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González JT, Thrush K, Meer M, Levine ME, Higgins-Chen AT. Age-Invariant Genes: Multi-Tissue Identification and Characterization of Murine Reference Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588721. [PMID: 38645168 PMCID: PMC11030416 DOI: 10.1101/2024.04.09.588721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Studies of the aging transcriptome focus on genes that change with age. But what can we learn from age-invariant genes-those that remain unchanged throughout the aging process? These genes also have a practical application: they serve as reference genes (often called housekeeping genes) in expression studies. Reference genes have mostly been identified and validated in young organisms, and no systematic investigation has been done across the lifespan. Here, we build upon a common pipeline for identifying reference genes in RNA-seq datasets to identify age-invariant genes across seventeen C57BL/6 mouse tissues (brain, lung, bone marrow, muscle, white blood cells, heart, small intestine, kidney, liver, pancreas, skin, brown, gonadal, marrow, and subcutaneous adipose tissue) spanning 1 to 21+ months of age. We identify 9 pan-tissue age-invariant genes and many tissue-specific age-invariant genes. These genes are stable across the lifespan and are validated in independent bulk RNA-seq datasets and RT-qPCR. We find age-invariant genes have shorter transcripts on average and are enriched for CpG islands. Interestingly, pathway enrichment analysis for age-invariant genes identifies an overrepresentation of molecular functions associated with some, but not all, hallmarks of aging. Thus, though hallmarks of aging typically involve changes in cell maintenance mechanisms, select genes associated with these hallmarks resist fluctuations in expression with age. Finally, our analysis concludes no classical reference gene is appropriate for aging studies in all tissues. Instead, we provide tissue-specific and pan-tissue genes for assays utilizing reference gene normalization (i.e., RT-qPCR) that can be applied to animals across the lifespan.
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Affiliation(s)
- John T. González
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Kyra Thrush
- Altos Labs, San Diego Institute of Sciences, San Diego, CA, USA
| | - Margarita Meer
- Altos Labs, San Diego Institute of Sciences, San Diego, CA, USA
| | - Morgan E. Levine
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Altos Labs, San Diego Institute of Sciences, San Diego, CA, USA
| | - Albert T. Higgins-Chen
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven CT, USA
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2
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Soheili-Nezhad S, Ibáñez-Solé O, Izeta A, Hoeijmakers JHJ, Stoeger T. Time is ticking faster for long genes in aging. Trends Genet 2024; 40:299-312. [PMID: 38519330 PMCID: PMC11003850 DOI: 10.1016/j.tig.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 03/24/2024]
Abstract
Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.
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Affiliation(s)
- Sourena Soheili-Nezhad
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Olga Ibáñez-Solé
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ander Izeta
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Tecnun-University of Navarra, 20018 Donostia-San Sebastian, Spain.
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands; University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany; Princess Maxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands.
| | - Thomas Stoeger
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA; Potocsnak Longevity Institute, Northwestern University, Chicago, IL, USA; Simpson Querrey Lung Institute for Translational Science, Chicago, IL, USA.
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3
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Yamanaka T, Matsui H. Modeling familial and sporadic Parkinson's disease in small fishes. Dev Growth Differ 2024; 66:4-20. [PMID: 37991125 DOI: 10.1111/dgd.12904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
The establishment of animal models for Parkinson's disease (PD) has been challenging. Nevertheless, once established, they will serve as valuable tools for elucidating the causes and pathogenesis of PD, as well as for developing new strategies for its treatment. Following the recent discovery of a series of PD causative genes in familial cases, teleost fishes, including zebrafish and medaka, have often been used to establish genetic PD models because of their ease of breeding and gene manipulation, as well as the high conservation of gene orthologs. Some of the fish lines can recapitulate PD phenotypes, which are often more pronounced than those in rodent genetic models. In addition, a new experimental teleost fish, turquoise killifish, can be used as a sporadic PD model, because it spontaneously manifests age-dependent PD phenotypes. Several PD fish models have already made significant contributions to the discovery of novel PD pathological features, such as cytosolic leakage of mitochondrial DNA and pathogenic phosphorylation in α-synuclein. Therefore, utilizing various PD fish models with distinct degenerative phenotypes will be an effective strategy for identifying emerging facets of PD pathogenesis and therapeutic modalities.
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Affiliation(s)
- Tomoyuki Yamanaka
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
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4
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Stoeger T. The Road Less Traveled: Uncovering the Convergence Toward Specific Pleiotropic Phenotypes in Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534472. [PMID: 37034589 PMCID: PMC10081180 DOI: 10.1101/2023.03.28.534472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Aging is a complex process influenced by a wide range of environmental and molecular factors. Despite this complexity, individuals tend to age in highly similar ways, leading to the question of what drives this convergence. Recent research, including my own discoveries, suggests that the length of transcript molecules plays a crucial role in age-dependent changes to the transcriptome. Drawing inspiration from the road trip analogy of cellular transcription, I propose that a non-linear scaling law drives convergence towards specific pleiotropic phenotypes in biological aging. This scaling law is based on the notion that molecular changes observed during aging may reflect unspecific damage to cellular physiology. By validating this hypothesis, I can improve our understanding of biological aging and identify new candidate compounds for anti-aging interventions, as well as re-identify one known intervention. This work has actionable implications for improving human health and extending lifespans.
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Affiliation(s)
- Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
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5
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Branicky R, Wang Y, Khaki A, Liu JL, Kramer-Drauberg M, Hekimi S. Stimulation of RAS-dependent ROS signaling extends longevity by modulating a developmental program of global gene expression. SCIENCE ADVANCES 2022; 8:eadc9851. [PMID: 36449615 PMCID: PMC9710873 DOI: 10.1126/sciadv.adc9851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
We show that elevation of mitochondrial superoxide generation increases Caenorhabditis elegans life span by enhancing a RAS-dependent ROS (reactive oxygen species) signaling pathway (RDRS) that controls the expression of half of the genome as well as animal composition and physiology. RDRS stimulation mimics a program of change in gene expression that is normally observed at the end of postembryonic development. We further show that RDRS is regulated by negative feedback from the superoxide dismutase 1 (SOD-1)-dependent conversion of superoxide into cytoplasmic hydrogen peroxide, which, in turn, acts on a redox-sensitive cysteine (C118) of RAS. Preventing C118 oxidation by replacement with serine, or mimicking oxidation by replacement with aspartic acid, leads to opposite changes in the expression of the same large set of genes that is affected when RDRS is stimulated by mitochondrial superoxide. The identities of these genes suggest that stimulation of the pathway extends life span by boosting turnover and repair while moderating damage from metabolic activity.
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6
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Stoeger T, Grant RA, McQuattie-Pimentel AC, Anekalla KR, Liu SS, Tejedor-Navarro H, Singer BD, Abdala-Valencia H, Schwake M, Tetreault MP, Perlman H, Balch WE, Chandel NS, Ridge KM, Sznajder JI, Morimoto RI, Misharin AV, Budinger GRS, Nunes Amaral LA. Aging is associated with a systemic length-associated transcriptome imbalance. NATURE AGING 2022; 2:1191-1206. [PMID: 37118543 PMCID: PMC10154227 DOI: 10.1038/s43587-022-00317-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/21/2022] [Indexed: 12/14/2022]
Abstract
Aging is among the most important risk factors for morbidity and mortality. To contribute toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data from multiple studies. Here, we show that transcript length alone explains most transcriptional changes observed with aging in mice and humans. We present three lines of evidence supporting the biological importance of the uncovered transcriptome imbalance. First, in vertebrates the length association primarily displays a lower relative abundance of long transcripts in aging. Second, eight antiaging interventions of the Interventions Testing Program of the National Institute on Aging can counter this length association. Third, we find that in humans and mice the genes with the longest transcripts enrich for genes reported to extend lifespan, whereas those with the shortest transcripts enrich for genes reported to shorten lifespan. Our study opens fundamental questions on aging and the organization of transcriptomes.
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Affiliation(s)
- Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA.
| | - Rogan A Grant
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | | | - Kishore R Anekalla
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Sophia S Liu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | | | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, IL, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Michael Schwake
- Department of Neurology, Northwestern University, Evanston, IL, USA
- Faculty of Chemistry, University of Bielefeld, Bielefeld, Germany
| | - Marie-Pier Tetreault
- Division of Gastroenterology and Hepatology, Northwestern University, Evanston, IL, USA
| | - Harris Perlman
- Division of Rheumatology, Northwestern University, Evanston, IL, USA
| | | | - Navdeep S Chandel
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, USA.
