaus Mittelhessen, Giessen, Germany
| | - Werner Seeger
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
| | - Rainer Schulz
- Institute of Physiology, Justus-Liebig University of Giessen, Giessen, Germany.
| | - Norbert Weissmann
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Natascha Sommer
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Oleg Pak
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
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Hossain MK, Kim HR, Chae HJ. Aging phenotype in AD brain organoids: Track to success and challenges. Ageing Res Rev 2024; 96:102256. [PMID: 38460555 DOI: 10.1016/j.arr.2024.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/11/2024]
Abstract
Alzheimer's disease (AD) poses a complex challenge, with abnormal protein accumulation in the brain causing memory loss and cognitive decline. Traditional models fall short in AD research, prompting interest in 3D brain organoids (BOs) from human stem cells. These findings hold promise for unveiling the mechanisms of AD, especially in relation to aging. However, an understanding of the aging impact of AD remains elusive. BOs offer insight but face challenges. This review delves into the role of BOs in deciphering aging-related AD and acknowledges limitations. Strategies to enhance BOs for accurate aging modeling in AD brains are suggested. Strengthened by molecular advancements, BOs have the potential to uncover the aging phenotype, advancing AD research.
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Affiliation(s)
| | - Hyung-Ryong Kim
- Department of Pharmacology, College of Dentistry, Jeonbuk National University, Jeonju 54896, Republic of Korea.
| | - Han Jung Chae
- School of Pharmacy, Jeonbuk National University, Jeonju 54896, Republic of Korea.
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5
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Sarver DC, Saqib M, Chen F, Wong GW. Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586781. [PMID: 38586038 PMCID: PMC10996676 DOI: 10.1101/2024.03.26.586781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Organ function declines with age, and large-scale transcriptomic analyses have highlighted differential aging trajectories across tissues. The mechanisms underlying shared and organ-selective functional changes across the lifespan, however, still remains poorly understood. Given the central role of mitochondria in powering cellular processes needed to maintain tissue health, we therefore undertook a systematic assessment of respiratory activity across 33 different tissues in young (2.5 months) and old (20 months) mice of both sexes. Our high-resolution mitochondrial respiration atlas reveals: 1) within any group of mice, mitochondrial activity varies widely across tissues, with the highest values consistently seen in heart, brown fat, and kidney; 2) biological sex is a significant but minor contributor to mitochondrial respiration, and its contributions are tissue-specific, with major differences seen in the pancreas, stomach, and white adipose tissue; 3) age is a dominant factor affecting mitochondrial activity, especially across different fat depots and skeletal muscle groups, and most brain regions; 4) age-effects can be sex- and tissue-specific, with some of the largest effects seen in pancreas, heart, adipose tissue, and skeletal muscle; and 5) while aging alters the functional trajectories of mitochondria in a majority of tissues, some are remarkably resilient to age-induced changes. Altogether, our data provide the most comprehensive compendium of mitochondrial respiration and illuminate functional signatures of aging across diverse tissues and organ systems.
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Affiliation(s)
- Dylan C. Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore
| | - Muzna Saqib
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore
| | - Fangluo Chen
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore
| | - G. William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore
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Tikhonov S, Batin M, Gladyshev VN, Dmitriev SE, Tyshkovskiy A. AgeMeta: Quantitative Gene Expression Database of Mammalian Aging. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:313-321. [PMID: 38622098 DOI: 10.1134/s000629792402010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/12/2023] [Accepted: 02/13/2024] [Indexed: 04/17/2024]
Abstract
AgeMeta is a database that provides systemic and quantitative description of mammalian aging at the level of gene expression. It encompasses transcriptomic changes with age across various tissues of humans, mice, and rats, based on a comprehensive meta-analysis of 122 publicly available gene expression datasets from 26 studies. AgeMeta provides an intuitive visual interface for quantification of aging-associated transcriptomics at the level of individual genes and functional groups of genes, allowing easy comparison among various species and tissues. Additionally, all the data in the database can be downloaded and analyzed independently. Overall, this work contributes to the understanding of the complex network of biological processes underlying mammalian aging and supports future advancements in this field. AgeMeta is freely available at: https://age-meta.com/.
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Affiliation(s)
- Stanislav Tikhonov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexander Tyshkovskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Zhang Y, Qian W, Zhang Y, Ma Y, Qian J, Li J, Wei X, Long Y, Wan X. Pediococcus acidilactici reduces tau pathology and ameliorates behavioral deficits in models of neurodegenerative disorders. Cell Commun Signal 2024; 22:84. [PMID: 38291511 PMCID: PMC10826277 DOI: 10.1186/s12964-023-01419-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/02/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD), affecting many elders worldwide, is characterized by A-beta and tau-related cognitive decline. Accumulating evidence suggests that brain iron accumulation is an important characteristic of AD. However, the function and mechanism of the iron-mediated gut-brain axis on AD is still unclear. METHODS A Caenorhabditis elegans model with tau-overexpression and a high-Fe diet mouse model of cognitive impairment was used for probiotic function evaluation. With the use of qPCR, and immunoblotting, the probiotic regulated differential expression of AD markers and iron related transporting genes was determined. Colorimetric kits, IHC staining, and immunofluorescence have been performed to explore the probiotic mechanism on the development of gut-brain links and brain iron accumulation. RESULTS In the present study, a high-Fe diet mouse model was used for evaluation in which cognitive impairment, higher A-beta, tau and phosphorylated (p)-tau expression, and dysfunctional phosphate distribution were observed. Considering the close crosstalk between intestine and brain, probiotics were then employed to delay the process of cognitive impairment in the HFe mouse model. Pediococcus acidilactici (PA), but not Bacillus subtilis (BN) administration in HFe-fed mice reduced brain iron accumulation, enhanced global alkaline phosphatase (AP) activity, accelerated dephosphorylation, lowered phosphate levels and increased brain urate production. In addition, because PA regulated cognitive behavior in HFe fed mice, we used the transgenic Caenorhabditis elegans with over-expressed human p-tau for model, and then PA fed worms became more active and longer lived than E.coli fed worms, as well as p-tau was down-regulated. These results suggest that brain iron accumulation influences AD risk proteins and various metabolites. Furthermore, PA was shown to reverse tau-induced pathogenesis via iron transporters and AP-urate interaction. CONCLUSIONS PA administration studies demonstrate that PA is an important mediator of tau protein reduction, p-tau expression and neurodegenerative behavior both in Caenorhabditis elegans and iron-overload mice. Finally, our results provide candidates for AP modulation strategies as preventive tools for promoting brain health. Video Abstract.
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Affiliation(s)
- Yong Zhang
- Shunde Innovation School, Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Weiyi Qian
- Shunde Innovation School, Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
| | - Yitong Zhang
- Shunde Innovation School, Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
| | - Yan Ma
- Shunde Innovation School, Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
| | - Jiamin Qian
- Shunde Innovation School, Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
| | - Jinping Li
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Xun Wei
- Shunde Innovation School, Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Yan Long
- Shunde Innovation School, Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China.
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China.
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China.
| | - Xiangyuan Wan
- Shunde Innovation School, Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing, 100083, China.
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China.
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China.
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8
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Gilad N, Mohanam MP, Darlyuk-Saadon I, Heng CKM, Plaschkes I, Benyamini H, Berezhnoy NV, Engelberg D. Asynchronous Pattern of MAPKs' Activity during Aging of Different Tissues and of Distinct Types of Skeletal Muscle. Int J Mol Sci 2024; 25:1713. [PMID: 38338990 PMCID: PMC10855984 DOI: 10.3390/ijms25031713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The MAPK p38α was proposed to be a prominent promoter of skeletal muscle aging. The skeletal muscle tissue is composed of various muscle types, and it is not known if p38α is associated with aging in all of them. It is also not known if p38α is associated with aging of other tissues. JNK and ERK were also proposed to be associated with aging of several tissues. Nevertheless, the pattern of p38α, JNK, and ERK activity during aging was not documented. Here, we documented the levels of phosphorylated/active p38α, Erk1/2, and JNKs in several organs as well as the soleus, tibialis anterior, quadriceps, gastrocnemius, and EDL muscles of 1-, 3-, 6-, 13-, 18-, and 24-month-old mice. We report that in most tissues and skeletal muscles, the MAPKs' activity does not change in the course of aging. In most tissues and muscles, p38α is in fact active at younger ages. The quadriceps and the lungs are exceptions, where p38α is significantly active only in mice 13 months old or older. Curiously, levels of active JNK and ERKs are also elevated in aged lungs and quadriceps. RNA-seq analysis of the quadriceps during aging revealed downregulation of proteins related to the extra-cellular matrix (ECM) and ERK signaling. A panel of mRNAs encoding cell cycle inhibitors and senescence-associated proteins, considered to be aging markers, was not found to be elevated. It seems that the pattern of MAPKs' activation in aging, as well as expression of known 'aging' components, are tissue- and muscle type-specific, supporting a notion that the process of aging is tissue- and even cell-specific.
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Affiliation(s)
- Nechama Gilad
- Department of Biological Chemistry, The Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
| | - Manju Payini Mohanam
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ilona Darlyuk-Saadon
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
| | - C. K. Matthew Heng
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Hadar Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Nikolay V. Berezhnoy
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - David Engelberg
- Department of Biological Chemistry, The Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
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9
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Lai J, Demirbas D, Kim J, Jeffries AM, Tolles A, Park J, Chittenden TW, Buckley PG, Yu TW, Lodato MA, Lee EA. ATM-deficiency-induced microglial activation promotes neurodegeneration in ataxia-telangiectasia. Cell Rep 2024; 43:113622. [PMID: 38159274 PMCID: PMC10908398 DOI: 10.1016/j.celrep.2023.113622] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/26/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024] Open
Abstract
While ATM loss of function has long been identified as the genetic cause of ataxia-telangiectasia (A-T), how it leads to selective and progressive degeneration of cerebellar Purkinje and granule neurons remains unclear. ATM expression is enriched in microglia throughout cerebellar development and adulthood. Here, we find evidence of microglial inflammation in the cerebellum of patients with A-T using single-nucleus RNA sequencing. Pseudotime analysis revealed that activation of A-T microglia preceded upregulation of apoptosis-related genes in granule and Purkinje neurons and that microglia exhibited increased neurotoxic cytokine signaling to granule and Purkinje neurons in A-T. To confirm these findings experimentally, we performed transcriptomic profiling of A-T induced pluripotent stem cell (iPSC)-derived microglia, which revealed cell-intrinsic microglial activation of cytokine production and innate immune response pathways compared to controls. Furthermore, A-T microglia co-culture with either control or A-T iPSC-derived neurons was sufficient to induce cytotoxicity. Taken together, these studies reveal that cell-intrinsic microglial activation may promote neurodegeneration in A-T.
