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Kedlian VR, Wang Y, Liu T, Chen X, Bolt L, Tudor C, Shen Z, Fasouli ES, Prigmore E, Kleshchevnikov V, Pett JP, Li T, Lawrence JEG, Perera S, Prete M, Huang N, Guo Q, Zeng X, Yang L, Polański K, Chipampe NJ, Dabrowska M, Li X, Bayraktar OA, Patel M, Kumasaka N, Mahbubani KT, Xiang AP, Meyer KB, Saeb-Parsy K, Teichmann SA, Zhang H. Human skeletal muscle aging atlas. NATURE AGING 2024; 4:727-744. [PMID: 38622407 PMCID: PMC11108788 DOI: 10.1038/s43587-024-00613-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Skeletal muscle aging is a key contributor to age-related frailty and sarcopenia with substantial implications for global health. Here we profiled 90,902 single cells and 92,259 single nuclei from 17 donors to map the aging process in the adult human intercostal muscle, identifying cellular changes in each muscle compartment. We found that distinct subsets of muscle stem cells exhibit decreased ribosome biogenesis genes and increased CCL2 expression, causing different aging phenotypes. Our atlas also highlights an expansion of nuclei associated with the neuromuscular junction, which may reflect re-innervation, and outlines how the loss of fast-twitch myofibers is mitigated through regeneration and upregulation of fast-type markers in slow-twitch myofibers with age. Furthermore, we document the function of aging muscle microenvironment in immune cell attraction. Overall, we present a comprehensive human skeletal muscle aging resource ( https://www.muscleageingcellatlas.org/ ) together with an in-house mouse muscle atlas to study common features of muscle aging across species.
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Affiliation(s)
- Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tianliang Liu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhuojian Shen
- Department of Thoracic Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Qin Guo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinrui Zeng
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xiaobo Li
- Core Facilities for Medical Science, Sun Yat-sen University, Guangzhou, China
| | - Omer Ali Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Andy Peng Xiang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
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2
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Michaud SA, Pětrošová H, Sinclair NJ, Kinnear AL, Jackson AM, McGuire JC, Hardie DB, Bhowmick P, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Smith D, Mohammed Y, Schibli D, Sickmann A, Borchers CH. Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues. Commun Biol 2024; 7:6. [PMID: 38168632 PMCID: PMC10762018 DOI: 10.1038/s42003-023-05687-0] [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: 09/16/2020] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Mouse is the mammalian model of choice to study human health and disease due to its size, ease of breeding and the natural occurrence of conditions mimicking human pathology. Here we design and validate multiple reaction monitoring mass spectrometry (MRM-MS) assays for quantitation of 2118 unique proteins in 20 murine tissues and organs. We provide open access to technical aspects of these assays to enable their implementation in other laboratories, and demonstrate their suitability for proteomic profiling in mice by measuring normal protein abundances in tissues from three mouse strains: C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. Sex- and strain-specific differences in protein abundances are identified and described, and the measured values are freely accessible via our MouseQuaPro database: http://mousequapro.proteincentre.com . Together, this large library of quantitative MRM-MS assays established in mice and the measured baseline protein abundances represent an important resource for research involving mouse models.
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Affiliation(s)
- Sarah A Michaud
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada.
| | - Helena Pětrošová
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Nicholas J Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Andrea L Kinnear
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Angela M Jackson
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Jamie C McGuire
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Pallab Bhowmick
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Milan Ganguly
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann M Flenniken
- The Center for Phenogenomics, Toronto, ON, Canada
- Sinai Health Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Derek Smith
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - David Schibli
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Department of Pathology, McGill University, Montreal, QC, Canada.