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - Luis A Nunes Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA.
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7
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Kwon K, Cho H, Lee S, Cho EJ, Yu W, Kok CYL, Je HS, Kim J, Cho HJ, Kwon T. Adaptive cellular response of the substantia nigra dopaminergic neurons upon age-dependent iron accumulation. Aging Cell 2022; 21:e13694. [PMID: 35984750 PMCID: PMC9470899 DOI: 10.1111/acel.13694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/20/2022] [Accepted: 07/28/2022] [Indexed: 01/25/2023] Open
Abstract
Progressive iron accumulation in the substantia nigra in the aged human brain is a major risk factor for Parkinson's disease and other neurodegenerative diseases. Heavy metals, such as iron, produce reactive oxygen species and consequently oxidative stress in cells. It is unclear, however, how neurons in the substantia nigra are protected against the age-related, excessive accumulation of iron. In this study, we examined the cellular response of the substantia nigra against age-related iron accumulation in rats of different ages. Magnetic resonance imaging confirmed the presence of iron in 6-month-old rats; in 15-month-old rats, iron accumulation significantly increased, particularly in the midbrain. Transcriptome analysis of the region, in which iron deposition was observed, revealed an increase in stress response genes in older animals. To identify the genes related to the cellular response to iron, independent of neurodevelopment, we exposed the neuroblastoma cell line SH-SY5Y to a similar quantity of iron and then analyzed their transcriptomic responses. Among various stress response pathways altered by iron overloading in the rat brain and SH-SY5Y cells, the genes associated with topologically incorrect protein responses were significantly upregulated. Knockdown of HERPUD1 and CLU in this pathway increased susceptibility to iron-induced cellular stress, thus demonstrating their roles in preventing iron overload-induced toxicity. The current study details the neuronal response to excessive iron accumulation, which is associated with age-related neurodegenerative diseases.
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Affiliation(s)
- Kujin Kwon
- Department of Biomedical Engineering, College of Information and BiotechnologyUlsan National Institute of Science and Technology (UNIST)UlsanKorea
| | - Hwapyeong Cho
- Department of Biomedical Engineering, College of Information and BiotechnologyUlsan National Institute of Science and Technology (UNIST)UlsanKorea
| | - Soyeon Lee
- Department of Biological Sciences, College of Information and BiotechnologyUlsan National Institute of Science and Technology (UNIST)UlsanKorea
| | - Eun Jeong Cho
- Department of Biological Sciences, College of Information and BiotechnologyUlsan National Institute of Science and Technology (UNIST)UlsanKorea
| | - Weonjin Yu
- Neuroscience and Behavioral Disorders ProgramDuke‐National University of Singapore (NUS) Medical SchoolSingapore CitySingapore
| | - Catherine Yen Li Kok
- Neuroscience and Behavioral Disorders ProgramDuke‐National University of Singapore (NUS) Medical SchoolSingapore CitySingapore
| | - Hyunsoo Shawn Je
- Neuroscience and Behavioral Disorders ProgramDuke‐National University of Singapore (NUS) Medical SchoolSingapore CitySingapore,Advanced Bioimaging Center, AcademiaSingapore CitySingapore
| | - Jae‐Ick Kim
- Department of Biological Sciences, College of Information and BiotechnologyUlsan National Institute of Science and Technology (UNIST)UlsanKorea
| | - Hyung Joon Cho
- Department of Biomedical Engineering, College of Information and BiotechnologyUlsan National Institute of Science and Technology (UNIST)UlsanKorea
| | - Taejoon Kwon
- Department of Biomedical Engineering, College of Information and BiotechnologyUlsan National Institute of Science and Technology (UNIST)UlsanKorea,Center for Genome IntegrityInstitute for Basic Science (IBS)UlsanKorea
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8
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Kluever V, Russo B, Mandad S, Kumar NH, Alevra M, Ori A, Rizzoli SO, Urlaub H, Schneider A, Fornasiero EF. Protein lifetimes in aged brains reveal a proteostatic adaptation linking physiological aging to neurodegeneration. SCIENCE ADVANCES 2022; 8:eabn4437. [PMID: 35594347 PMCID: PMC9122331 DOI: 10.1126/sciadv.abn4437] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/07/2022] [Indexed: 05/27/2023]
Abstract
Aging is a prominent risk factor for neurodegenerative disorders (NDDs); however, the molecular mechanisms rendering the aged brain particularly susceptible to neurodegeneration remain unclear. Here, we aim to determine the link between physiological aging and NDDs by exploring protein turnover using metabolic labeling and quantitative pulse-SILAC proteomics. By comparing protein lifetimes between physiologically aged and young adult mice, we found that in aged brains protein lifetimes are increased by ~20% and that aging affects distinct pathways linked to NDDs. Specifically, a set of neuroprotective proteins are longer-lived in aged brains, while some mitochondrial proteins linked to neurodegeneration are shorter-lived. Strikingly, we observed a previously unknown alteration in proteostasis that correlates to parsimonious turnover of proteins with high biosynthetic costs, revealing an overall metabolic adaptation that preludes neurodegeneration. Our findings suggest that future therapeutic paradigms, aimed at addressing these metabolic adaptations, might be able to delay NDD onset.
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Affiliation(s)
- Verena Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Belisa Russo
- German Center for Neurodegenerative Diseases, DZNE Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - Sunit Mandad
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Nisha Hemandhar Kumar
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mihai Alevra
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Silvio O. Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Anja Schneider
- German Center for Neurodegenerative Diseases, DZNE Bonn, Venusberg Campus 1, 53127 Bonn, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, 53127 Bonn, Germany
| | - Eugenio F. Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
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9
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Lin J, McCann AP, Sereesongsaeng N, Burden JM, Alsa'd AA, Burden RE, Micu I, Williams R, Van Schaeybroeck S, Evergren E, Mullan P, Simpson JC, Scott CJ, Burrows JF. USP17 is required for peripheral trafficking of lysosomes. EMBO Rep 2022; 23:e51932. [PMID: 35080333 PMCID: PMC8982589 DOI: 10.15252/embr.202051932] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022] Open
Abstract
Expression of the deubiquitinase USP17 is induced by multiple stimuli, including cytokines (IL‐4/6), chemokines (IL‐8, SDF1), and growth factors (EGF), and several studies indicate it is required for cell proliferation and migration. However, the mechanisms via which USP17 impacts upon these cellular functions are unclear. Here, we demonstrate that USP17 depletion prevents peripheral lysosome positioning, as well as trafficking of lysosomes to the cell periphery in response to EGF stimulation. Overexpression of USP17 also increases secretion of the lysosomal protease cathepsin D. In addition, USP17 depletion impairs plasma membrane repair in cells treated with the pore‐forming toxin streptolysin O, further indicating that USP17 is required for lysosome trafficking to the plasma membrane. Finally, we demonstrate that USP17 can deubiquitinate p62, and we propose that USP17 can facilitate peripheral lysosome trafficking by opposing the E3 ligase RNF26 to untether lysosomes from the ER and facilitate lysosome peripheral trafficking, lysosome protease secretion, and plasma membrane repair.
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Affiliation(s)
- Jia Lin
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Aidan P McCann
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | | | | | | | | | - Ileana Micu
- Advanced Imaging Core Technology Unit, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Richard Williams
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Sandra Van Schaeybroeck
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Emma Evergren
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Paul Mullan
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Jeremy C Simpson
- School of Biology and Environmental Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Christopher J Scott
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
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10
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Mora I, Arola L, Caimari A, Escoté X, Puiggròs F. Structured Long-Chain Omega-3 Fatty Acids for Improvement of Cognitive Function during Aging. Int J Mol Sci 2022; 23:ijms23073472. [PMID: 35408832 PMCID: PMC8998232 DOI: 10.3390/ijms23073472] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/07/2023] Open
Abstract
Although the human lifespan has increased in the past century owing to advances in medicine and lifestyle, the human healthspan has not kept up the same pace, especially in brain aging. Consequently, the role of preventive health interventions has become a crucial strategy, in particular, the identification of nutritional compounds that could alleviate the deleterious effects of aging. Among nutrients to cope with aging in special cognitive decline, the long-chain omega-3 polyunsaturated fatty acids (ω-3 LCPUFAs) docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), have emerged as very promising ones. Due to their neuroinflammatory resolving effects, an increased status of DHA and EPA in the elderly has been linked to better cognitive function and a lower risk of dementia. However, the results from clinical studies do not show consistent evidence and intake recommendations for old adults are lacking. Recently, supplementation with structured forms of EPA and DHA, which can be derived natural forms or targeted structures, have proven enhanced bioavailability and powerful benefits. This review summarizes present and future perspectives of new structures of ω-3 LCPUFAs and the role of "omic" technologies combined with the use of high-throughput in vivo models to shed light on the relationships and underlying mechanisms between ω-3 LCPUFAs and healthy aging.