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Affiliation(s)
- Jenny Lai
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Neuroscience, Harvard University, Boston, MA 02115, USA
| | - Didem Demirbas
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Junho Kim
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ailsa M Jeffries
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Allie Tolles
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Junseok Park
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas W Chittenden
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Computational Statistics and Bioinformatics Group, Genuity AI Research Institute, Genuity Science, Boston, MA 02114, USA
| | | | - Timothy W Yu
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael A Lodato
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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10
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Huang K, Liu X, Zhang Z, Wang T, Xu H, Li Q, Jia Y, Huang L, Kim P, Zhou X. AgeAnnoMO: a knowledgebase of multi-omics annotation for animal aging. Nucleic Acids Res 2024; 52:D822-D834. [PMID: 37850649 PMCID: PMC10767957 DOI: 10.1093/nar/gkad884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/16/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
Aging entails gradual functional decline influenced by interconnected factors. Multiple hallmarks proposed as common and conserved underlying denominators of aging on the molecular, cellular and systemic levels across multiple species. Thus, understanding the function of aging hallmarks and their relationships across species can facilitate the translation of anti-aging drug development from model organisms to humans. Here, we built AgeAnnoMO (https://relab.xidian.edu.cn/AgeAnnoMO/#/), a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8596 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, proteins, metabolites, mitochondrial genes, microbiotas and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. AgeAnnoMO not only facilitates a deeper and more generalizable understanding of aging mechanisms, but also provides potential insights of the specificity across tissues and species in aging process, which is important to develop the effective anti-aging interventions for diverse populations. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology and identifying the targetable biomarkers for aging research.
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Affiliation(s)
- Kexin Huang
- The Center of Gerontology and Geriatrics and West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Xi Liu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Zhaocan Zhang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Tiangang Wang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Haixia Xu
- The Center of Gerontology and Geriatrics and West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Qingxuan Li
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Yuhao Jia
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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11
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Dørum G, Hänggi NV, Burri D, Marti Y, Banemann R, Kulstein G, Courts C, Gosch A, Hadrys T, Haas C, Neubauer J. Selecting mRNA markers in blood for age estimation of the donor of a biological stain. Forensic Sci Int Genet 2024; 68:102976. [PMID: 38000161 DOI: 10.1016/j.fsigen.2023.102976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/13/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023]
Abstract
RNA has gained a substantial amount of attention within the forensic field over the last decade. There is evidence that RNAs are differentially expressed with biological age. Since RNA can be co-extracted with DNA from the same piece of evidence, RNA-based analysis appears as a promising molecular alternative for predicting the biological age and hence inferring the chronological age of a person. Using RNA-Seq data we searched for markers in blood potentially associated with age. We used our own RNA-Seq data from dried blood stains as well as publicly available RNA-Seq data from whole blood, and compared two different approaches to select candidate markers. The first approach focused on individual gene analysis with DESeq2 to select the genes most correlated with age, while the second approach employed lasso regression to select a set of genes for optimal prediction of age. We present two lists with 270 candidate markers, one for each approach.
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Affiliation(s)
- Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | - Dario Burri
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Yael Marti
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | | | - Cornelius Courts
- University Hospital of Cologne, Institute of Legal Medicine, Cologne, Germany
| | - Annica Gosch
- University Hospital of Cologne, Institute of Legal Medicine, Cologne, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office (BLKA), Munich, Germany
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Jacqueline Neubauer
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
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12
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Huang W, Bates R, Zou X, Queen NJ, Mo X, Arnold WD, Ray A, Owendoff G, Cao L. Environmental Enrichment Improves Motor Function and Muscle Transcriptome of Aged Mice. Adv Biol (Weinh) 2024; 8:e2300148. [PMID: 37518850 PMCID: PMC10825065 DOI: 10.1002/adbi.202300148] [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: 04/14/2023] [Revised: 06/29/2023] [Indexed: 08/01/2023]
Abstract
Aging results in the progressive decline of muscle strength. Interventions to maintain muscle strength may mitigate the age-related loss of physical function, thus maximizing health span. The work on environmental enrichment (EE), an experimental paradigm recapitulating aspects of an active lifestyle, has revealed EE-induced metabolic benefits mediated by a brain-fat axis across the lifespan of mice. EE initiated at 18-month of age shows a trend toward an increased mean lifespan. While previous work described EE's influences on the aging dynamics of several central-peripheral processes, its influence on muscle remained understudied. Here, the impact of EE is investigated on motor function, neuromuscular physiology, and the skeletal muscle transcriptome. EE is initiated in 20-month-old mice for a five-month period. EE mice exhibit greater relative lean mass that is associated with improved mobility and hindlimb grip strength. Transcriptomic profiling of muscle tissue reveals an EE-associated enrichment of gene expression within several metabolic pathways related to oxidative phosphorylation and the TCA cycle. Many mitochondrial-related genes-several of which participate in the electron transport chain-are upregulated. Stress-responsive signaling pathways are downregulated because of EE. The results suggest that EE improves motor function-possibly through preservation of mitochondrial function-even late in life.
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Affiliation(s)
- Wei Huang
- Department of Cancer Biology & Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Rhiannon Bates
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Xunchang Zou
- Department of Cancer Biology & Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Nicholas J. Queen
- Department of Cancer Biology & Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Xiaokui Mo
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - W. David Arnold
- Department of Neurology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Alissa Ray
- Department of Neurology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Gregory Owendoff
- Department of Neurology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Lei Cao
- Department of Cancer Biology & Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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13
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Oh HSH, Rutledge J, Nachun D, Pálovics R, Abiose O, Moran-Losada P, Channappa D, Urey DY, Kim K, Sung YJ, Wang L, Timsina J, Western D, Liu M, Kohlfeld P, Budde J, Wilson EN, Guen Y, Maurer TM, Haney M, Yang AC, He Z, Greicius MD, Andreasson KI, Sathyan S, Weiss EF, Milman S, Barzilai N, Cruchaga C, Wagner AD, Mormino E, Lehallier B, Henderson VW, Longo FM, Montgomery SB, Wyss-Coray T. Organ aging signatures in the plasma proteome track health and disease. Nature 2023; 624:164-172. [PMID: 38057571 PMCID: PMC10700136 DOI: 10.1038/s41586-023-06802-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/31/2023] [Indexed: 12/08/2023]
Abstract
Animal studies show aging varies between individuals as well as between organs within an individual1-4, but whether this is true in humans and its effect on age-related diseases is unknown. We utilized levels of human blood plasma proteins originating from specific organs to measure organ-specific aging differences in living individuals. Using machine learning models, we analysed aging in 11 major organs and estimated organ age reproducibly in five independent cohorts encompassing 5,676 adults across the human lifespan. We discovered nearly 20% of the population show strongly accelerated age in one organ and 1.7% are multi-organ agers. Accelerated organ aging confers 20-50% higher mortality risk, and organ-specific diseases relate to faster aging of those organs. We find individuals with accelerated heart aging have a 250% increased heart failure risk and accelerated brain and vascular aging predict Alzheimer's disease (AD) progression independently from and as strongly as plasma pTau-181 (ref. 5), the current best blood-based biomarker for AD. Our models link vascular calcification, extracellular matrix alterations and synaptic protein shedding to early cognitive decline. We introduce a simple and interpretable method to study organ aging using plasma proteomics data, predicting diseases and aging effects.
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Affiliation(s)
- Hamilton Se-Hwee Oh
- Graduate Program in Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Jarod Rutledge
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Graduate Program in Genetics, Stanford University, Stanford, CA, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Róbert Pálovics
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Olamide Abiose
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia Moran-Losada
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Divya Channappa
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Deniz Yagmur Urey
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University School of Engineering, Stanford, CA, USA
| | - Kate Kim
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Dan Western
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Menghan Liu
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Edward N Wilson
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Yann Guen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Taylor M Maurer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Haney
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew C Yang
- Departments of Neurology and Anatomy, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Bakar Aging Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Katrin I Andreasson
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sanish Sathyan
- Departments of Medicine and Genetics, Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, USA
| | - Erica F Weiss
- Department of Neurology, Montefiore Medical Center, New York, NY, USA
| | - Sofiya Milman
- Departments of Medicine and Genetics, Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, USA
| | - Nir Barzilai
- Departments of Medicine and Genetics, Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Anthony D Wagner
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Elizabeth Mormino
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Victor W Henderson
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Frank M Longo
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Tony Wyss-Coray
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
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14
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Hahn O, Foltz AG, Atkins M, Kedir B, Moran-Losada P, Guldner IH, Munson C, Kern F, Pálovics R, Lu N, Zhang H, Kaur A, Hull J, Huguenard JR, Grönke S, Lehallier B, Partridge L, Keller A, Wyss-Coray T. Atlas of the aging mouse brain reveals white matter as vulnerable foci. Cell 2023; 186:4117-4133.e22. [PMID: 37591239 PMCID: PMC10528304 DOI: 10.1016/j.cell.2023.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/17/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]
Abstract
Aging is the key risk factor for cognitive decline, yet the molecular changes underlying brain aging remain poorly understood. Here, we conducted spatiotemporal RNA sequencing of the mouse brain, profiling 1,076 samples from 15 regions across 7 ages and 2 rejuvenation interventions. Our analysis identified a brain-wide gene signature of aging in glial cells, which exhibited spatially defined changes in magnitude. By integrating spatial and single-nucleus transcriptomics, we found that glial aging was particularly accelerated in white matter compared with cortical regions, whereas specialized neuronal populations showed region-specific expression changes. Rejuvenation interventions, including young plasma injection and dietary restriction, exhibited distinct effects on gene expression in specific brain regions. Furthermore, we discovered differential gene expression patterns associated with three human neurodegenerative diseases, highlighting the importance of regional aging as a potential modulator of disease. Our findings identify molecular foci of brain aging, providing a foundation to target age-related cognitive decline.