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3
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Li Y, Khan N, Ritzel RM, Lei Z, Allen S, Faden AI, Wu J. Sexually dimorphic extracellular vesicle responses after chronic spinal cord injury are associated with neuroinflammation and neurodegeneration in the aged brain. J Neuroinflammation 2023; 20:197. [PMID: 37653491 PMCID: PMC10469550 DOI: 10.1186/s12974-023-02881-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Medical advances have made it increasingly possible for spinal cord injury (SCI) survivors to survive decades after the insult. But how SCI affects aging changes and aging impacts the injury process have received limited attention. Extracellular vesicles (EVs) are recognized as critical mediators of neuroinflammation after CNS injury, including at a distance from the lesion site. We have previously shown that SCI in young male mice leads to robust changes in plasma EV count and microRNA (miR) content. Here, our goal was to investigate the impact of biological sex and aging on EVs and brain after SCI. METHODS Young adult age-matched male and female C57BL/6 mice were subjected to SCI. At 19 months post-injury, total plasma EVs were isolated by ultracentrifugation and characterized by nanoparticle tracking analysis (NTA). EVs miR cargo was examined using the Fireplex® assay. The transcriptional changes in the brain were assessed by a NanoString nCounter Neuropathology panel and validated by Western blot (WB) and flow cytometry (FC). A battery of behavioral tests was performed for assessment of neurological function. RESULTS Transcriptomic changes showed a high number of changes between sham and those with SCI. Sex-specific changes were found in transcription networks related to disease association, activated microglia, and vesicle trafficking. FC showed higher microglia and myeloid counts in the injured tissue of SCI/Female compared to their male counterparts, along with higher microglial production of ROS in both injured site and the brain. In the latter, increased levels of TNF and mitochondrial membrane potential were seen in microglia from SCI/Female. WB and NTA revealed that EV markers are elevated in the plasma of SCI/Male. Particle concentration in the cortex increased after injury, with SCI/Female showing higher counts than SCI/Male. EVs cargo analysis revealed changes in miR content related to injury and sex. Behavioral testing confirmed impairment of cognition and depression at chronic time points after SCI in both sexes, without significant differences between males and females. CONCLUSIONS Our study is the first to show sexually dimorphic changes in brain after very long-term SCI and supports a potential sex-dependent EV-mediated mechanism that contributes to SCI-induced brain changes.
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Affiliation(s)
- Yun Li
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore Street, MSTF, Room 6-034D, Baltimore, MD, 21201, USA
| | - Niaz Khan
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore Street, MSTF, Room 6-034D, Baltimore, MD, 21201, USA
| | - Rodney M Ritzel
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore Street, MSTF, Room 6-034D, Baltimore, MD, 21201, USA
| | - Zhuofan Lei
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore Street, MSTF, Room 6-034D, Baltimore, MD, 21201, USA
| | - Samantha Allen
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore Street, MSTF, Room 6-034D, Baltimore, MD, 21201, USA
| | - Alan I Faden
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore Street, MSTF, Room 6-034D, Baltimore, MD, 21201, USA
| | - Junfang Wu
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore Street, MSTF, Room 6-034D, Baltimore, MD, 21201, USA.
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4
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Graber TG, Maroto R, Thompson JK, Widen SG, Man Z, Pajski ML, Rasmussen BB. Skeletal Muscle Transcriptome Alterations Related to Declining Physical Function in Older Mice. JOURNAL OF AGEING AND LONGEVITY 2023; 3:159-178. [PMID: 37876943 PMCID: PMC10597580 DOI: 10.3390/jal3020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
One inevitable consequence of aging is the gradual deterioration of physical function and exercise capacity, driven in part by the adverse effect of age on muscle tissue. We hypothesized that relationships exist between age-related differentially expressed genes (DEGs) in skeletal muscle and age-associated declines in physical function and exercise capacity. Previously, male C57BL/6mice (6m, months old, 24m, and 28m) were tested for physical function using a composite scoring system (comprehensive functional assessment battery, CFAB) comprised of five well-validated tests of physical function. In this study, total RNA was isolated from tibialis anterior samples (n = 8) randomly selected from each age group in the parent study. Using Next Generation Sequencing RNAseq to determine DEGs during aging (6m vs. 28m, and 6m vs. 24m), we found a greater than five-fold increase in DEGs in 28m compared to the 24m. Furthermore, regression of the normalized expression of each DEG with the CFAB score of the corresponding mouse revealed many more DEGs strongly associated (R ≥ |0.70|) with functional status in the older mice. Gene ontology results indicate highly enriched axon guidance and acetyl choline receptor gene sets, suggesting that denervation/reinnervation flux might potentially play a critical role in functional decline. We conclude that specific age-related DEG patterns are associated with declines in physical function, and the data suggest accelerated aging occurring between 24 and 28 months.