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Affiliation(s)
- Ignasi Mora
- Brudy Technology S.L., 08006 Barcelona, Spain
- Correspondence: (I.M.); (L.A.)
| | - Lluís Arola
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Correspondence: (I.M.); (L.A.)
| | - Antoni Caimari
- Eurecat, Centre Tecnològic de Catalunya, Biotechnology Area, 43204 Reus, Spain; (A.C.); (F.P.)
| | - Xavier Escoté
- Eurecat, Centre Tecnològic de Catalunya, Nutrition and Health Unit, 43204 Reus, Spain;
| | - Francesc Puiggròs
- Eurecat, Centre Tecnològic de Catalunya, Biotechnology Area, 43204 Reus, Spain; (A.C.); (F.P.)
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11
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Williams EG, Pfister N, Roy S, Statzer C, Haverty J, Ingels J, Bohl C, Hasan M, Čuklina J, Bühlmann P, Zamboni N, Lu L, Ewald CY, Williams RW, Aebersold R. Multiomic profiling of the liver across diets and age in a diverse mouse population. Cell Syst 2022; 13:43-57.e6. [PMID: 34666007 PMCID: PMC8776606 DOI: 10.1016/j.cels.2021.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/12/2021] [Accepted: 09/14/2021] [Indexed: 01/21/2023]
Abstract
We profiled the liver transcriptome, proteome, and metabolome in 347 individuals from 58 isogenic strains of the BXD mouse population across age (7 to 24 months) and diet (low or high fat) to link molecular variations to metabolic traits. Several hundred genes are affected by diet and/or age at the transcript and protein levels. Orthologs of two aging-associated genes, St7 and Ctsd, were knocked down in C. elegans, reducing longevity in wild-type and mutant long-lived strains. The multiomics data were analyzed as segregating gene networks according to each independent variable, providing causal insight into dietary and aging effects. Candidates were cross-examined in an independent diversity outbred mouse liver dataset segregating for similar diets, with ∼80%-90% of diet-related candidate genes found in common across datasets. Together, we have developed a large multiomics resource for multivariate analysis of complex traits and demonstrate a methodology for moving from observational associations to causal connections.
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Affiliation(s)
- Evan G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Niklas Pfister
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Cyril Statzer
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Jack Haverty
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jesse Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Casey Bohl
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Moaraj Hasan
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Jelena Čuklina
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Peter Bühlmann
- Department of Mathematics, Seminar for Statistics, ETH Zürich, Zurich, Switzerland
| | - Nicola Zamboni
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Collin Y Ewald
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland; Faculty of Science, University of Zürich, Zurich, Switzerland
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12
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Vanhunsel S, Bergmans S, Beckers A, Etienne I, Van Bergen T, De Groef L, Moons L. The age factor in optic nerve regeneration: Intrinsic and extrinsic barriers hinder successful recovery in the short-living killifish. Aging Cell 2022; 21:e13537. [PMID: 34927348 PMCID: PMC8761009 DOI: 10.1111/acel.13537] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 01/06/2023] Open
Abstract
As the mammalian central nervous system matures, its regenerative ability decreases, leading to incomplete or non-recovery from the neurodegenerative diseases and central nervous system insults that we are increasingly facing in our aging world population. Current neuroregenerative research is largely directed toward identifying the molecular and cellular players that underlie central nervous system repair, yet it repeatedly ignores the aging context in which many of these diseases appear. Using an optic nerve crush model in a novel biogerontology model, that is, the short-living African turquoise killifish, the impact of aging on injury-induced optic nerve repair was investigated. This work reveals an age-related decline in axonal regeneration in female killifish, with different phases of the repair process being affected depending on the age. Interestingly, as in mammals, both a reduced intrinsic growth potential and a non-supportive cellular environment seem to lie at the basis of this impairment. Overall, we introduce the killifish visual system and its age-dependent regenerative ability as a model to identify new targets for neurorepair in non-regenerating individuals, thereby also considering the effects of aging on neurorepair.
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Affiliation(s)
- Sophie Vanhunsel
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
| | - Steven Bergmans
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
| | - An Beckers
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
| | | | | | - Lies De Groef
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
- Leuven Brain InstituteLeuvenBelgium
| | - Lieve Moons
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
- Leuven Brain InstituteLeuvenBelgium
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13
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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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14
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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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15
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Clemens Z, Sivakumar S, Pius A, Sahu A, Shinde S, Mamiya H, Luketich N, Cui J, Dixit P, Hoeck JD, Kreuz S, Franti M, Barchowsky A, Ambrosio F. The biphasic and age-dependent impact of klotho on hallmarks of aging and skeletal muscle function. eLife 2021; 10:e61138. [PMID: 33876724 PMCID: PMC8118657 DOI: 10.7554/elife.61138] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
Aging is accompanied by disrupted information flow, resulting from accumulation of molecular mistakes. These mistakes ultimately give rise to debilitating disorders including skeletal muscle wasting, or sarcopenia. To derive a global metric of growing 'disorderliness' of aging muscle, we employed a statistical physics approach to estimate the state parameter, entropy, as a function of genes associated with hallmarks of aging. Escalating network entropy reached an inflection point at old age, while structural and functional alterations progressed into oldest-old age. To probe the potential for restoration of molecular 'order' and reversal of the sarcopenic phenotype, we systemically overexpressed the longevity protein, Klotho, via AAV. Klotho overexpression modulated genes representing all hallmarks of aging in old and oldest-old mice, but pathway enrichment revealed directions of changes were, for many genes, age-dependent. Functional improvements were also age-dependent. Klotho improved strength in old mice, but failed to induce benefits beyond the entropic tipping point.
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Affiliation(s)
- Zachary Clemens
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
- Department of Environmental and Occupational Health, University of PittsburghPittsburghUnited States
| | - Sruthi Sivakumar
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
- Department of Bioengineering, University of PittsburghPittsburghUnited States
| | - Abish Pius
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
- Department of Computational & Systems Biology, School of Medicine, University of PittsburghPittsburghUnited States
| | - Amrita Sahu
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
| | - Sunita Shinde
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
| | - Hikaru Mamiya
- Department of Bioengineering, University of PittsburghPittsburghUnited States
| | - Nathaniel Luketich
- Department of Bioengineering, University of PittsburghPittsburghUnited States
| | - Jian Cui
- Department of Computational & Systems Biology, School of Medicine, University of PittsburghPittsburghUnited States
| | - Purushottam Dixit
- Department of Physics, University of FloridaGainesvilleUnited States
| | - Joerg D Hoeck
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, IncRheinGermany
| | - Sebastian Kreuz
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, IncRheinGermany
| | - Michael Franti
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, IncRheinGermany
| | - Aaron Barchowsky
- Department of Environmental and Occupational Health, University of PittsburghPittsburghUnited States
| | - Fabrisia Ambrosio
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
- Department of Environmental and Occupational Health, University of PittsburghPittsburghUnited States
- Department of Bioengineering, University of PittsburghPittsburghUnited States
- McGowan Institute for Regenerative Medicine, University of PittsburghPittsburghUnited States
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16
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Takemon Y, Chick JM, Gerdes Gyuricza I, Skelly DA, Devuyst O, Gygi SP, Churchill GA, Korstanje R. Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney. eLife 2021; 10:e62585. [PMID: 33687326 PMCID: PMC8096428 DOI: 10.7554/elife.62585] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/06/2021] [Indexed: 01/10/2023] Open
Abstract
Little is known about the molecular changes that take place in the kidney during the aging process. In order to better understand these changes, we measured mRNA and protein levels in genetically diverse mice at different ages. We observed distinctive change in mRNA and protein levels as a function of age. Changes in both mRNA and protein are associated with increased immune infiltration and decreases in mitochondrial function. Proteins show a greater extent of change and reveal changes in a wide array of biological processes including unique, organ-specific features of aging in kidney. Most importantly, we observed functionally important age-related changes in protein that occur in the absence of corresponding changes in mRNA. Our findings suggest that mRNA profiling alone provides an incomplete picture of molecular aging in the kidney and that examination of changes in proteins is essential to understand aging processes that are not transcriptionally regulated.