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Affiliation(s)
- Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Aulden G Foltz
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Micaiah Atkins
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Blen Kedir
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia Moran-Losada
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ian H Guldner
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Christy Munson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA; Vilcek Institute of Graduate Biomedical Sciences, NYU Langone Health, New York City, NY, USA
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Róbert Pálovics
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nannan Lu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hui Zhang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Achint Kaur
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob Hull
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Cologne, Germany; Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA; Stanford University, The Phil and Penny Knight Initiative for Brain Resilience, Stanford, CA, USA.
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15
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Takasugi M, Yoshida Y, Nonaka Y, Ohtani N. Gene expressions associated with longer lifespan and aging exhibit similarity in mammals. Nucleic Acids Res 2023; 51:7205-7219. [PMID: 37351606 PMCID: PMC10415134 DOI: 10.1093/nar/gkad544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Although molecular features underlying aging and species maximum lifespan (MLS) have been comprehensively studied by transcriptome analyses, the actual impact of transcriptome on aging and MLS remains elusive. Here, we found that transcriptional signatures that are associated with mammalian MLS exhibited significant similarity to those of aging. Moreover, transcriptional signatures of longer MLS and aging both exhibited significant similarity to that of longer-lived mouse strains, suggesting that gene expression patterns associated with species MLS contribute to extended lifespan even within a species and that aging-related gene expression changes overall represent adaptations that extend lifespan rather than deterioration. Finally, we found evidence of co-evolution of MLS and promoter sequences of MLS-associated genes, highlighting the evolutionary contribution of specific transcription factor binding motifs such as that of E2F1 in shaping MLS-associated gene expression signature. Our results highlight the importance of focusing on adaptive aspects of aging transcriptome and demonstrate that cross-species genomics can be a powerful approach for understanding adaptive aging transcriptome.
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Affiliation(s)
- Masaki Takasugi
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Yuya Yoshida
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Yoshiki Nonaka
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Naoko Ohtani
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
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16
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Abstract
Organismal aging exhibits wide-ranging hallmarks in divergent cell types across tissues, organs, and systems. The advancement of single-cell technologies and generation of rich datasets have afforded the scientific community the opportunity to decode these hallmarks of aging at an unprecedented scope and resolution. In this review, we describe the technological advancements and bioinformatic methodologies enabling data interpretation at the cellular level. Then, we outline the application of such technologies for decoding aging hallmarks and potential intervention targets and summarize common themes and context-specific molecular features in representative organ systems across the body. Finally, we provide a brief summary of available databases relevant for aging research and present an outlook on the opportunities in this emerging field.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xu Chi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Zhejun Ji
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China;
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jie Ren
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;
- University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China;
- University of Chinese Academy of Sciences, Beijing, China
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17
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Statistical inference on the significance of rows and columns for matrix-valued data in an additive model. TEST-SPAIN 2023. [DOI: 10.1007/s11749-023-00852-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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18
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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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19
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Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs. PLoS One 2023; 18:e0281286. [PMID: 36745614 PMCID: PMC9901809 DOI: 10.1371/journal.pone.0281286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/19/2023] [Indexed: 02/07/2023] Open
Abstract
Having observed that gene expressions have a correlation, the Library of Integrated Network-based Cell-Signature program selects 1000 landmark genes to predict the remaining gene expression value. Further works have improved the prediction result by using deep learning models. However, these models ignore the latent structure of genes, limiting the accuracy of the experimental results. We therefore propose a novel neural network named Neighbour Connection Neural Network(NCNN) to utilize the gene interaction graph information. Comparing to the popular GCN model, our model incorperates the graph information in a better manner. We validate our model under two different settings and show that our model promotes prediction accuracy comparing to the other models.
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20
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Wolff CA, Gutierrez-Monreal MA, Meng L, Zhang X, Douma LG, Costello HM, Douglas CM, Ebrahimi E, Pham A, Oliveira AC, Fu C, Nguyen A, Alava BR, Hesketh SJ, Morris AR, Endale MM, Crislip GR, Cheng KY, Schroder EA, Delisle BP, Bryant AJ, Gumz ML, Huo Z, Liu AC, Esser KA. Defining the age-dependent and tissue-specific circadian transcriptome in male mice. Cell Rep 2023; 42:111982. [PMID: 36640301 PMCID: PMC9929559 DOI: 10.1016/j.celrep.2022.111982] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/01/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023] Open
Abstract
Cellular circadian clocks direct a daily transcriptional program that supports homeostasis and resilience. Emerging evidence has demonstrated age-associated changes in circadian functions. To define age-dependent changes at the systems level, we profile the circadian transcriptome in the hypothalamus, lung, heart, kidney, skeletal muscle, and adrenal gland in three age groups. We find age-dependent and tissue-specific clock output changes. Aging reduces the number of rhythmically expressed genes (REGs), indicative of weakened circadian control. REGs are enriched for the hallmarks of aging, adding another dimension to our understanding of aging. Analyzing differential gene expression within a tissue at four different times of day identifies distinct clusters of differentially expressed genes (DEGs). Increased variability of gene expression across the day is a common feature of aged tissues. This analysis extends the landscape for understanding aging and highlights the impact of aging on circadian clock function and temporal changes in gene expression.
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Affiliation(s)
- Christopher A Wolff
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Miguel A Gutierrez-Monreal
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA; Claude D. Pepper Older Americans Independence Center, University of Florida, Gainesville, FL 32610, USA
| | - Lingsong Meng
- Department of Biostatistics, University of Florida, Gainesville, FL 32610, USA
| | - Xiping Zhang
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lauren G Douma
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Hannah M Costello
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Collin M Douglas
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Elnaz Ebrahimi
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ann Pham
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Aline C Oliveira
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Chunhua Fu
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Amy Nguyen
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Bryan R Alava
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Stuart J Hesketh
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Andrew R Morris
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mehari M Endale
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - G Ryan Crislip
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Kit-Yan Cheng
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Elizabeth A Schroder
- Internal Medicine, Pulmonary, University of Kentucky, Lexington, KY 40506, USA; Department of Physiology, University of Kentucky, Lexington, KY 40506, USA
| | - Brian P Delisle
- Department of Physiology, University of Kentucky, Lexington, KY 40506, USA
| | - Andrew J Bryant
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Michelle L Gumz
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; Center for Integrative Cardiovascular and Metabolic Disease, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL 32610, USA.
| | - Andrew C Liu
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
| | - Karyn A Esser
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA; Claude D. Pepper Older Americans Independence Center, University of Florida, Gainesville, FL 32610, USA.
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21
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Huang K, Gong H, Guan J, Zhang L, Hu C, Zhao W, Huang L, Zhang W, Kim P, Zhou X. AgeAnno: a knowledgebase of single-cell annotation of aging in human. Nucleic Acids Res 2023; 51:D805-D815. [PMID: 36200838 PMCID: PMC9825500 DOI: 10.1093/nar/gkac847] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 01/30/2023] Open
Abstract
Aging is a complex process that accompanied by molecular and cellular alterations. The identification of tissue-/cell type-specific biomarkers of aging and elucidation of the detailed biological mechanisms of aging-related genes at the single-cell level can help to understand the heterogeneous aging process and design targeted anti-aging therapeutics. Here, we built AgeAnno (https://relab.xidian.edu.cn/AgeAnno/#/), a knowledgebase of single cell annotation of aging in human, aiming to provide comprehensive characterizations for aging-related genes across diverse tissue-cell types in human by using single-cell RNA and ATAC sequencing data (scRNA and scATAC). The current version of AgeAnno houses 1 678 610 cells from 28 healthy tissue samples with ages ranging from 0 to 110 years. We collected 5580 aging-related genes from previous resources and performed dynamic functional annotations of the cellular context. For the scRNA data, we performed analyses include differential gene expression, gene variation coefficient, cell communication network, transcription factor (TF) regulatory network, and immune cell proportionc. AgeAnno also provides differential chromatin accessibility analysis, motif/TF enrichment and footprint analysis, and co-accessibility peak analysis for scATAC data. AgeAnno will be a unique resource to systematically characterize aging-related genes across diverse tissue-cell types in human, and it could facilitate antiaging and aging-related disease research.
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Affiliation(s)
- Kexin Huang
- West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Med-X Center for Informatics, Sichuan University,Chengdu,Sichuan 610041, P.R. China
| | - Hoaran Gong
- West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Med-X Center for Informatics, Sichuan University,Chengdu,Sichuan 610041, P.R. China
| | - Jingjing Guan
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, P.R. China
| | - Lingxiao Zhang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, P.R. China
| | - Changbao Hu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, P.R. China
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, P.R. China
| | - Wei Zhang
- West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Med-X Center for Informatics, Sichuan University,Chengdu,Sichuan 610041, P.R. China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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22
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Ashton KJ, Kiessling CJ, Thompson JLM, Aziz AY, Thomas WG, Headrick JP, Reichelt ME. Early cardiac aging linked to impaired stress-resistance and transcriptional control of stress response, quality control and mitochondrial pathways. Exp Gerontol 2023; 171:112011. [PMID: 36347360 DOI: 10.1016/j.exger.2022.112011] [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: 03/20/2022] [Revised: 10/18/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
Abstract
Phenotypic and transcriptomic evidence of early cardiac aging, and associated mechanisms, were investigated in young to middle-aged male mice (C57Bl/6; ages 8, 16, 32, 48 wks). Left ventricular gene expression (profiled via Illumina MouseWG-6 BeadChips), contractile and coronary function, and stress-resistance were assessed in Langendorff perfused hearts under normoxic conditions and following ischemic insult (20 min global ischemia-45 min reperfusion; I-R). Baseline or normoxic contractile function was unaltered by age, while cardiac and coronary 'reserves' (during β-adrenoceptor stimulation; 1 μM isoproterenol) declined by 48 wks. Resistance to I-R injury fell from 16 to 32 wks. Age-dependent transcriptional changes In un-stressed hearts were limited to 104 genes (>1.3-fold; 0.05 FDR), supporting: up-regulated innate defenses (glutathione and xenobiotic metabolism, chemotaxis, interleukins) and catecholamine secretion; and down-regulated extracellular matrix (ECM), growth factor and survival (PI3K/Akt) signaling. In stressed (post-ischemic) myocardium, ∼15-times as many genes (1528) were age-dependent, grouped into 6 clusters (>1.3-fold change; 0.05 FDR): most changing from 16 wks (45 % up/44 % down), a further 5 % declining from 32 wks. Major age-dependent Biological Processes in I-R hearts reveal: declining ATP metabolism, oxidative phosphorylation, cardiac contraction and morphogenesis, phospholipid metabolism and calcineurin signaling; increasing proteolysis and negative control of MAPK; and mixed changes in nuclear transport and angiogenic genes. Pathway analysis supports reductions in: autophagy, stress response, ER protein processing, mRNA surveillance and ribosome/translation genes; with later falls in mitochondrial biogenesis, oxidative phosphorylation and proteasome genes in I-R hearts. Summarizing, early cardiac aging is evident from 16 to 32 wks in male mice, characterized by: declining cardiovascular reserve and stress-resistance, transcriptomic evidence of constitutive stress and altered catecholamine and survival/growth signaling in healthy hearts; and declining stress response, quality control, mitochondrial energy metabolism and cardiac modeling processes in stressed hearts. These very early changes, potentially key substrate for advanced aging, may inform approaches to healthy aging and cardioprotection in the adult heart.