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Affiliation(s)
- Ted G. Graber
- Department of Physical Therapy, East Carolina University, Greenville, NC 27834, USA
| | - Rosario Maroto
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jill K. Thompson
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven G. Widen
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Zhaohui Man
- Bioinformatics and Analytics Research Collaborative, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Megan L. Pajski
- Department of Physical Therapy, East Carolina University, Greenville, NC 27834, USA
| | - Blake B. Rasmussen
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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5
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Gyenis A, Chang J, Demmers JJPG, Bruens ST, Barnhoorn S, Brandt RMC, Baar MP, Raseta M, Derks KWJ, Hoeijmakers JHJ, Pothof J. Genome-wide RNA polymerase stalling shapes the transcriptome during aging. Nat Genet 2023; 55:268-279. [PMID: 36658433 PMCID: PMC9925383 DOI: 10.1038/s41588-022-01279-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/07/2022] [Indexed: 01/21/2023]
Abstract
Gene expression profiling has identified numerous processes altered in aging, but how these changes arise is largely unknown. Here we combined nascent RNA sequencing and RNA polymerase II chromatin immunoprecipitation followed by sequencing to elucidate the underlying mechanisms triggering gene expression changes in wild-type aged mice. We found that in 2-year-old liver, 40% of elongating RNA polymerases are stalled, lowering productive transcription and skewing transcriptional output in a gene-length-dependent fashion. We demonstrate that this transcriptional stress is caused by endogenous DNA damage and explains the majority of gene expression changes in aging in most mainly postmitotic organs, specifically affecting aging hallmark pathways such as nutrient sensing, autophagy, proteostasis, energy metabolism, immune function and cellular stress resilience. Age-related transcriptional stress is evolutionary conserved from nematodes to humans. Thus, accumulation of stochastic endogenous DNA damage during aging deteriorates basal transcription, which establishes the age-related transcriptome and causes dysfunction of key aging hallmark pathways, disclosing how DNA damage functionally underlies major aspects of normal aging.
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Affiliation(s)
- Akos Gyenis
- 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
| | - Jiang Chang
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris J P G Demmers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Serena T Bruens
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marjolein P Baar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marko Raseta
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kasper W J Derks
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics and School for Oncology & Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - 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
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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6
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Bresilla D, Habisch H, Pritišanac I, Zarse K, Parichatikanond W, Ristow M, Madl T, Madreiter-Sokolowski CT. The sex-specific metabolic signature of C57BL/6NRj mice during aging. Sci Rep 2022; 12:21050. [PMID: 36473898 PMCID: PMC9726821 DOI: 10.1038/s41598-022-25396-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Due to intact reactive oxygen species homeostasis and glucose metabolism, C57BL/6NRj mice are especially suitable to study cellular alterations in metabolism. We applied Nuclear Magnetic resonance spectroscopy to analyze five different tissues of this mouse strain during aging and included female and male mice aged 3, 6, 12, and 24 months. Metabolite signatures allowed separation between the age groups in all tissues, and we identified the most prominently changing metabolites in female and male tissues. A refined analysis of individual metabolite levels during aging revealed an early onset of age-related changes at 6 months, sex-specific differences in the liver, and a biphasic pattern for various metabolites in the brain, heart, liver, and lung. In contrast, a linear decrease of amino acids was apparent in muscle tissues. Based on these results, we assume that age-related metabolic alterations happen at a comparably early aging state and are potentially associated with a metabolic switch. Moreover, identified differences between female and male tissues stress the importance of distinguishing between sexes when studying age-related changes and developing new treatment approaches. Besides, metabolomic features seem to be highly dependent on the genetic background of mouse strains.