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Affiliation(s)
| | - Joel M Chick
- Harvard Medical SchoolBostonUnited States
- VividionTherapeuticsSan DiegoUnited States
| | | | | | - Olivier Devuyst
- Institute of Physiology, University of ZurichZurichSwitzerland
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17
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Börsch A, Ham DJ, Mittal N, Tintignac LA, Migliavacca E, Feige JN, Rüegg MA, Zavolan M. Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. Commun Biol 2021; 4:194. [PMID: 33580198 PMCID: PMC7881157 DOI: 10.1038/s42003-021-01723-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Sarcopenia, the age-related loss of skeletal muscle mass and function, affects 5-13% of individuals aged over 60 years. While rodents are widely-used model organisms, which aspects of sarcopenia are recapitulated in different animal models is unknown. Here we generated a time series of phenotypic measurements and RNA sequencing data in mouse gastrocnemius muscle and analyzed them alongside analogous data from rats and humans. We found that rodents recapitulate mitochondrial changes observed in human sarcopenia, while inflammatory responses are conserved at pathway but not gene level. Perturbations in the extracellular matrix are shared by rats, while mice recapitulate changes in RNA processing and autophagy. We inferred transcription regulators of early and late transcriptome changes, which could be targeted therapeutically. Our study demonstrates that phenotypic measurements, such as muscle mass, are better indicators of muscle health than chronological age and should be considered when analyzing aging-related molecular data.
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Affiliation(s)
- Anastasiya Börsch
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Daniel J Ham
- Biozentrum, University of Basel, Basel, Switzerland
| | - Nitish Mittal
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Lionel A Tintignac
- Department of Biomedicine, Pharmazentrum, University of Basel, Basel, Switzerland
| | | | - Jérôme N Feige
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | | | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
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18
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Rivero-Segura NA, Bello-Chavolla OY, Barrera-Vázquez OS, Gutierrez-Robledo LM, Gomez-Verjan JC. Promising biomarkers of human aging: In search of a multi-omics panel to understand the aging process from a multidimensional perspective. Ageing Res Rev 2020; 64:101164. [PMID: 32977058 DOI: 10.1016/j.arr.2020.101164] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
Abstract
The aging process has been linked to the occurrence of chronic diseases and functional impairments, including cancer, sarcopenia, frailty, metabolic, cardiovascular, and neurodegenerative diseases. Nonetheless, aging is highly variable and heterogeneous and represents a challenge for its characterization. In this sense, intrinsic capacity (IC) stands as a novel perspective by the World Health Organization, which integrates the individual wellbeing, environment, and risk factors to understand aging. However, there is a lack of quantitative and qualitative attributes to define it objectively. Therefore, in this review we attempt to summarize the most relevant and promising biomarkers described in clinical studies at date over different molecular levels, including epigenomics, transcriptomics, proteomics, metabolomics, and the microbiome. To aid gerontologists, geriatricians, and biomedical researchers to understand the aging process through the IC. Aging biomarkers reflect the physiological state of individuals and the underlying mechanisms related to homeostatic changes throughout an individual lifespan; they demonstrated that aging could be measured independently of time (that may explain its heterogeneity) and to be helpful to predict age-related syndromes and mortality. In summary, we highlight the areas of opportunity and gaps of knowledge that must be addressed to fully integrate biomedical findings into clinically useful tools and interventions.
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Affiliation(s)
| | - O Y Bello-Chavolla
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico; Department of Physiology, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - O S Barrera-Vázquez
- Departamento de Famacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - J C Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico.
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19
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Proteomic Profiling of Fibroblasts Isolated from Chronic Wounds Identifies Disease-Relevant Signaling Pathways. J Invest Dermatol 2020; 140:2280-2290.e4. [DOI: 10.1016/j.jid.2020.02.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 12/13/2022]
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20
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Espada L, Dakhovnik A, Chaudhari P, Martirosyan A, Miek L, Poliezhaieva T, Schaub Y, Nair A, Döring N, Rahnis N, Werz O, Koeberle A, Kirkpatrick J, Ori A, Ermolaeva MA. Loss of metabolic plasticity underlies metformin toxicity in aged Caenorhabditis elegans. Nat Metab 2020; 2:1316-1331. [PMID: 33139960 DOI: 10.1038/s42255-020-00307-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022]
Abstract
Current clinical trials are testing the life-extending benefits of the diabetes drug metformin in healthy individuals without diabetes. However, the metabolic response of a non-diabetic cohort to metformin treatment has not been studied. Here, we show in C. elegans and human primary cells that metformin shortens lifespan when provided in late life, contrary to its positive effects in young organisms. We find that metformin exacerbates ageing-associated mitochondrial dysfunction, causing respiratory failure. Age-related failure to induce glycolysis and activate the dietary-restriction-like mobilization of lipid reserves in response to metformin result in lethal ATP exhaustion in metformin-treated aged worms and late-passage human cells, which can be rescued by ectopic stabilization of cellular ATP content. Metformin toxicity is alleviated in worms harbouring disruptions in insulin-receptor signalling, which show enhanced resilience to mitochondrial distortions at old age. Together, our data show that metformin induces deleterious changes of conserved metabolic pathways in late life, which could bring into question its benefits for older individuals without diabetes.
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Affiliation(s)
- Lilia Espada
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Prerana Chaudhari
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Asya Martirosyan
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Laura Miek
- Institute of Pharmacy, Friedrich Schiller University Jena, Jena, Germany
| | | | - Yvonne Schaub
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Ashish Nair
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Nadia Döring
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Norman Rahnis
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Oliver Werz
- Institute of Pharmacy, Friedrich Schiller University Jena, Jena, Germany
| | - Andreas Koeberle
- Institute of Pharmacy, Friedrich Schiller University Jena, Jena, Germany
- Michael Popp Research Institute, University of Innsbruck, Innsbruck, Austria
| | | | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Maria A Ermolaeva
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
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21
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Sun Y, Li M, Zhao D, Li X, Yang C, Wang X. Lysosome activity is modulated by multiple longevity pathways and is important for lifespan extension in C. elegans. eLife 2020; 9:55745. [PMID: 32482227 PMCID: PMC7274789 DOI: 10.7554/elife.55745] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Lysosomes play important roles in cellular degradation to maintain cell homeostasis. In order to understand whether and how lysosomes alter with age and contribute to lifespan regulation, we characterized multiple properties of lysosomes during the aging process in C. elegans. We uncovered age-dependent alterations in lysosomal morphology, motility, acidity and degradation activity, all of which indicate a decline in lysosome function with age. The age-associated lysosomal changes are suppressed in the long-lived mutants daf-2, eat-2 and isp-1, which extend lifespan by inhibiting insulin/IGF-1 signaling, reducing food intake and impairing mitochondrial function, respectively. We found that 43 lysosome genes exhibit reduced expression with age, including genes encoding subunits of the proton pump V-ATPase and cathepsin proteases. The expression of lysosome genes is upregulated in the long-lived mutants, and this upregulation requires the functions of DAF-16/FOXO and SKN-1/NRF2 transcription factors. Impairing lysosome function affects clearance of aggregate-prone proteins and disrupts lifespan extension in daf-2, eat-2 and isp-1 worms. Our data indicate that lysosome function is modulated by multiple longevity pathways and is important for lifespan extension.