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Affiliation(s)
- Kevin J Ashton
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, QLD, Australia
| | - Can J Kiessling
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, QLD, Australia
| | - Jamie-Lee M Thompson
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, QLD, Australia
| | - Aliah Y Aziz
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, QLD, Australia
| | - Walter G Thomas
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
| | - John P Headrick
- School of Medical Science, Griffith University, Southport, QLD, Australia
| | - Melissa E Reichelt
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia.
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23
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Abstract
Age is the key risk factor for diseases and disabilities of the elderly. Efforts to tackle age-related diseases and increase healthspan have suggested targeting the ageing process itself to 'rejuvenate' physiological functioning. However, achieving this aim requires measures of biological age and rates of ageing at the molecular level. Spurred by recent advances in high-throughput omics technologies, a new generation of tools to measure biological ageing now enables the quantitative characterization of ageing at molecular resolution. Epigenomic, transcriptomic, proteomic and metabolomic data can be harnessed with machine learning to build 'ageing clocks' with demonstrated capacity to identify new biomarkers of biological ageing.
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Affiliation(s)
- Jarod Rutledge
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
| | - Hamilton Oh
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
- Graduate Program in Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
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24
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Möller S, Saul N, Projahn E, Barrantes I, Gézsi A, Walter M, Antal P, Fuellen G. Gene co-expression analyses of health(span) across multiple species. NAR Genom Bioinform 2022; 4:lqac083. [PMID: 36458022 PMCID: PMC9706456 DOI: 10.1093/nargab/lqac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/20/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
Health(span)-related gene clusters/modules were recently identified based on knowledge about the cross-species genetic basis of health, to interpret transcriptomic datasets describing health-related interventions. However, the cross-species comparison of health-related observations reveals a lot of heterogeneity, not least due to widely varying health(span) definitions and study designs, posing a challenge for the exploration of conserved healthspan modules and, specifically, their transfer across species. To improve the identification and exploration of conserved/transferable healthspan modules, here we apply an established workflow based on gene co-expression network analyses employing GEO/ArrayExpress data for human and animal models, and perform a comprehensive meta-study of the resulting modules related to health(span), yielding a small set of literature backed health(span) candidate genes. For each experiment, WGCNA (weighted gene correlation network analysis) was used to infer modules of genes which correlate in their expression with a 'health phenotype score' and to determine the most-connected (hub) genes (and their interactions) for each such module. After mapping these hub genes to their human orthologs, 12 health(span) genes were identified in at least two species (ACTN3, ANK1, MRPL18, MYL1, PAXIP1, PPP1CA, SCN3B, SDCBP, SKIV2L, TUBG1, TYROBP, WIPF1), for which enrichment analysis by g:profiler found an association with actin filament-based movement and associated organelles, as well as muscular structures. We conclude that a meta-study of hub genes from co-expression network analyses for the complex phenotype health(span), across multiple species, can yield molecular-mechanistic insights and can direct experimentalists to further investigate the contribution of individual genes and their interactions to health(span).
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Affiliation(s)
- Steffen Möller
- To whom correspondence should be addressed. Tel: +49 381 494 7361; Fax: +49 381 494 7203;
| | - Nadine Saul
- Humboldt-University of Berlin, Institute of Biology, Berlin, Germany
| | - Elias Projahn
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
| | - Israel Barrantes
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
| | - András Gézsi
- Budapest University of Technology and Economics, Department of Measurement and Information Systems, Budapest, Hungary
| | - Michael Walter
- Rostock University Medical Center, Institute for Clinical Chemistry and Laboratory Medicine, Rostock, Germany
| | - Péter Antal
- Budapest University of Technology and Economics, Department of Measurement and Information Systems, Budapest, Hungary
| | - Georg Fuellen
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
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25
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Treatment effects of phosphorylated Chrysanthemum indicum polysaccharides on duck virus hepatitis by protecting mitochondrial function from oxidative damage. Vet Microbiol 2022; 275:109600. [DOI: 10.1016/j.vetmic.2022.109600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/28/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
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26
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Chung EJ, Kwon S, Shankavaram U, White AO, Das S, Citrin DE. Natural variation in macrophage polarization and function impact pneumocyte senescence and susceptibility to fibrosis. Aging (Albany NY) 2022; 14:7692-7717. [PMID: 36173617 PMCID: PMC9596223 DOI: 10.18632/aging.204309] [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: 05/26/2022] [Accepted: 09/17/2022] [Indexed: 11/25/2022]
Abstract
Radiation-induced pulmonary fibrosis (RIPF), a late adverse event of radiation therapy, is characterized by infiltration of inflammatory cells, progressive loss of alveolar structure, secondary to the loss of pneumocytes and accumulation of collagenous extracellular matrix, and senescence of alveolar stem cells. Differential susceptibility to lung injury from radiation and other toxic insults across mouse strains is well described but poorly understood. The accumulation of alternatively activated macrophages (M2) has previously been implicated in the progression of lung fibrosis. Using fibrosis prone strain (C57L), a fibrosis-resistant strain (C3H/HeN), and a strain with intermediate susceptibility (C57BL6/J), we demonstrate that the accumulation of M2 macrophages correlates with the manifestation of fibrosis. A comparison of primary macrophages derived from each strain identified phenotypic and functional differences, including differential expression of NADPH Oxidase 2 and production of superoxide in response to M2 polarization and activation. Further, the sensitivity of primary AECII to senescence after coculture with M2 macrophages was strain dependent and correlated to observations of sensitivity to fibrosis and senescence in vivo. Taken together, these data support that the relative susceptibility of different strains to RIPF is closely related to distinct senescence responses induced through pulmonary M2 macrophages after thoracic irradiation.
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Affiliation(s)
- Eun Joo Chung
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seokjoo Kwon
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Uma Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ayla O White
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shaoli Das
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah E Citrin
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Patil S, Reedy JL, Scroggins BT, White AO, Kwon S, Shankavaram U, López-Coral A, Chung EJ, Citrin DE. Senescence-associated tumor growth is promoted by 12-Lipoxygenase. Aging (Albany NY) 2022; 14:1068-1086. [PMID: 35158337 PMCID: PMC8876904 DOI: 10.18632/aging.203890] [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: 10/20/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022]
Abstract
Radiation therapy is a commonly used treatment modality for cancer. Although effective in providing local tumor control, radiation causes oxidative stress, inflammation, immunomodulatory and mitogenic cytokine production, extracellular matrix production, and premature senescence in lung parenchyma. The senescence associated secretory phenotype (SASP) can promote inflammation and stimulate alterations in the surrounding tissue. Therefore, we hypothesized that radiation-induced senescent parenchymal cells in irradiated lung would enhance tumor growth. Using a murine syngeneic tumor model of melanoma and non-small cell lung cancer lung metastasis, we demonstrate that radiation causes a significant increase in markers of premature senescence in lung parenchyma within 4 to 8 weeks. Further, injection of B16F0 (melanoma) or Lewis Lung carcinoma (epidermoid lung cancer) cells at these time points after radiation results in an increase in the number and size of pulmonary tumor nodules relative to unirradiated mice. Treatment of irradiated mice with a senolytic agent (ABT-737) or agents that prevent senescence (rapamycin, INK-128) was sufficient to reduce radiation-induced lung parenchymal senescence and to mitigate radiation-enhanced tumor growth. These agents abrogated radiation-induced expression of 12-Lipoxygenase (12-LOX), a molecule implicated in several deleterious effects of senescence. Deficiency of 12-LOX prevented radiation-enhanced tumor growth. Together, these data demonstrate the pro-tumorigenic role of radiation-induced senescence, introduces the dual TORC inhibitor INK-128 as an effective agent for prevention of radiation-induced normal tissue senescence, and identifies senescence-associated 12-LOX activity as an important component of the pro-tumorigenic irradiated tissue microenvironment. These studies suggest that combining senotherapeutic agents with radiotherapy may decrease post-therapy tumor growth.
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Affiliation(s)
- Shilpa Patil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jessica L Reedy
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bradley T Scroggins
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ayla O White
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seokjoo Kwon
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Uma Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alfonso López-Coral
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Joo Chung
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah E Citrin
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Young AP, Denovan-Wright EM. The Dynamic Role of Microglia and the Endocannabinoid System in Neuroinflammation. Front Pharmacol 2022; 12:806417. [PMID: 35185547 PMCID: PMC8854262 DOI: 10.3389/fphar.2021.806417] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/24/2021] [Indexed: 12/13/2022] Open
Abstract
Microglia, the resident immune cells of the brain, can take on a range of pro- or anti-inflammatory phenotypes to maintain homeostasis. However, the sustained activation of pro-inflammatory microglia can lead to a state of chronic neuroinflammation characterized by high concentrations of neurotoxic soluble factors throughout the brain. In healthy brains, the inflammatory processes cease and microglia transition to an anti-inflammatory phenotype, but failure to halt the pro-inflammatory processes is a characteristic of many neurological disorders. The endocannabinoid system has been identified as a promising therapeutic target for chronic neuroinflammation as there is evidence that synthetic and endogenously produced cannabinoids temper the pro-inflammatory response of microglia and may encourage a switch to an anti-inflammatory phenotype. Activation of cannabinoid type 2 (CB2) receptors has been proposed as the mechanism of action responsible for these effects. The abundance of components of the endocannabinoid system in microglia also change dynamically in response to several brain pathologies. This can impact the ability of microglia to synthesize and degrade endocannabinoids or react to endogenous and exogenous cannabinoids. Cannabinoid receptors also participate in the formation of receptor heteromers which influences their function specifically in cells that express both receptors, such as microglia. This creates opportunities for drug-drug interactions between CB2 receptor-targeted therapies and other classes of drugs. In this article, we review the roles of pro- and anti-inflammatory microglia in the development and resolution of neuroinflammation. We also discuss the fluctuations observed in the components of the endocannabinoid in microglia and examine the potential of CB2 receptors as a therapeutic target in this context.