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Affiliation(s)
- Doruntina Bresilla
- grid.11598.340000 0000 8988 2476Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/VI, 8010 Graz, Austria
| | - Hansjoerg Habisch
- grid.11598.340000 0000 8988 2476Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/VI, 8010 Graz, Austria
| | - Iva Pritišanac
- grid.11598.340000 0000 8988 2476Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/VI, 8010 Graz, Austria
| | - Kim Zarse
- grid.5801.c0000 0001 2156 2780Laboratory of Energy Metabolism, Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zurich, Schorenstrasse 16, 8603 Schwerzenbach, Switzerland
| | - Warisara Parichatikanond
- grid.10223.320000 0004 1937 0490Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok, 10400 Thailand ,grid.10223.320000 0004 1937 0490Faculty of Pharmacy, Center of Biopharmaceutical Science for Healthy Ageing (BSHA), Mahidol University, Bangkok, 10400 Thailand
| | - Michael Ristow
- grid.5801.c0000 0001 2156 2780Laboratory of Energy Metabolism, Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zurich, Schorenstrasse 16, 8603 Schwerzenbach, Switzerland
| | - Tobias Madl
- grid.11598.340000 0000 8988 2476Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/VI, 8010 Graz, Austria ,grid.452216.6BioTechMed-Graz, Graz, Austria
| | - Corina T. Madreiter-Sokolowski
- grid.11598.340000 0000 8988 2476Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/VI, 8010 Graz, Austria ,grid.452216.6BioTechMed-Graz, Graz, Austria
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7
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Tong X, Li WX, Liang J, Zheng Y, Dai SX. Two different aging paths in human blood revealed by integrated analysis of gene Expression, mutation and alternative splicing. Gene 2022; 829:146501. [PMID: 35452709 DOI: 10.1016/j.gene.2022.146501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 11/04/2022]
Abstract
Aging is a complex life process that human organs and tissues steadily and continuously decline. Aging has huge heterogeneity, which shows different aging rates among different individuals and in different tissues of the same individual. Many studies of aging are often contradictory and show little common signature. The integrated analysis of these transcriptome datasets will provide an unbiased global view of the aging process. Here, we integrated 8 transcriptome datasets including 757 samples from healthy human blood to study aging from three aspects of gene expression, mutations, and alternative splicing. Surprisingly, we found that transcriptome changes in blood are relatively independent of the chronological age. Further pseudotime analysis revealed two different aging paths (AgingPath1 and AgingPath2) in human blood. The differentially expressed genes (DEGs) along the two paths showed a limited overlap and are enriched in different biological processes. The mutations of DEGs in AgingPath1 are significantly increased in the aging process, while the opposite trend was observed in AgingPath2. Expression quantitative trait loci (eQTL) and splicing quantitative trait loci (sQTL) analysis identified 304 important mutations that can affect both gene expression and alternative splicing during aging. Finally, by comparison between aging and Alzheimer's disease, we identified 37 common DEGs in AgingPath1, AgingPath2 and Alzheimer's disease. These genes may contribute to the shift from aging state to Alzheimer's disease. In summary, this study revealed the two aging paths and the related genes and mutations, which provides a new insight into aging and aging-related disease.
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Affiliation(s)
- Xin Tong
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Wen-Xing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jihao Liang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yang Zheng
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Shao-Xing Dai
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
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8
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Webb JL, Moe SM, Bolstad AK, McNeill EM. Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive. PLoS One 2021; 16:e0255085. [PMID: 34379632 PMCID: PMC8357136 DOI: 10.1371/journal.pone.0255085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 07/09/2021] [Indexed: 11/19/2022] Open
Abstract
Aging is universal, yet characterizing the molecular changes that occur in aging which lead to an increased risk for neurological disease remains a challenging problem. Aging affects the prefrontal cortex (PFC), which governs executive function, learning, and memory. Previous sequencing studies have demonstrated that aging alters gene expression in the PFC, however the extent to which these changes are conserved across species and are meaningful in neurodegeneration is unknown. Identifying conserved, age-related genetic and morphological changes in the brain allows application of the wealth of tools available to study underlying mechanisms in model organisms such as Drosophila melanogaster. RNA sequencing data from human PFC and fly heads were analyzed to determine conserved transcriptome signatures of age. Our analysis revealed that expression of 50 conserved genes can accurately determine age in Drosophila (R2 = 0.85) and humans (R2 = 0.46). These transcriptome signatures were also able to classify Drosophila into three age groups with a mean accuracy of 88% and classify human samples with a mean accuracy of 69%. Overall, this work identifies 50 highly conserved aging-associated genetic changes in the brain that can be further studied in model organisms and demonstrates a novel approach to uncovering genetic changes conserved across species from multi-study public databases.