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Affiliation(s)
- Yanan Sun
- College of Life science, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Meijiao Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Dongfeng Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xin Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chonglin Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Xiaochen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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22
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Kelmer Sacramento E, Kirkpatrick JM, Mazzetto M, Baumgart M, Bartolome A, Di Sanzo S, Caterino C, Sanguanini M, Papaevgeniou N, Lefaki M, Childs D, Bagnoli S, Terzibasi Tozzini E, Di Fraia D, Romanov N, Sudmant PH, Huber W, Chondrogianni N, Vendruscolo M, Cellerino A, Ori A. Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation. Mol Syst Biol 2020; 16:e9596. [PMID: 32558274 PMCID: PMC7301280 DOI: 10.15252/msb.20209596] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/18/2022] Open
Abstract
A progressive loss of protein homeostasis is characteristic of aging and a driver of neurodegeneration. To investigate this process quantitatively, we characterized proteome dynamics during brain aging in the short-lived vertebrate Nothobranchius furzeri combining transcriptomics and proteomics. We detected a progressive reduction in the correlation between protein and mRNA, mainly due to post-transcriptional mechanisms that account for over 40% of the age-regulated proteins. These changes cause a progressive loss of stoichiometry in several protein complexes, including ribosomes, which show impaired assembly/disassembly and are enriched in protein aggregates in old brains. Mechanistically, we show that reduction of proteasome activity is an early event during brain aging and is sufficient to induce proteomic signatures of aging and loss of stoichiometry in vivo. Using longitudinal transcriptomic data, we show that the magnitude of early life decline in proteasome levels is a major risk factor for mortality. Our work defines causative events in the aging process that can be targeted to prevent loss of protein homeostasis and delay the onset of age-related neurodegeneration.
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Affiliation(s)
| | - Joanna M Kirkpatrick
- Leibniz Institute on Aging‐Fritz Lipmann Institute (FLI)JenaGermany
- Present address:
Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Mariateresa Mazzetto
- Leibniz Institute on Aging‐Fritz Lipmann Institute (FLI)JenaGermany
- Bio@SNSScuola Normale SuperiorePisaItaly
| | - Mario Baumgart
- Leibniz Institute on Aging‐Fritz Lipmann Institute (FLI)JenaGermany
| | | | - Simone Di Sanzo
- Leibniz Institute on Aging‐Fritz Lipmann Institute (FLI)JenaGermany
| | - Cinzia Caterino
- Leibniz Institute on Aging‐Fritz Lipmann Institute (FLI)JenaGermany
- Bio@SNSScuola Normale SuperiorePisaItaly
| | - Michele Sanguanini
- Centre for Misfolding DiseasesDepartment of ChemistryUniversity of CambridgeCambridgeUK
| | | | - Maria Lefaki
- Institute of Chemical BiologyNational Hellenic Research FoundationAthensGreece
| | | | | | | | | | - Natalie Romanov
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
Max Planck Institute of BiophysicsFrankfurt am MainGermany
| | | | | | - Niki Chondrogianni
- Institute of Chemical BiologyNational Hellenic Research FoundationAthensGreece
| | - Michele Vendruscolo
- Centre for Misfolding DiseasesDepartment of ChemistryUniversity of CambridgeCambridgeUK
| | - Alessandro Cellerino
- Leibniz Institute on Aging‐Fritz Lipmann Institute (FLI)JenaGermany
- Bio@SNSScuola Normale SuperiorePisaItaly
| | - Alessandro Ori
- Leibniz Institute on Aging‐Fritz Lipmann Institute (FLI)JenaGermany
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23
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Yu Q, Xiao H, Jedrychowski MP, Schweppe DK, Navarrete-Perea J, Knott J, Rogers J, Chouchani ET, Gygi SP. Sample multiplexing for targeted pathway proteomics in aging mice. Proc Natl Acad Sci U S A 2020; 117:9723-9732. [PMID: 32332170 PMCID: PMC7211924 DOI: 10.1073/pnas.1919410117] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pathway proteomics strategies measure protein expression changes in specific cellular processes that carry out related functions. Using targeted tandem mass tags-based sample multiplexing, hundreds of proteins can be quantified across 10 or more samples simultaneously. To facilitate these highly complex experiments, we introduce a strategy that provides complete control over targeted sample multiplexing experiments, termed Tomahto, and present its implementation on the Orbitrap Tribrid mass spectrometer platform. Importantly, this software monitors via the external desktop computer to the data stream and inserts optimized MS2 and MS3 scans in real time based on an application programming interface with the mass spectrometer. Hundreds of proteins of interest from diverse biological samples can be targeted and accurately quantified in a sensitive and high-throughput fashion. It achieves sensitivity comparable to, if not better than, deep fractionation and requires minimal total sample input (∼10 µg). As a proof-of-principle experiment, we selected four pathways important in metabolism- and inflammation-related processes (260 proteins/520 peptides) and measured their abundance across 90 samples (nine tissues from five old and five young mice) to explore effects of aging. Tissue-specific aging is presented here and we highlight the role of inflammation- and metabolism-related processes in white adipose tissue. We validated our approach through comparison with a global proteome survey across the tissues, work that we also provide as a general resource for the community.
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Affiliation(s)
- Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Haopeng Xiao
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Mark P Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Devin K Schweppe
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | | | | | - John Rogers
- Thermo Fisher Scientific, Rockford, IL 61101
| | - Edward T Chouchani
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115;
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24
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Dabrowski R, Ripa R, Latza C, Annibal A, Antebi A. Optimization of mass spectrometry settings for steroidomic analysis in young and old killifish. Anal Bioanal Chem 2020; 412:4089-4099. [PMID: 32333075 PMCID: PMC7320053 DOI: 10.1007/s00216-020-02640-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/02/2020] [Accepted: 04/03/2020] [Indexed: 12/27/2022]
Abstract
Steroids are essential structural components of cell membranes that organize lipid rafts and modulate membrane fluidity. They can also act as signalling molecules that work through nuclear and G protein–coupled receptors to impact health and disease. Notably, changes in steroid levels have been implicated in metabolic, cardiovascular and neurodegenerative diseases, but how alterations in the steroid pool affect ageing is less well understood. One of the major challenges in steroidomic analysis is the ability to simultaneously detect and distinguish various steroids due to low in vivo concentrations and naturally occurring stereoisomers. Here, we established such a method to study the mass spectrometry behaviour of nine sterols/steroids and related molecules (cholesterol precursors: squalene, lanosterol; sterol metabolites; 7 Dehydrocholesterol, 24, 25 and 27 Hydroxycholesterol; and steroids: progesterone, testosterone, and corticosterone) during ageing in the African turquoise killifish, a new model for studying vertebrate longevity. We find that levels of all tested steroids change significantly with age in multiple tissues, suggesting that specific steroids could be used as biomarkers of ageing. These findings pave the way for use of Nothobranchius furzeri as a novel model organism to unravel the role of sterols/steroids in ageing and age-related diseases. Graphical abstract ![]()
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Affiliation(s)
- Rahel Dabrowski
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9 b, 50931, Cologne, Germany
| | - Roberto Ripa
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9 b, 50931, Cologne, Germany
| | - Christian Latza
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9 b, 50931, Cologne, Germany
| | - Andrea Annibal
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9 b, 50931, Cologne, Germany.
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9 b, 50931, Cologne, Germany. .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Josef-Stelzmann-Strasse 26, 50931, Cologne, Germany.
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25
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Coux O, Zieba BA, Meiners S. The Proteasome System in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:55-100. [DOI: 10.1007/978-3-030-38266-7_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Marttila S, Chatsirisupachai K, Palmer D, de Magalhães JP. Ageing-associated changes in the expression of lncRNAs in human tissues reflect a transcriptional modulation in ageing pathways. Mech Ageing Dev 2020; 185:111177. [PMID: 31706952 PMCID: PMC6961210 DOI: 10.1016/j.mad.2019.111177] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/18/2022]
Abstract
Ageing-associated changes in the protein coding transcriptome have been extensively characterised, but less attention has been paid to the non-coding portion of the human genome, especially to long non-coding RNAs (lncRNAs). Only a minority of known lncRNAs have been functionally characterised; however, a handful of these lncRNAs have already been linked to ageing-associated processes. To gain more information on the effects of ageing on lncRNAs, we identified from GTEx data lncRNAs that show ageing-associated expression patterns (age-lncRNAs) in 29 human tissues in 20-79-year-old individuals. The age-lncRNAs identified were highly tissue-specific, but the protein coding genes co-expressed with the age-lncRNAs and the functional categories associated with the age-lncRNAs showed significant overlap across tissues. Functions associated with the age-lncRNAs, including immune system processes and transcription, were similar to what has previously been reported for protein coding genes with ageing-associated expression pattern. As the tissue-specific age-lncRNAs were associated with shared functions across tissues, they may reflect the tissue-specific fine-tuning of the common ageing-associated processes. The present study can be utilised as a resource when selecting and prioritising lncRNAs for further functional analyses.