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Boche D, Gordon MN. Diversity of transcriptomic microglial phenotypes in aging and Alzheimer's disease. Alzheimers Dement 2022; 18:360-376. [PMID: 34223696 PMCID: PMC9059230 DOI: 10.1002/alz.12389] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 02/03/2023]
Abstract
The morphological plasticity of microglia has fascinated neuroscientists for 100 years. Attempts to classify functional phenotypes are hampered by similarities between endogenous brain microglia and peripheral myeloid cells that can enter the brain under pathological conditions. Recent advances in single-cell -omic methodologies have led to an explosion of data regarding gene expression in microglia. Herein, we review the diversity of microglial phenotypes in healthy brains, aging, and Alzheimer's disease (AD); identify knowledge gaps in the body of evidence; and suggest areas in which new knowledge would be useful. Data from human samples and mouse models are compared and contrasted. Understanding the molecular complexity of the microglial response repertoire will suggest new avenues for therapeutic treatments in AD.
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Affiliation(s)
- Delphine Boche
- Clinical Neurosciences, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Marcia N. Gordon
- Translational Neuroscience, Michigan State University College of Human Medicine, Grand Rapids, MI, USA,corresponding author: Marcia N. Gordon, PhD, Michigan State University GRRC, 400 Monroe Ave NW, Grand Rapids, MI, 49503 USA, , Telephone: (616) 234-2837
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Izgi H, Han D, Isildak U, Huang S, Kocabiyik E, Khaitovich P, Somel M, Dönertaş HM. Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity. eLife 2022; 11:68048. [PMID: 35098922 PMCID: PMC8880995 DOI: 10.7554/elife.68048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Developmental trajectories of gene expression may reverse in their direction during ageing, a phenomenon previously linked to cellular identity loss. Our analysis of cerebral cortex, lung, liver and muscle transcriptomes of 16 mice, covering development and ageing intervals, revealed widespread but tissue-specific ageing-associated expression reversals. Cumulatively, these reversals create a unique phenomenon: mammalian tissue transcriptomes diverge from each other during postnatal development, but during ageing, they tend to converge towards similar expression levels, a process we term Divergence followed by Convergence, or DiCo. We found that DiCo was most prevalent among tissue-specific genes and associated with loss of tissue identity, which is confirmed using data from independent mouse and human datasets. Further, using publicly available single-cell transcriptome data, we showed that DiCo could be driven both by alterations in tissue cell type composition and also by cell-autonomous expression changes within particular cell types.
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Affiliation(s)
- Hamit Izgi
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - DingDing Han
- CAS Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Ulas Isildak
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Shuyun Huang
- CAS Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Ece Kocabiyik
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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Watson ER, Taherian Fard A, Mar JC. Computational Methods for Single-Cell Imaging and Omics Data Integration. Front Mol Biosci 2022; 8:768106. [PMID: 35111809 PMCID: PMC8801747 DOI: 10.3389/fmolb.2021.768106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Integrating single cell omics and single cell imaging allows for a more effective characterisation of the underlying mechanisms that drive a phenotype at the tissue level, creating a comprehensive profile at the cellular level. Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques such as MRI, CT, and PET. These imaging technologies complement omics-based data in biomedical research because they are helpful for identifying associations between genotype and phenotype, along with functional changes occurring at the tissue level. Single cell imaging can act as an intermediary between these levels. Meanwhile new technologies continue to arrive that can be used to interrogate the genome of single cells and its related omics datasets. As these two areas, single cell imaging and single cell omics, each advance independently with the development of novel techniques, the opportunity to integrate these data types becomes more and more attractive. This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further our understanding of complex biological phenomena like ageing. We include an emphasis on machine learning algorithms because of their ability to identify complex patterns in large multidimensional data.
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Affiliation(s)
| | - Atefeh Taherian Fard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Jessica Cara Mar
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
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Edara VV, Manning KE, Ellis M, Lai L, Moore KM, Foster SL, Floyd K, Davis-Gardner ME, Mantus G, Nyhoff LE, Bechnak S, Alaaeddine G, Naji A, Samaha H, Lee M, Bristow L, Hussaini L, Ciric CR, Nguyen PV, Gagne M, Roberts-Torres J, Henry AR, Godbole S, Grakoui A, Sexton M, Piantadosi A, Waggoner JJ, Douek DC, Anderson EJ, Rouphael N, Wrammert J, Suthar MS. mRNA-1273 and BNT162b2 mRNA vaccines have reduced neutralizing activity against the SARS-CoV-2 Omicron variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34981056 DOI: 10.1101/2021.09.09.459619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines generate potent neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the global emergence of SARS-CoV-2 variants with mutations in the spike protein, the principal antigenic target of these vaccines, has raised concerns over the neutralizing activity of vaccine-induced antibody responses. The Omicron variant, which emerged in November 2021, consists of over 30 mutations within the spike protein. Here, we used an authentic live virus neutralization assay to examine the neutralizing activity of the SARS-CoV-2 Omicron variant against mRNA vaccine-induced antibody responses. Following the 2nd dose, we observed a 30-fold reduction in neutralizing activity against the omicron variant. Through six months after the 2nd dose, none of the sera from naïve vaccinated subjects showed neutralizing activity against the Omicron variant. In contrast, recovered vaccinated individuals showed a 22-fold reduction with more than half of the subjects retaining neutralizing antibody responses. Following a booster shot (3rd dose), we observed a 14-fold reduction in neutralizing activity against the omicron variant and over 90% of boosted subjects showed neutralizing activity against the omicron variant. These findings show that a 3rd dose is required to provide robust neutralizing antibody responses against the Omicron variant.
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Kluever V, Fornasiero EF. Principles of brain aging: Status and challenges of modeling human molecular changes in mice. Ageing Res Rev 2021; 72:101465. [PMID: 34555542 DOI: 10.1016/j.arr.2021.101465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023]
Abstract
Due to the extension of human life expectancy, the prevalence of cognitive impairment is rising in the older portion of society. Developing new strategies to delay or attenuate cognitive decline is vital. For this purpose, it is imperative to understand the cellular and molecular events at the basis of brain aging. While several organs are directly accessible to molecular analysis through biopsies, the brain constitutes a notable exception. Most of the molecular studies are performed on postmortem tissues, where cell death and tissue damage have already occurred. Hence, the study of the molecular aspects of cognitive decline largely relies on animal models and in particular on small mammals such as mice. What have we learned from these models? Do these animals recapitulate the changes observed in humans? What should we expect from future mouse studies? In this review we answer these questions by summarizing the state of the research that has addressed cognitive decline in mice from several perspectives, including genetic manipulation and omics strategies. We conclude that, while extremely valuable, mouse models have limitations that can be addressed by the optimal design of future studies and by ensuring that results are cross-validated in the human context.
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34
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Tabibzadeh S. CircadiOmic medicine and aging. Ageing Res Rev 2021; 71:101424. [PMID: 34389481 DOI: 10.1016/j.arr.2021.101424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 01/15/2023]
Abstract
The earth displays daily, seasonal and annual environmental cycles that have led to evolutionarily adapted ultradian, circadian and infradian rhythmicities in the entire biosphere. All biological organisms must adapt to these cycles that synchronize the function of their circadiome. The objective of this review is to discuss the latest knowledge regarding the role of circadiomics in health and aging. The biological timekeepers are responsive to the environmental cues at microsecond to seasonal time-scales and act with precision of a clock machinery. The robustness of these rhythms is essential to normal daily function of cells, tissues and organs. Mis-alignment of circadian rhythms makes the individual prone to aging, sleep disorders, cancer, diabetes, and neuro-degenerative diseases. Circadian and CircadiOmic medicine are emerging fields that leverage our in-depth understanding of health issues, that arise as a result of disturbances in circadian rhythms, towards establishing better therapeutic approaches in personalized medicine and for geroprotection.
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Affiliation(s)
- Siamak Tabibzadeh
- Frontiers in Bioscience Research Institute in Aging and Cancer, 16471 Scientific Way, Irvine, CA 92618, United States.