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Affiliation(s)
- Joe L. Webb
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
| | - Simon M. Moe
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
| | - Andrew K. Bolstad
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States of America
| | - Elizabeth M. McNeill
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
- Neuroscience Interdepartmental Graduate program, Iowa State University, Ames, IA, United States of America
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9
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Satou-Kobayashi Y, Kim JD, Fukamizu A, Asashima M. Temporal transcriptomic profiling reveals dynamic changes in gene expression of Xenopus animal cap upon activin treatment. Sci Rep 2021; 11:14537. [PMID: 34267234 PMCID: PMC8282838 DOI: 10.1038/s41598-021-93524-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
Activin, a member of the transforming growth factor-β (TGF-β) superfamily of proteins, induces various tissues from the amphibian presumptive ectoderm, called animal cap explants (ACs) in vitro. However, it remains unclear how and to what extent the resulting cells recapitulate in vivo development. To comprehensively understand whether the molecular dynamics during activin-induced ACs differentiation reflect the normal development, we performed time-course transcriptome profiling of Xenopus ACs treated with 50 ng/mL of activin A, which predominantly induced dorsal mesoderm. The number of differentially expressed genes (DEGs) in response to activin A increased over time, and totally 9857 upregulated and 6663 downregulated DEGs were detected. 1861 common upregulated DEGs among all Post_activin samples included several Spemann's organizer genes. In addition, the temporal transcriptomes were clearly classified into four distinct groups in correspondence with specific features, reflecting stepwise differentiation into mesoderm derivatives, and a decline in the regulation of nuclear envelop and golgi. From the set of early responsive genes, we also identified the suppressor of cytokine signaling 3 (socs3) as a novel activin A-inducible gene. Our transcriptome data provide a framework to elucidate the transcriptional dynamics of activin-driven AC differentiation, reflecting the molecular characteristics of early normal embryogenesis.
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Affiliation(s)
- Yumeko Satou-Kobayashi
- grid.264706.10000 0000 9239 9995Strategic Innovation and Research Center, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605 Japan ,grid.264706.10000 0000 9239 9995Advanced Comprehensive Research Organization, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605 Japan ,grid.20515.330000 0001 2369 4728Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1, Tsukuba, Tennoudai Ibaraki 305-8577 Japan
| | - Jun-Dal Kim
- grid.20515.330000 0001 2369 4728Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1, Tsukuba, Tennoudai Ibaraki 305-8577 Japan ,grid.267346.20000 0001 2171 836XDivision of Complex Bioscience Research, Department of Research and Development, Institute of National Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194 Japan
| | - Akiyoshi Fukamizu
- grid.20515.330000 0001 2369 4728Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1, Tsukuba, Tennoudai Ibaraki 305-8577 Japan
| | - Makoto Asashima
- grid.264706.10000 0000 9239 9995Strategic Innovation and Research Center, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605 Japan ,grid.264706.10000 0000 9239 9995Advanced Comprehensive Research Organization, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605 Japan ,grid.20515.330000 0001 2369 4728Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1, Tsukuba, Tennoudai Ibaraki 305-8577 Japan
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10
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Balkenhol J, Kaltdorf KV, Mammadova-Bach E, Braun A, Nieswandt B, Dittrich M, Dandekar T. Comparison of the central human and mouse platelet signaling cascade by systems biological analysis. BMC Genomics 2020; 21:897. [PMID: 33353544 PMCID: PMC7756956 DOI: 10.1186/s12864-020-07215-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is involved in major responses to exogenous factors. This is defined by systemsbiological pathway analysis as the central regulating signaling cascade of platelets (CC). Results The CC is systematically compared here between mouse and human and major differences were found. Genetic differences were analysed comparing orthologous human and mouse genes. We next analyzed different expression levels of mRNAs. Considering 4 mouse and 7 human high-quality proteome data sets, we identified then those major mRNA expression differences (81%) which were supported by proteome data. CC is conserved regarding genetic completeness, but we observed major differences in mRNA and protein levels between both species. Looking at central interactors, human PLCB2, MMP9, BDNF, ITPR3 and SLC25A6 (always Entrez notation) show absence in all murine datasets. CC interactors GNG12, PRKCE and ADCY9 occur only in mice. Looking at the common proteins, TLN1, CALM3, PRKCB, APP, SOD2 and TIMP1 are higher abundant in human, whereas RASGRP2, ITGB2, MYL9, EIF4EBP1, ADAM17, ARRB2, CD9 and ZYX are higher abundant in mouse. Pivotal kinase SRC shows different regulation on mRNA and protein level as well as ADP receptor P2RY12. Conclusions Our results highlight species-specific differences in platelet signaling and points of specific fine-tuning in human platelets as well as murine-specific signaling differences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07215-4.
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Affiliation(s)
- Johannes Balkenhol
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074, Würzburg, Germany
| | - Kristin V Kaltdorf
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074, Würzburg, Germany
| | - Elmina Mammadova-Bach
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Centre, University of Würzburg, Würzburg, Germany.,Present address: Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig, Maximilian University of Munich, D-80336, Munich, Germany
| | - Attila Braun
- Member of the German Center for Lung Research (DZL), Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians University Munich, Munich, Germany
| | - Bernhard Nieswandt
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Centre, University of Würzburg, Würzburg, Germany
| | - Marcus Dittrich
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074, Würzburg, Germany.,Dept of Genetics, Biocenter, Am Hubland, University of Würzburg, Am Hubland, D 97074, Würzburg, Germany
| | - Thomas Dandekar
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074, Würzburg, Germany.