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Affiliation(s)
- Saara Marttila
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Daniel Palmer
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
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27
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Romero-Ortuno R, Kenny RA, McManus R. Collagens and elastin genetic variations and their potential role in aging-related diseases and longevity in humans. Exp Gerontol 2019; 129:110781. [PMID: 31740390 DOI: 10.1016/j.exger.2019.110781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
Abstract
Collagens and elastin are 'building blocks' of tissues and extracellular matrix. Mutations in these proteins cause severe congenital syndromes. Adverse genetic variations may accelerate the aging process in adults contributing to premature morbidity, disability and/or mortality. Favorable variants may contribute to longevity and/or healthy aging, but this is much less studied. We reviewed the association between variation in the genes of collagens and elastin and premature aging, accelerated aging, age-related diseases and/or frailty; and the association between genetic variation in those and longevity and/or healthy aging in humans. A systematic search was conducted in MEDLINE and other online databases (OMIM, Genetics Home Reference, Orphanet, ClinVar). Results suggest that genetic variants lead to aging phenotypes of known congenital disease, but also to association with common age-related diseases in adults without known congenital disease. This may be due to the variable penetrance and expressivity of many variants. Some collagen variants have been associated with longevity or healthy aging. A limitation is that most studies had <1000 participants and their criterion for statistical significance was p < 0.05. Results highlight the importance of adopting a lifecourse approach to the study of the genomics of aging. Gerontology can help with new methodologies that operationalize biological aging.
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Affiliation(s)
- Roman Romero-Ortuno
- Trinity College Dublin, Discipline of Medical Gerontology, Mercer's Institute for Successful Ageing, St James's Hospital, Dublin 8, Ireland; The Irish Longitudinal Study on Ageing (TILDA), Trinity College Dublin, Dublin, Ireland..
| | - Rose Anne Kenny
- Trinity College Dublin, Discipline of Medical Gerontology, Mercer's Institute for Successful Ageing, St James's Hospital, Dublin 8, Ireland; The Irish Longitudinal Study on Ageing (TILDA), Trinity College Dublin, Dublin, Ireland
| | - Ross McManus
- Trinity College Dublin, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St James's Hospital, Dublin 8, Ireland
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28
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Cencioni C, Heid J, Krepelova A, Rasa SMM, Kuenne C, Guenther S, Baumgart M, Cellerino A, Neri F, Spallotta F, Gaetano C. Aging Triggers H3K27 Trimethylation Hoarding in the Chromatin of Nothobranchius furzeri Skeletal Muscle. Cells 2019; 8:cells8101169. [PMID: 31569376 PMCID: PMC6829443 DOI: 10.3390/cells8101169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/15/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
Aging associates with progressive loss of skeletal muscle function, sometimes leading to sarcopenia, a process characterized by impaired mobility and weakening of muscle strength. Since aging associates with profound epigenetic changes, epigenetic landscape alteration analysis in the skeletal muscle promises to highlight molecular mechanisms of age-associated alteration in skeletal muscle. This study was conducted exploiting the short-lived turquoise killifish Nothobranchius furzeri (Nfu), a relatively new model for aging studies. The epigenetic analysis suggested a less accessible and more condensed chromatin in old Nfu skeletal muscle. Specifically, an accumulation of heterochromatin regions was observed as a consequence of increased levels of H3K27me3, HP1α, polycomb complex subunits, and senescence-associated heterochromatic foci (SAHFs). Consistently, euchromatin histone marks, including H3K9ac, were significantly reduced. In this context, integrated bioinformatics analysis of RNASeq and ChIPSeq, related to skeletal muscle of Nfu at different ages, revealed a down-modulation of genes involved in cell cycle, differentiation, and DNA repair and an up-regulation of inflammation and senescence genes. Undoubtedly, more studies are needed to disclose the detailed mechanisms; however, our approach enlightened unprecedented features of Nfu skeletal muscle aging, potentially associated with swimming impairment and reduced mobility typical of old Nfu.
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Affiliation(s)
- Chiara Cencioni
- National Research Council, Institute for Systems Analysis and Computer Science, 00185 Rome, Italy.
| | - Johanna Heid
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Anna Krepelova
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | | | - Carsten Kuenne
- ECCPS Bioinformatics and deep sequencing platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.
| | - Stefan Guenther
- ECCPS Bioinformatics and deep sequencing platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.
| | - Mario Baumgart
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | - Alessandro Cellerino
- Laboratory of Biology (Bio@SNS), Scuola Normale Superiore, c/o Istituto di Biofisica del CNR, 56124 Pisa, Italy.
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | - Francesco Spallotta
- Department of Oncology, University of Turin, 10060 Candiolo (TO), Italy.
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (TO), Italy.
| | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy.
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29
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Ermolaeva M, Neri F, Ori A, Rudolph KL. Cellular and epigenetic drivers of stem cell ageing. Nat Rev Mol Cell Biol 2019; 19:594-610. [PMID: 29858605 DOI: 10.1038/s41580-018-0020-3] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adult tissue stem cells have a pivotal role in tissue maintenance and regeneration throughout the lifespan of multicellular organisms. Loss of tissue homeostasis during post-reproductive lifespan is caused, at least in part, by a decline in stem cell function and is associated with an increased incidence of diseases. Hallmarks of ageing include the accumulation of molecular damage, failure of quality control systems, metabolic changes and alterations in epigenome stability. In this Review, we discuss recent evidence in support of a novel concept whereby cell-intrinsic damage that accumulates during ageing and cell-extrinsic changes in ageing stem cell niches and the blood result in modifications of the stem cell epigenome. These cumulative epigenetic alterations in stem cells might be the cause of the deregulation of developmental pathways seen during ageing. In turn, they could confer a selective advantage to mutant and epigenetically drifted stem cells with altered self-renewal and functions, which contribute to the development of ageing-associated organ dysfunction and disease.
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Affiliation(s)
- Maria Ermolaeva
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
| | - K Lenhard Rudolph
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany. .,Medical Faculty Jena, University Hospital Jena (UKJ), Jena, Germany.
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30
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Hunt NJ, Kang SWS, Lockwood GP, Le Couteur DG, Cogger VC. Hallmarks of Aging in the Liver. Comput Struct Biotechnol J 2019; 17:1151-1161. [PMID: 31462971 PMCID: PMC6709368 DOI: 10.1016/j.csbj.2019.07.021] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 02/07/2023] Open
Abstract
While the liver demonstrates remarkable resilience during aging, there is growing evidence that it undergoes all the cellular hallmarks of aging, which increases the risk of liver and systemic disease. The aging process in the liver is driven by alterations of the genome and epigenome that contribute to dysregulation of mitochondrial function and nutrient sensing pathways, leading to cellular senescence and low-grade inflammation. These changes promote multiple phenotypic changes in all liver cells (hepatocytes, liver sinusoidal endothelial, hepatic stellate and Küpffer cells) and impairment of hepatic function. In particular, age-related changes in the liver sinusoidal endothelial cells are a significant but under-recognized risk factor for the development of age-related cardiometabolic disease. Liver aging is driven by transcription and metabolic epigenome alterations. This leads to cellular senescence and low-grade inflammation. Hepatocyte, sinusoidal endothelial, stellate and Küpffer cells undergoes the hallmarks of aging. Each cell type demonstrates phenotypical cellular changes with age.