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35
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Beyer AM, Norwood Toro LE, Hughes WE, Young M, Clough AV, Gao F, Medhora M, Audi SH, Jacobs ER. Autophagy, TERT, and mitochondrial dysfunction in hyperoxia. Am J Physiol Heart Circ Physiol 2021; 321:H985-H1003. [PMID: 34559580 PMCID: PMC8616608 DOI: 10.1152/ajpheart.00166.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/31/2021] [Accepted: 09/16/2021] [Indexed: 02/06/2023]
Abstract
Ventilation with gases containing enhanced fractions of oxygen is the cornerstone of therapy for patients with hypoxia and acute respiratory distress syndrome. Yet, hyperoxia treatment increases free reactive oxygen species (ROS)-induced lung injury, which is reported to disrupt autophagy/mitophagy. Altered extranuclear activity of the catalytic subunit of telomerase, telomerase reverse transcriptase (TERT), plays a protective role in ROS injury and autophagy in the systemic and coronary endothelium. We investigated interactions between autophagy/mitophagy and TERT that contribute to mitochondrial dysfunction and pulmonary injury in cultured rat lung microvascular endothelial cells (RLMVECs) exposed in vitro, and rat lungs exposed in vivo to hyperoxia for 48 h. Hyperoxia-induced mitochondrial damage in rat lungs [TOMM20, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)], which was paralleled by increased markers of inflammation [myeloperoxidase (MPO), IL-1β, TLR9], impaired autophagy signaling (Beclin-1, LC3B-II/1, and p62), and decreased the expression of TERT. Mitochondrial-specific autophagy (mitophagy) was not altered, as hyperoxia increased expression of Pink1 but not Parkin. Hyperoxia-induced mitochondrial damage (TOMM20) was more pronounced in rats that lack the catalytic subunit of TERT and resulted in a reduction in cellular proliferation rather than cell death in RLMVECs. Activation of TERT or autophagy individually offset mitochondrial damage (MTT). Combined activation/inhibition failed to alleviate hyperoxic-induced mitochondrial damage in vitro, whereas activation of autophagy in vivo decreased mitochondrial damage (MTT) in both wild type (WT) and rats lacking TERT. Functionally, activation of either TERT or autophagy preserved transendothelial membrane resistance. Altogether, these observations show that activation of autophagy/mitophagy and/or TERT mitigate loss of mitochondrial function and barrier integrity in hyperoxia.NEW & NOTEWORTHY In cultured pulmonary artery endothelial cells and in lungs exposed in vivo to hyperoxia, autophagy is activated, but clearance of autophagosomes is impaired in a manner that suggests cross talk between TERT and autophagy. Stimulation of autophagy prevents hyperoxia-induced decreases in mitochondrial metabolism and sustains monolayer resistance. Hyperoxia increases mitochondrial outer membrane (TOMM20) protein, decreases mitochondrial function, and reduces cellular proliferation without increasing cell death.
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Affiliation(s)
- Andreas M Beyer
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Laura E Norwood Toro
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - William E Hughes
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Micaela Young
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Anne V Clough
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
- Research Service, Zablocki Veterans Affairs Medical Center, Milwaukee Wisconsin
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, Wisconsin
| | - Feng Gao
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Meetha Medhora
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
- Research Service, Zablocki Veterans Affairs Medical Center, Milwaukee Wisconsin
| | - Said H Audi
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
- Research Service, Zablocki Veterans Affairs Medical Center, Milwaukee Wisconsin
- Department of Biomedical Engineering, Marquette University, Milwaukee, Wisconsin
| | - Elizabeth R Jacobs
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
- Research Service, Zablocki Veterans Affairs Medical Center, Milwaukee Wisconsin
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36
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Randhawa V, Kumar M. An integrated network analysis approach to identify potential key genes, transcription factors, and microRNAs regulating human hematopoietic stem cell aging. Mol Omics 2021; 17:967-984. [PMID: 34605522 DOI: 10.1039/d1mo00199j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hematopoietic stem cells (HSCs) undergo functional deterioration with increasing age that causes loss of their self-renewal and regenerative potential. Despite various efforts, significant success in identifying molecular regulators of HSC aging has not been achieved, one prime reason being the non-availability of appropriate human HSC samples. To demonstrate the scope of integrating and re-analyzing the HSC transcriptomics data available, we used existing tools and databases to structure a sequential data analysis pipeline to predict potential candidate genes, transcription factors, and microRNAs simultaneously. This sequential approach comprises (i) collecting matched young and aged mice HSC sample datasets, (ii) identifying differentially expressed genes, (iii) identifying human homologs of differentially expressed genes, (iv) inferring gene co-expression network modules, and (v) inferring the microRNA-transcription factor-gene regulatory network. Systems-level analyses of HSC interaction networks provided various insights based on which several candidates were predicted. For example, 16 HSC aging-related candidate genes were predicted (e.g., CD38, BRCA1, AGTR1, GSTM1, etc.) from GCN analysis. Following this, the shortest path distance-based analyses of the regulatory network predicted several novel candidate miRNAs and TFs. Among these, miR-124-3p was a common regulator in candidate gene modules, while TFs MYC and SP1 were identified to regulate various candidate genes. Based on the regulatory interactions among candidate genes, TFs, and miRNAs, a potential regulation model of biological processes in each of the candidate modules was predicted, which provided systems-level insights into the molecular complexity of each module to regulate HSC aging.
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Affiliation(s)
- Vinay Randhawa
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific & Industrial Research, Chandigarh-160036, India.
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific & Industrial Research, Chandigarh-160036, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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Rizvi F, Preston CC, Emelyanova L, Yousufuddin M, Viqar M, Dakwar O, Ross GR, Faustino RS, Holmuhamedov EL, Jahangir A. Effects of Aging on Cardiac Oxidative Stress and Transcriptional Changes in Pathways of Reactive Oxygen Species Generation and Clearance. J Am Heart Assoc 2021; 10:e019948. [PMID: 34369184 PMCID: PMC8475058 DOI: 10.1161/jaha.120.019948] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/13/2021] [Indexed: 11/30/2022]
Abstract
Background Age-related heart diseases are significant contributors to increased morbidity and mortality. Emerging evidence indicates that mitochondria within cardiomyocytes contribute to age-related increased reactive oxygen species (ROS) generation that plays an essential role in aging-associated cardiac diseases. Methods and Results The present study investigated differences between ROS production in cardiomyocytes isolated from adult (6 months) and aged (24 months) Fischer 344 rats, and in cardiac tissue of adult (18-65 years) and elderly (>65 years) patients with preserved cardiac function. Superoxide dismutase inhibitable ferricytochrome c reduction assay (1.32±0.63 versus 0.76±0.31 nMol/mg per minute; P=0.001) superoxide and H2O2 production, measured as dichlorofluorescein diacetate fluorescence (1646±428 versus 699±329, P=0.04), were significantly higher in the aged versus adult cardiomyocytes. Similarity in age-related alteration between rats and humans was identified in mitochondrial-electron transport chain-complex-I-associated increased oxidative-stress by MitoSOX fluorescence (53.66±18.58 versus 22.81±12.60; P=0.03) and in 4-HNE adduct levels (187.54±54.8 versus 47.83±16.7 ng/mg protein, P=0.0063), indicative of increased peroxidation in the elderly. These differences correlated with changes in functional enrichment of genes regulating ROS homeostasis pathways in aged human and rat hearts. Functional merged collective network and pathway enrichment analysis revealed common genes prioritized in human and rat aging-associated networks that underlay enriched functional terms of mitochondrial complex I and common pathways in the aging human and rat heart. Conclusions Aging sensitizes mitochondrial and extramitochondrial mechanisms of ROS buildup within the heart. Network analysis of the transcriptome highlights the critical elements involved with aging-related ROS homeostasis pathways common in rat and human hearts as targets.
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Affiliation(s)
- Farhan Rizvi
- Center for Integrative Research on Cardiovascular Aging (CIRCA)Aurora Research InstituteMilwaukeeWI
| | - Claudia C. Preston
- Division of Cardiovascular DiseasesDepartment of MedicineMayo Clinic RochesterRochesterMN
- Genetics and Genomics GroupSanford ResearchSioux FallsSD
| | - Larisa Emelyanova
- Center for Integrative Research on Cardiovascular Aging (CIRCA)Aurora Research InstituteMilwaukeeWI
| | | | - Maria Viqar
- Division of Cardiovascular DiseasesDepartment of MedicineMayo Clinic RochesterRochesterMN
| | - Omar Dakwar
- Center for Advanced Atrial Fibrillation TherapiesAdvocate Aurora HealthMilwaukeeWI
| | - Gracious R. Ross
- Center for Integrative Research on Cardiovascular Aging (CIRCA)Aurora Research InstituteMilwaukeeWI
| | | | - Ekhson L. Holmuhamedov
- Center for Integrative Research on Cardiovascular Aging (CIRCA)Aurora Research InstituteMilwaukeeWI
| | - Arshad Jahangir
- Center for Integrative Research on Cardiovascular Aging (CIRCA)Aurora Research InstituteMilwaukeeWI
- Division of Cardiovascular DiseasesDepartment of MedicineMayo Clinic RochesterRochesterMN
- Center for Advanced Atrial Fibrillation TherapiesAdvocate Aurora HealthMilwaukeeWI
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Ferreira M, Francisco S, Soares AR, Nobre A, Pinheiro M, Reis A, Neto S, Rodrigues AJ, Sousa N, Moura G, Santos MAS. Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues. Aging (Albany NY) 2021; 13:18150-18190. [PMID: 34330884 PMCID: PMC8351669 DOI: 10.18632/aging.203379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/21/2021] [Indexed: 02/06/2023]
Abstract
Gene expression alterations occurring with aging have been described for a multitude of species, organs, and cell types. However, most of the underlying studies rely on static comparisons of mean gene expression levels between age groups and do not account for the dynamics of gene expression throughout the lifespan. These studies also tend to disregard the pairwise relationships between gene expression profiles, which may underlie commonly altered pathways and regulatory mechanisms with age. To overcome these limitations, we have combined segmented regression analysis with weighted gene correlation network analysis (WGCNA) to identify high-confidence signatures of aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice in a publicly available RNA-Seq dataset (GSE132040). Functional enrichment analysis of the overlap of genes identified in both approaches showed that immune- and inflammation-related responses are prominently altered in the brain and the liver, while in the heart and the muscle, aging affects amino and fatty acid metabolism, and tissue regeneration, respectively, which reflects an age-related global loss of tissue function. We also explored sexual dimorphism in the aging mouse transcriptome and found the liver and the muscle to have the most pronounced gender differences in gene expression throughout the lifespan, particularly in proteostasis-related pathways. While the data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, which we highlight as important features of murine tissue physiological aging.
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Affiliation(s)
- Margarida Ferreira
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Stephany Francisco
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana R. Soares
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana Nobre
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Andreia Reis
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Sonya Neto
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana João Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Gabriela Moura
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Manuel A. S. Santos
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
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39
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Ravel-Godreuil C, Massiani-Beaudoin O, Mailly P, Prochiantz A, Joshi RL, Fuchs J. Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death. iScience 2021; 24:102756. [PMID: 34278264 PMCID: PMC8264156 DOI: 10.1016/j.isci.2021.102756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/14/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Age is a major risk factor for neurodegenerative diseases like Parkinson's disease, but few studies have explored the contribution of key hallmarks of aging, namely DNA methylation changes and heterochromatin destructuration, in the neurodegenerative process. Here, we investigated the consequences of viral overexpression of Gadd45b, a multifactorial protein involved in DNA demethylation, in the mouse midbrain. Gadd45b overexpression induced global and stable changes in DNA methylation, particularly in introns of genes related to neuronal functions, as well as on LINE-1 transposable elements. This was paralleled by disorganized heterochromatin, increased DNA damage, and vulnerability to oxidative stress. LINE-1 de-repression, a potential source of DNA damage, preceded Gadd45b-induced neurodegeneration, whereas prolonged Gadd45b expression deregulated expression of genes related to heterochromatin maintenance, DNA methylation, or Parkinson's disease. Our data indicates that aging-related alterations contribute to dopaminergic neuron degeneration with potential implications for Parkinson's disease.