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11
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Zhou Q, Wan Q, Jiang Y, Liu J, Qiang L, Sun L. A Landscape of Murine Long Non-Coding RNAs Reveals the Leading Transcriptome Alterations in Adipose Tissue during Aging. Cell Rep 2020; 31:107694. [PMID: 32460027 PMCID: PMC7603645 DOI: 10.1016/j.celrep.2020.107694] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/09/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
Aging is an inevitable process that involves profound physiological changes. Long non-coding RNAs (lncRNAs) are emerging as important regulators in various biological processes but are not systemically studied in aging. To provide an organism-wide lncRNA landscape during aging, we conduct comprehensive RNA sequencing (RNA-seq) analyses across the mouse lifespan. Of the 1,675 aging-regulated lncRNAs (AR-lncRNAs) identified, the majority are connected to inflammation-related biological pathways. AR-lncRNAs exhibit high tissue specificity; conversely, those with higher tissue specificity are preferentially regulated during aging. White adipose tissue (WAT) displays the highest number of AR-lncRNAs and develops the most dynamic crosstalk between AR-lncRNA and AR-mRNA during aging. An adipose-enriched AR-lncRNA, lnc-adipoAR1, is negatively correlated with aging, and knocking it down inhibits adipogenesis, phenocopying the compromised adipogenic capacity of aged fat. Our works together reveal AR-lncRNAs as essential components in aging and suggest that although each tissue ages in a distinct manner, WAT is a leading contributor to aging-related health decline.
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Affiliation(s)
- Qiuzhong Zhou
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Qianfen Wan
- Naomi Berrie Diabetes Center, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yuxi Jiang
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, Zhejiang 325035, China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jin Liu
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Li Qiang
- Naomi Berrie Diabetes Center, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
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12
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D'Souza RF, Woodhead JST, Hedges CP, Zeng N, Wan J, Kumagai H, Lee C, Cohen P, Cameron-Smith D, Mitchell CJ, Merry TL. Increased expression of the mitochondrial derived peptide, MOTS-c, in skeletal muscle of healthy aging men is associated with myofiber composition. Aging (Albany NY) 2020; 12:5244-5258. [PMID: 32182209 PMCID: PMC7138593 DOI: 10.18632/aging.102944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 03/09/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria putatively regulate the aging process, in part, through the small regulatory peptide, mitochondrial open reading frame of the 12S rRNA-c (MOTS-c) that is encoded by the mitochondrial genome. Here we investigated the regulation of MOTS-c in the plasma and skeletal muscle of healthy aging men. Circulating MOTS-c reduced with age, but older (70-81 y) and middle-aged (45-55 y) men had ~1.5-fold higher skeletal muscle MOTS-c expression than young (18-30 y). Plasma MOTS-c levels only correlated with plasma in young men, was associated with markers of slow-type muscle, and associated with improved muscle quality in the older group (maximal leg-press load relative to thigh cross-sectional area). Using small mRNA assays we provide evidence that MOTS-c transcription may be regulated independently of the full length 12S rRNA gene in which it is encoded, and expression is not associated with antioxidant response element (ARE)-related genes as previously seen in culture. Our results suggest that plasma and muscle MOTS-c are differentially regulated with aging, and the increase in muscle MOTS-c expression with age is consistent with fast-to-slow type muscle fiber transition. Further research is required to determine the molecular targets of endogenous MOTS-c in human muscle but they may relate to factors that maintain muscle quality.
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Affiliation(s)
- Randall F D'Souza
- Discipline of Nutrition, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Jonathan S T Woodhead
- Discipline of Nutrition, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Christopher P Hedges
- Discipline of Nutrition, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Nina Zeng
- Liggins Institute, The University of Auckland, Auckland, New Zealand.,Department of Physiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Junxiang Wan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Hiroshi Kumagai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,Japan Society for the Promotion of Science, Tokyo, Japan.,Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA.,Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Cameron J Mitchell
- Liggins Institute, The University of Auckland, Auckland, New Zealand.,School of Kinesiology, University of British Colombia, Vancouver, BC V6T 1Z1, Canada
| | - Troy L Merry
- Discipline of Nutrition, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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