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Key Words
- AMPK, 5′ adenosine monophosphate-activated protein kinase
- CR, caloric restriction
- Endothelial
- FOXO, forkhead box O
- Genetic
- HSC, hepatic stellate cell
- Hepatocyte
- IGF-1, insulin like growth factor 1
- IL-6, interleukin 6
- IL-8, interleukin 8
- KC, Küpffer cell
- LSEC, liver sinusoidal endothelial cell
- Mitochondrial dysfunction
- NAD, nicotinamide adenine dinucleotide
- NAFLD, non-alcoholic fatty liver disease
- NO, nitric oxide
- Nutrient sensing pathways
- PDGF, platelet derived growth factor
- PGC-1α, peroxisome proliferator-activated receptor gamma coactivator 1-α
- ROS, reactive oxygen species
- SIRT1, sirtuin 1
- Senescence
- TNFα, tumor necrosis factor alpha
- VEGF, vascular endothelial growth factor
- mTOR, mammalian target of rapamycin
- miR, microRNA
- αSMA, alpha smooth muscle actin
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Affiliation(s)
- Nicholas J Hunt
- ANZAC Research Institute, Aging and Alzheimer's Institute, Centre for Education and Research on Ageing, Concord Repatriation General Hospital, Concord, NSW, Australia.,The University of Sydney, Concord Clinical School, Sydney Medical School, Sydney, NSW, Australia.,The University of Sydney, Nutrition Ecology, Charles Perkins Centre, Sydney, NSW, Australia
| | - Sun Woo Sophie Kang
- ANZAC Research Institute, Aging and Alzheimer's Institute, Centre for Education and Research on Ageing, Concord Repatriation General Hospital, Concord, NSW, Australia.,The University of Sydney, Nutrition Ecology, Charles Perkins Centre, Sydney, NSW, Australia
| | - Glen P Lockwood
- ANZAC Research Institute, Aging and Alzheimer's Institute, Centre for Education and Research on Ageing, Concord Repatriation General Hospital, Concord, NSW, Australia.,The University of Sydney, Nutrition Ecology, Charles Perkins Centre, Sydney, NSW, Australia
| | - David G Le Couteur
- ANZAC Research Institute, Aging and Alzheimer's Institute, Centre for Education and Research on Ageing, Concord Repatriation General Hospital, Concord, NSW, Australia.,The University of Sydney, Concord Clinical School, Sydney Medical School, Sydney, NSW, Australia.,The University of Sydney, Nutrition Ecology, Charles Perkins Centre, Sydney, NSW, Australia
| | - Victoria C Cogger
- ANZAC Research Institute, Aging and Alzheimer's Institute, Centre for Education and Research on Ageing, Concord Repatriation General Hospital, Concord, NSW, Australia.,The University of Sydney, Concord Clinical School, Sydney Medical School, Sydney, NSW, Australia.,The University of Sydney, Nutrition Ecology, Charles Perkins Centre, Sydney, NSW, Australia
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31
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McIntyre RL, Daniels EG, Molenaars M, Houtkooper RH, Janssens GE. From molecular promise to preclinical results: HDAC inhibitors in the race for healthy aging drugs. EMBO Mol Med 2019; 11:e9854. [PMID: 31368626 PMCID: PMC6728603 DOI: 10.15252/emmm.201809854] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 06/13/2019] [Accepted: 07/11/2019] [Indexed: 12/18/2022] Open
Abstract
Reversing or slowing the aging process brings great promise to treat or prevent age‐related disease, and targeting the hallmarks of aging is a strategy to achieve this. Epigenetics affects several if not all of the hallmarks of aging and has therefore emerged as a central target for intervention. One component of epigenetic regulation involves histone deacetylases (HDAC), which include the “classical” histone deacetylases (of class I, II, and IV) and sirtuin deacetylases (of class III). While targeting sirtuins for healthy aging has been extensively reviewed elsewhere, this review focuses on pharmacologically inhibiting the classical HDACs to promote health and longevity. We describe the theories of how classical HDAC inhibitors may operate to increase lifespan, supported by studies in model organisms. Furthermore, we explore potential mechanisms of how HDAC inhibitors may have such a strong grasp on health and longevity, summarizing their links to other hallmarks of aging. Finally, we show the wide range of age‐related preclinical disease models, ranging from neurodegeneration to heart disease, diabetes to sarcopenia, which show improvement upon HDAC inhibition.
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Affiliation(s)
- Rebecca L McIntyre
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eileen G Daniels
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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32
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de Jong TV, Moshkin YM, Guryev V. Gene expression variability: the other dimension in transcriptome analysis. Physiol Genomics 2019; 51:145-158. [DOI: 10.1152/physiolgenomics.00128.2018] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Transcriptome sequencing is a powerful technique to study molecular changes that underlie the differences in physiological conditions and disease progression. A typical question that is posed in such studies is finding genes with significant changes between sample groups. In this respect expression variability is regarded as a nuisance factor that is primarily of technical origin and complicates the data analysis. However, it is becoming apparent that the biological variation in gene expression might be an important molecular phenotype that can affect physiological parameters. In this review we explore the recent literature on technical and biological variability in gene expression, sources of expression variability, (epi-)genetic hallmarks, and evolutionary constraints in genes with robust and variable gene expression. We provide an overview of recent findings on effects of external cues, such as diet and aging, on expression variability and on other biological phenomena that can be linked to it. We discuss metrics and tools that were developed for quantification of expression variability and highlight the importance of future studies in this direction. To assist the adoption of expression variability analysis, we also provide a detailed description and computer code, which can easily be utilized by other researchers. We also provide a reanalysis of recently published data to highlight the value of the analysis method.
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Affiliation(s)
- Tristan V. de Jong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Yuri M. Moshkin
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
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33
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Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P. Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals. Cell 2019; 177:1308-1318.e10. [PMID: 31031010 PMCID: PMC6988111 DOI: 10.1016/j.cell.2019.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/18/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
Proteotypes, like genotypes, have been found to vary between individuals in several studies, but consistent molecular functional traits across studies remain to be quantified. In a meta-analysis of 11 proteomics datasets from humans and mice, we use co-variation of proteins in known functional modules across datasets and individuals to obtain a consensus landscape of proteotype variation. We find that individuals differ considerably in both protein complex abundances and stoichiometry. We disentangle genetic and environmental factors impacting these metrics, with genetic sex and specific diets together explaining 13.5% and 11.6% of the observed variation of complex abundance and stoichiometry, respectively. Sex-specific differences, for example, include various proteins and complexes, where the respective genes are not located on sex-specific chromosomes. Diet-specific differences, added to the individual genetic backgrounds, might become a starting point for personalized proteotype modulation toward desired features. Benchmarking of datasets on human and mouse proteotypes Consistent co-variation landscape of functional modules across individuals Protein complexes vary in their stoichiometry across individuals Quantifying effects of genetic sex and specific diets on complexes
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Affiliation(s)
- Natalie Romanov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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34
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Bens M, Szafranski K, Holtze S, Sahm A, Groth M, Kestler HA, Hildebrandt TB, Platzer M. Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging. BMC Biol 2018; 16:77. [PMID: 30068345 PMCID: PMC6090939 DOI: 10.1186/s12915-018-0546-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/28/2018] [Indexed: 12/25/2022] Open
Abstract
Background Naked mole-rats (NMRs) are eusocially organized in colonies. Although breeders carry the additional metabolic load of reproduction, they are extremely long-lived and remain fertile throughout their lifespan. This phenomenon contrasts the disposable soma theory of aging stating that organisms can invest their resources either in somatic maintenance, enabling a longer lifespan, or in reproduction, at the cost of longevity. Here, we present a comparative transcriptome analysis of breeders vs. non-breeders of the eusocial, long-lived NMR vs. the polygynous and shorter-lived guinea pig (GP). Results Comparative transcriptome analysis of tissue samples from ten organs showed, in contrast to GPs, low levels of differentiation between sexes in adult NMR non-breeders. After transition into breeders, NMR transcriptomes are markedly sex-specific, show pronounced feedback signaling via gonadal steroids, and have similarities to reproductive phenotypes in African cichlid fish, which also exhibit social status changes between dominant and subordinate phenotypes. Further, NMRs show functional enrichment of status-related expression differences associated with aging. Lipid metabolism and oxidative phosphorylation—molecular networks known to be linked to aging—were identified among most affected gene sets. Remarkably and in contrast to GPs, transcriptome patterns associated with longevity are reinforced in NMR breeders. Conclusion Our results provide comprehensive and unbiased molecular insights into interspecies differences between NMRs and GPs, both in sexual maturation and in the impact of reproduction on longevity. We present molecular evidence that sexual maturation in NMRs is socially suppressed. In agreement with evolutionary theories of aging in eusocial organisms, we have identified transcriptome patterns in NMR breeders that—in contrast to the disposable soma theory of aging—may slow down aging rates and potentially contribute to their exceptional long life- and healthspan. Electronic supplementary material The online version of this article (10.1186/s12915-018-0546-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Bens
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenberg Str. 11, 07745, Jena, Germany.