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Affiliation(s)
- Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Mailly
- Orion Imaging Facility, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Labex Memolife, Université PSL, Paris, France
| | - Alain Prochiantz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rajiv L. Joshi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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40
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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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41
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Emechebe U, Nelson JW, Alkayed NJ, Kaul S, Adey AC, Barnes AP. Age-dependent transcriptional alterations in cardiac endothelial cells. Physiol Genomics 2021; 53:295-308. [PMID: 34097533 PMCID: PMC8321782 DOI: 10.1152/physiolgenomics.00037.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 02/08/2023] Open
Abstract
Aging is a significant risk factor for cardiovascular disease. Despite the fact that endothelial cells play critical roles in cardiovascular function and disease, the molecular impact of aging on this cell population in many organ systems remains unknown. In this study, we sought to determine age-associated transcriptional alterations in cardiac endothelial cells. Highly enriched populations of endothelial cells (ECs) isolated from the heart, brain, and kidney of young (3 mo) and aged (24 mo) C57/BL6 mice were profiled for RNA expression via bulk RNA sequencing. Approximately 700 cardiac endothelial transcripts significantly differ by age. Gene set enrichment analysis indicated similar patterns for cellular pathway perturbations. Receptor-ligand comparisons indicated parallel alterations in age-affected circulating factors and cardiac endothelial-expressed receptors. Gene and pathway enrichment analyses show that age-related transcriptional response of cardiac endothelial cells is distinct from that of endothelial cells derived from the brain or kidney vascular bed. Furthermore, single-cell analysis identified nine distinct EC subtypes and shows that the Apelin Receptor-enriched subtype is reduced with age in mouse heart. Finally, we identify age-dysregulated genes in specific aged cardiac endothelial subtypes.
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Affiliation(s)
- Uchenna Emechebe
- The Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon
| | - Jonathan W Nelson
- The Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon
| | - Nabil J Alkayed
- The Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, Oregon
| | - Sanjiv Kaul
- The Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon
| | - Andrew C Adey
- The Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
- Cancer Early Detection Advanced Research Institute, Oregon Health and Science University, Portland, Oregon
| | - Anthony P Barnes
- The Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, Oregon
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
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42
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Han Q, Li H, Jia M, Wang L, Zhao Y, Zhang M, Zhang Q, Meng Z, Shao J, Yang Y, Zhu L. Age-related changes in metabolites in young donor livers and old recipient sera after liver transplantation from young to old rats. Aging Cell 2021; 20:e13425. [PMID: 34157207 PMCID: PMC8282239 DOI: 10.1111/acel.13425] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/14/2021] [Accepted: 06/09/2021] [Indexed: 12/18/2022] Open
Abstract
Liver ageing not only damages liver function but also harms systemic metabolism. To better understand the mechanisms underlying liver ageing, we transplanted the livers of young rats to young and old rats and performed untargeted metabolomics to detect changes in the metabolites in the liver tissues and sera. A total of 153 metabolites in the livers and 83 metabolites in the sera were different between the old and young rats that did not undergo liver transplantation; among these metabolites, 7 different metabolites were observed in both the livers and sera. Five weeks after liver transplantation, the levels of 25 metabolites in the young donor livers were similar to those in the old rats, and this result probably occurred due to the effect of the whole‐body environment of the older recipients on the young livers. The 25 altered metabolites included organic acids and derivatives, lipids and lipid‐like molecules, etc. In the sera, the differences in 78 metabolites, which were significant between the young and old rats, were insignificant in the old recipient rats and made the metabolic profile of the old recipients more similar to that of the young recipients. Finally, combining the above metabolomic data with the transcriptomic data from the GEO, we found that the altered metabolites and genes in the liver were enriched in 9 metabolic pathways, including glycerophospholipid, arachidonic acid, histidine and linoleate. Thus, this study revealed important age‐related metabolites and potential pathways as well as the interaction between the liver and the whole‐body environment.
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Affiliation(s)
- Qunhua Han
- Department of Geriatrics The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic‐chemical Injury Diseases The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Hui Li
- NHFPC Key Laboratory of Combined Multi‐Organ Transplantation The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Mengyuan Jia
- Department of Geriatrics The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic‐chemical Injury Diseases The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Lin Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Yulan Zhao
- Zhejiang Provincial Key Laboratory of Pancreatic Disease The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Mangli Zhang
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Qin Zhang
- Department of Geriatrics The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic‐chemical Injury Diseases The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Zhuoxian Meng
- Zhejiang Provincial Key Laboratory of Pancreatic Disease The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Department of Pathology and Pathophysiology, and Key Laboratory of Disease Proteomics of Zhejiang Province Zhejiang University School of Medicine Hangzhou China
| | - Jimin Shao
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Department of Pathology and Pathophysiology, and Key Laboratory of Disease Proteomics of Zhejiang Province Zhejiang University School of Medicine Hangzhou China
- Zhejiang University Cancer Center Hangzhou China
| | - Yunmei Yang
- Department of Geriatrics The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic‐chemical Injury Diseases The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Lijun Zhu
- Department of Geriatrics The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic‐chemical Injury Diseases The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
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43
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Molecular evolution and the decline of purifying selection with age. Nat Commun 2021; 12:2657. [PMID: 33976227 PMCID: PMC8113359 DOI: 10.1038/s41467-021-22981-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Life history theory predicts that the intensity of selection declines with age, and this trend should impact how genes expressed at different ages evolve. Here we find consistent relationships between a gene’s age of expression and patterns of molecular evolution in two mammals (the human Homo sapiens and the mouse Mus musculus) and two insects (the malaria mosquito Anopheles gambiae and the fruit fly Drosophila melanogaster). When expressed later in life, genes fix nonsynonymous mutations more frequently, are more polymorphic for nonsynonymous mutations, and have shorter evolutionary lifespans, relative to those expressed early. The latter pattern is explained by a simple evolutionary model. Further, early-expressed genes tend to be enriched in similar gene ontology terms across species, while late-expressed genes show no such consistency. In humans, late-expressed genes are more likely to be linked to cancer and to segregate for dominant disease-causing mutations. Last, the effective strength of selection (Nes) decreases and the fraction of beneficial mutations increases with a gene’s age of expression. These results are consistent with the diminishing efficacy of purifying selection with age, as proposed by Medawar’s classic hypothesis for the evolution of senescence, and provide links between life history theory and molecular evolution. A fundamental principle of evolutionary theory is that the force of natural selection is weaker on traits expressed late in life relative to traits expressed early. Here, the authors find strong and consistent patterns of molecular evolution reflecting this principle in four species of animals, including humans.
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44
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Analysis of aging-related protein interactome and cross-network module comparisons across tissues provide new insights into aging. Comput Biol Chem 2021; 92:107506. [PMID: 34020164 DOI: 10.1016/j.compbiolchem.2021.107506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/09/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022]
Abstract
Delaying the human aging process and thus eliminating the risk factors for age-related diseases is one of the prime objectives. While various aging-associated genes and proteins have been characterized, which provide a significant understanding of the human aging process, a significant success in regulating aging is not achieved yet. Understanding how aging proteins interact with each other and also with other proteins could provide important insights into the underlying mechanisms governing the aging process. Therefore, in this work, information of gene expression was included to the static aging-related protein interactome to understand the network-based relationships among aging-related essential (AE) proteins, aging-related non-essential (ANE) proteins, and housekeeping-proteins that could regulate or influence aging. Comprehensive analyses provided various systems-level insights into the regulatory characteristics of aging; for example, (i) network-based correlation analysis predicted functional relationships among AE proteins and ANE proteins; (ii) network variability analysis predicted aging to affect different tissues in strikingly different ways by differentially regulating various regulatory interactions; (iii) cross-network comparisons identified two aging-related modules to be significantly conserved across most of the tissues. Overall, the findings obtained during this study could be helpful for researchers to delay, prevent, or even reverse various aspects of the aging.
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45
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Sándor S, Tátrai K, Czeibert K, Egyed B, Kubinyi E. CDKN2A Gene Expression as a Potential Aging Biomarker in Dogs. Front Vet Sci 2021; 8:660435. [PMID: 33981746 PMCID: PMC8107359 DOI: 10.3389/fvets.2021.660435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/18/2021] [Indexed: 12/04/2022] Open
Abstract
Describing evolutionary conserved physiological or molecular patterns, which can reliably mark the age of both model organisms and humans or predict the onset of age-related pathologies has become a priority in aging research. The age-related gene-expression changes of the Cyclin Dependent Kinase Inhibitor 2A (CDKN2A) gene have been well-documented in humans and rodents. However, data is lacking from other relevant species, including dogs. Therefore, we quantified the CDKN2A mRNA abundance in dogs of different ages, in four tissue types: the frontal cortex of the brain, temporal muscle, skin, and blood. We found a significant, positive correlation between CDKN2A relative expression values and age in the brain, muscle, and blood; however, no correlation was detected in the skin. The strongest correlation was detected in the brain tissue (CDKN2A/GAPDH: r = 0.757, p < 0.001), similarly to human findings, while the muscle and blood showed weaker, but significant correlation. Our results suggest that CDKN2A might be a potential blood-borne biomarker of aging in dogs, although the validation and optimization will require further, more focused research. Our current results also clearly demonstrate that the role of CDKN2A in aging is conserved in dogs, regarding both tissue specificity and a pivotal role of CDKN2A in brain aging.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, Senior Family Dog Project, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Kitti Tátrai
- Department of Ethology, Senior Family Dog Project, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Kálmán Czeibert
- Department of Ethology, Senior Family Dog Project, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Balázs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Enikő Kubinyi
- Department of Ethology, Senior Family Dog Project, ELTE Eötvös Loránd University, Budapest, Hungary
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46
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Koch SC, Nelson A, Hartenstein V. Structural aspects of the aging invertebrate brain. Cell Tissue Res 2021; 383:931-947. [PMID: 33409654 PMCID: PMC7965346 DOI: 10.1007/s00441-020-03314-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/28/2020] [Indexed: 11/26/2022]
Abstract
Aging is characterized by a decline in neuronal function in all animal species investigated so far. Functional changes are accompanied by and may be in part caused by, structurally visible degenerative changes in neurons. In the mammalian brain, normal aging shows abnormalities in dendrites and axons, as well as ultrastructural changes in synapses, rather than global neuron loss. The analysis of the structural features of aging neurons, as well as their causal link to molecular mechanisms on the one hand, and the functional decline on the other hand is crucial in order to understand the aging process in the brain. Invertebrate model organisms like Drosophila and C. elegans offer the opportunity to apply a forward genetic approach to the analysis of aging. In the present review, we aim to summarize findings concerning abnormalities in morphology and ultrastructure in invertebrate brains during normal aging and compare them to what is known for the mammalian brain. It becomes clear that despite of their considerably shorter life span, invertebrates display several age-related changes very similar to the mammalian condition, including the retraction of dendritic and axonal branches at specific locations, changes in synaptic density and increased accumulation of presynaptic protein complexes. We anticipate that continued research efforts in invertebrate systems will significantly contribute to reveal (and possibly manipulate) the molecular/cellular pathways leading to neuronal aging in the mammalian brain.
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Affiliation(s)
- Sandra C Koch
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Annie Nelson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA.
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47
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Cordeiro AV, Brícola RS, Braga RR, Lenhare L, Silva VRR, Anaruma CP, Katashima CK, Crisol BM, Simabuco FM, Silva ASR, Cintra DE, Moura LP, Pauli JR, Ropelle ER. Aerobic Exercise Training Induces the Mitonuclear Imbalance and UPRmt in the Skeletal Muscle of Aged Mice. J Gerontol A Biol Sci Med Sci 2021; 75:2258-2261. [PMID: 32173728 DOI: 10.1093/gerona/glaa059] [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: 06/26/2019] [Indexed: 12/27/2022] Open
Abstract
The impairment of the mitochondrial functions is a hallmark of aging. During aging, there is a downregulation of two mechanisms strictly associated with mitochondrial integrity, including the mitonuclear imbalance (eg, imbalance in mitochondrial- versus nuclear-encoded mitochondrial proteins) and the mitochondrial unfolded protein response (UPRmt). Here, we evaluated the effects of aerobic exercise in the mitonuclear imbalance and UPRmt markers in the skeletal muscle of old mice. We combined the physiological tests, molecular and bioinformatic analyzes to evaluate the effects of 4 weeks of aerobic exercise training on mitonuclear imbalance and UPRmt markers in the skeletal muscle of young (2 months) and aged (24 months) C57BL/6J mice. Initially, we found that aging reduced several mitochondrial genes in the gastrocnemius muscle, and it was accompanied by the low levels of UPRmt markers, including Yme1l1 and Clpp mRNA. As expected, physical training improved the whole-body metabolism and physical performance of aged mice. The aerobic exercise increased key proteins involved in the mitochondrial biogenesis/functions (VDAC and SIRT1) along with mitochondrial-encoded genes (mtNd1, mtCytB, and mtD-Loop) in the skeletal muscle of old mice. Interestingly, aerobic exercise induced the mitonuclear imbalance, increasing MTCO1/ATP5a ratio and UPRmt markers in the skeletal muscle, including HSP60, Lonp1, and Yme1L1 protein levels in the gastrocnemius muscle of aged mice. These data demonstrate that aerobic exercise training induced mitonuclear imbalance and UPRmt in the skeletal muscle during aging. These phenomena could be involved in the improvement of the mitochondrial metabolism and oxidative capacity in aged individuals.
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Affiliation(s)
- André V Cordeiro
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil
| | - Rafael S Brícola
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil
| | - Renata R Braga
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil
| | - Luciene Lenhare
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil
| | - Vagner R R Silva
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil
| | - Chadi P Anaruma
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil.,Department of Physical Education, Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
| | - Carlos K Katashima
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil
| | - Barbara M Crisol
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil
| | - Fernando M Simabuco
- Laboratory of Functional Properties in Foods, University of Campinas, Limeira, Brazil
| | - Adelino S R Silva
- Postgraduate Program in Rehabilitation and Functional Performance, University of São Paulo, Ribeirão Preto, Brazil.,School of Physical Education and Sport of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Dennys E Cintra
- Laboratory of Nutritional Genomics, University of Campinas, Limeira, Brazil
| | - Leandro P Moura
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil.,Department of Physical Education, Institute of Biosciences, São Paulo State University, Rio Claro, Brazil.,CEPECE - Center of Research in Sport Sciences, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
| | - José R Pauli
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil.,CEPECE - Center of Research in Sport Sciences, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
| | - Eduardo R Ropelle
- Laboratory of Molecular Biology of Exercise, University of Campinas, Limeira, Brazil.,CEPECE - Center of Research in Sport Sciences, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil.,Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
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48
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Palmer D, Fabris F, Doherty A, Freitas AA, de Magalhães JP. Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues. Aging (Albany NY) 2021; 13:3313-3341. [PMID: 33611312 PMCID: PMC7906136 DOI: 10.18632/aging.202648] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/29/2020] [Indexed: 12/22/2022]
Abstract
By combining transcriptomic data with other data sources, inferences can be made about functional changes during ageing. Thus, we conducted a meta-analysis on 127 publicly available microarray and RNA-Seq datasets from mice, rats and humans, identifying a transcriptomic signature of ageing across species and tissues. Analyses on subsets of these datasets produced transcriptomic signatures of ageing for brain, heart and muscle. We then applied enrichment analysis and machine learning to functionally describe these signatures, revealing overexpression of immune and stress response genes and underexpression of metabolic and developmental genes. Further analyses revealed little overlap between genes differentially expressed with age in different tissues, despite ageing differentially expressed genes typically being widely expressed across tissues. Additionally we show that the ageing gene expression signatures (particularly the overexpressed signatures) of the whole meta-analysis, brain and muscle tend to include genes that are central in protein-protein interaction networks. We also show that genes underexpressed with age in the brain are highly central in a co-expression network, suggesting that underexpression of these genes may have broad phenotypic consequences. In sum, we show numerous functional similarities between the ageing transcriptomes of these important tissues, along with unique network properties of genes differentially expressed with age in both a protein-protein interaction and co-expression networks.
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Affiliation(s)
- Daniel Palmer
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.,Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
| | - Fabio Fabris
- School of Computing, University of Kent, Canterbury, Kent, UK
| | - Aoife Doherty
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Alex A Freitas
- School of Computing, University of Kent, Canterbury, Kent, UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
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49
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Liu GH, Bao Y, Qu J, Zhang W, Zhang T, Kang W, Yang F, Ji Q, Jiang X, Ma Y, Ma S, Liu Z, Chen S, Wang S, Sun S, Geng L, Yan K, Yan P, Fan Y, Song M, Ren J, Wang Q, Yang S, Yang Y, Xiong M, Liang C, Li LZ, Cao T, Hu J, Yang P, Ping J, Hu H, Zheng Y, Sun G, Li J, Liu L, Zou Z, Ding Y, Li M, Liu D, Wang M, Ji Q, Sun X, Wang C, Bi S, Shan H, Zhuo X. Aging Atlas: a multi-omics database for aging biology. Nucleic Acids Res 2021; 49:D825-D830. [PMID: 33119753 PMCID: PMC7779027 DOI: 10.1093/nar/gkaa894] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Organismal aging is driven by interconnected molecular changes encompassing internal and extracellular factors. Combinational analysis of high-throughput 'multi-omics' datasets (gathering information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and pharmacogenomics), at either populational or single-cell levels, can provide a multi-dimensional, integrated profile of the heterogeneous aging process with unprecedented throughput and detail. These new strategies allow for the exploration of the molecular profile and regulatory status of gene expression during aging, and in turn, facilitate the development of new aging interventions. With a continually growing volume of valuable aging-related data, it is necessary to establish an open and integrated database to support a wide spectrum of aging research. The Aging Atlas database aims to provide a wide range of life science researchers with valuable resources that allow access to a large-scale of gene expression and regulation datasets created by various high-throughput omics technologies. The current implementation includes five modules: transcriptomics (RNA-seq), single-cell transcriptomics (scRNA-seq), epigenomics (ChIP-seq), proteomics (protein-protein interaction), and pharmacogenomics (geroprotective compounds). Aging Atlas provides user-friendly functionalities to explore age-related changes in gene expression, as well as raw data download services. Aging Atlas is freely available at https://bigd.big.ac.cn/aging/index.
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50
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Dilated cardiomyopathy impairs mitochondrial biogenesis and promotes inflammation in an age- and sex-dependent manner. Aging (Albany NY) 2020; 12:24117-24133. [PMID: 33303703 PMCID: PMC7762497 DOI: 10.18632/aging.202283] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022]
Abstract
Dilated cardiomyopathy (DCM) belongs to the myocardial diseases associated with a severe impairment of cardiac function, but the question of how sex and age affect this pathology has not been fully explored. Impaired energy homeostasis, mitochondrial dysfunction, and systemic inflammation are well-described phenomena associated with aging. In this study, we investigated if DCM affects these phenomena in a sex- and age-related manner. We analyzed the expression of mitochondrial and antioxidant proteins and the inflammatory state in DCM heart tissue from younger and older women and men. A significant downregulation of Sirt1 expression was detected in older DCM patients. Sex-related differences were observed in the phosphorylation of AMPK that only appeared in older males with DCM, possibly due to an alternative Sirt1 regulation mechanism. Furthermore, reduced expression of several mitochondrial proteins (TOM40, TIM23, Sirt3, and SOD2) and genes (cox1, nd4) was only detected in old DCM patients, suggesting that age has a greater effect than DCM on these alterations. Finally, an increased expression of inflammatory markers in older, failing hearts, with a stronger pro-inflammatory response in men, was observed. Together, these findings indicate that age- and sex-related increased inflammation and disturbance of mitochondrial homeostasis occurs in male individuals with DCM.
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