| | - Karol Szafranski
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenberg Str. 11, 07745, Jena, Germany
| | - Susanne Holtze
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Arne Sahm
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenberg Str. 11, 07745, Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenberg Str. 11, 07745, Jena, Germany
| | - Hans A Kestler
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenberg Str. 11, 07745, Jena, Germany.,Institute of Medical Systems Biology, Ulm University, James-Franck-Ring, 89069, Ulm, Germany
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenberg Str. 11, 07745, Jena, Germany
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Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging. BMC Biol 2018; 16:82. [PMID: 30068331 PMCID: PMC6090990 DOI: 10.1186/s12915-018-0547-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/28/2018] [Indexed: 12/04/2022] Open
Abstract
Background Mammals display a wide range of variation in their lifespan. Investigating the molecular networks that distinguish long- from short-lived species has proven useful to identify determinants of longevity. Here, we compared the livers of young and old long-lived naked mole-rats (NMRs) and the phylogenetically closely related, shorter-lived, guinea pigs using an integrated omics approach. Results We found that NMR livers display a unique expression pattern of mitochondrial proteins that results in distinct metabolic features of their mitochondria. For instance, we observed a generally reduced respiration rate associated with lower protein levels of respiratory chain components, particularly complex I, and increased capacity to utilize fatty acids. Interestingly, we show that the same molecular networks are affected during aging in both NMRs and humans, supporting a direct link to the extraordinary longevity of both species. Finally, we identified a novel detoxification pathway linked to longevity and validated it experimentally in the nematode Caenorhabditis elegans. Conclusions Our work demonstrates the benefits of integrating proteomic and transcriptomic data to perform cross-species comparisons of longevity-associated networks. Using a multispecies approach, we show at the molecular level that livers of NMRs display progressive age-dependent changes that recapitulate typical signatures of aging despite the negligible senescence and extraordinary longevity of these rodents. Electronic supplementary material The online version of this article (10.1186/s12915-018-0547-y) contains supplementary material, which is available to authorized users.
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Parca L, Beck M, Bork P, Ori A. Quantifying compartment-associated variations of protein abundance in proteomics data. Mol Syst Biol 2018; 14:e8131. [PMID: 29967062 PMCID: PMC6056770 DOI: 10.15252/msb.20178131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 12/22/2022] Open
Abstract
Quantitative mass spectrometry enables to monitor the abundance of thousands of proteins across biological conditions. Currently, most data analysis approaches rely on the assumption that the majority of the observed proteins remain unchanged across compared samples. Thus, gross morphological differences between cell states, deriving from, e.g., differences in size or number of organelles, are often not taken into account. Here, we analyzed multiple published datasets and frequently observed that proteins associated with a particular cellular compartment collectively increase or decrease in their abundance between conditions tested. We show that such effects, arising from underlying morphological differences, can skew the outcome of differential expression analysis. We propose a method to detect and normalize morphological effects underlying proteomics data. We demonstrate the applicability of our method to different datasets and biological questions including the analysis of sub-cellular proteomes in the context of Caenorhabditis elegans aging. Our method provides a complementary perspective to classical differential expression analysis and enables to uncouple overall abundance changes from stoichiometric variations within defined group of proteins.
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Affiliation(s)
- Luca Parca
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
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Müller C, Zidek LM, Ackermann T, de Jong T, Liu P, Kliche V, Zaini MA, Kortman G, Harkema L, Verbeek DS, Tuckermann JP, von Maltzahn J, de Bruin A, Guryev V, Wang ZQ, Calkhoven CF. Reduced expression of C/EBPβ-LIP extends health and lifespan in mice. eLife 2018; 7:34985. [PMID: 29708496 PMCID: PMC5986274 DOI: 10.7554/elife.34985] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023] Open
Abstract
Ageing is associated with physical decline and the development of age-related diseases such as metabolic disorders and cancer. Few conditions are known that attenuate the adverse effects of ageing, including calorie restriction (CR) and reduced signalling through the mechanistic target of rapamycin complex 1 (mTORC1) pathway. Synthesis of the metabolic transcription factor C/EBPβ-LIP is stimulated by mTORC1, which critically depends on a short upstream open reading frame (uORF) in the Cebpb-mRNA. Here, we describe that reduced C/EBPβ-LIP expression due to genetic ablation of the uORF delays the development of age-associated phenotypes in mice. Moreover, female C/EBPβΔuORF mice display an extended lifespan. Since LIP levels increase upon aging in wild type mice, our data reveal an important role for C/EBPβ in the aging process and suggest that restriction of LIP expression sustains health and fitness. Thus, therapeutic strategies targeting C/EBPβ-LIP may offer new possibilities to treat age-related diseases and to prolong healthspan. The risks of major diseases including type II diabetes, cancer and Alzheimer’s are linked to the biological process of ageing. By finding ways to slow ageing, we can help more people to live longer healthier lives while avoiding these illnesses. Placing some animals on a diet that contains only two-thirds as many calories as they would normally eat can improve their fitness during old age and delay the onset of many age-related problems. It is unrealistic to expect people to control their diet to this extent, yet there may be other ways to bring about the same effects. Calorie restriction affects the activity of many different genes; for example, it causes a gene that produces a protein known as Liver-enriched Inhibitory Protein (LIP for short) to shut down. LIP controls the activity of many genes involved in metabolism, so it could be a key target for drugs to control ageing. Müller, Zidek et al. used mice that are unable to produce LIP to study this protein’s effect on ageing. The life expectancy of female mice lacking LIP increased by up to 20%. These mice were leaner, fitter, more resistant to cancer, had stronger immune systems and controlled their blood sugar levels better than normal mice. Male mice that lacked LIP did not live longer but did experience some ageing-related benefits. Genetic analysis also showed that gene activity particularly of metabolic genes is more robust in old female LIP-deficient mice and thus more similar to young control mice than old control mice. The results presented by Müller, Zidek et al. suggest that targeting the activity of the LIP gene could help to slow the ageing process. It is not yet clear whether shutting off LIP has similar beneficial effects in humans. Further research is also needed to investigate why female mice gain more benefits from a lack of LIP than males do.
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Affiliation(s)
- Christine Müller
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands.,Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Laura M Zidek
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Tobias Ackermann
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Tristan de Jong
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Peng Liu
- Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Verena Kliche
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Mohamad Amr Zaini
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Gertrud Kortman
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Liesbeth Harkema
- Dutch Molecular Pathology Centre, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jan P Tuckermann
- Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | | | - Alain de Bruin
- Dutch Molecular Pathology Centre, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Cornelis F Calkhoven
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands.,Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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Mukherjee S, Saxena R, Palmer LJ. The genetics of obstructive sleep apnoea. Respirology 2018; 23:18-27. [PMID: 29113020 PMCID: PMC7308164 DOI: 10.1111/resp.13212] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/11/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022]
Abstract
Obstructive sleep apnoea (OSA) is a common chronic disease and is associated with high social and economic costs. OSA is heritable, and there is evidence of both direct genetic contributions to OSA susceptibility and indirect contributions via 'intermediate' phenotypes such as obesity, craniofacial structure, neurological control of upper airway muscles and of sleep and circadian rhythm. Investigation of the genetics of OSA is an important research area and may lead to improved understanding of disease aetiology, pathogenesis, adverse health consequences and new preventive strategies and treatments. Genetic studies of OSA have lagged behind other chronic diseases; however recent gene discovery efforts have been successful in finding genetic loci contributing to OSA-associated intermediate phenotypes. Nevertheless, many of the seminal questions relating to the genetic epidemiology of OSA and associated factors remain unanswered. This paper reviews the current state of knowledge of the genetics of OSA, with a focus on genomic approaches to understanding sleep apnoea.
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Affiliation(s)
- Sutapa Mukherjee
- Sleep Health Service, Respiratory and Sleep Services, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
- Adelaide Institute for Sleep Health, Flinders University, Adelaide, South Australia, Australia
| | - Richa Saxena
- Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Lyle J Palmer
- School of Public Health, University of Adelaide, North Terrace, Adelaide, South Australia, Australia
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