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Chen R, Zhang Z, Ma J, Liu B, Huang Z, Hu G, Huang J, Xu Y, Wang GZ. Circadian-driven tissue specificity is constrained under caloric restricted feeding conditions. Commun Biol 2024; 7:752. [PMID: 38902439 DOI: 10.1038/s42003-024-06421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024] Open
Abstract
Tissue specificity is a fundamental property of an organ that affects numerous biological processes, including aging and longevity, and is regulated by the circadian clock. However, the distinction between circadian-affected tissue specificity and other tissue specificities remains poorly understood. Here, using multi-omics data on circadian rhythms in mice, we discovered that approximately 35% of tissue-specific genes are directly affected by circadian regulation. These circadian-affected tissue-specific genes have higher expression levels and are associated with metabolism in hepatocytes. They also exhibit specific features in long-reads sequencing data. Notably, these genes are associated with aging and longevity at both the gene level and at the network module level. The expression of these genes oscillates in response to caloric restricted feeding regimens, which have been demonstrated to promote longevity. In addition, aging and longevity genes are disrupted in various circadian disorders. Our study indicates that the modulation of circadian-affected tissue specificity is essential for understanding the circadian mechanisms that regulate aging and longevity at the genomic level.
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Affiliation(s)
- Renrui Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziang Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bing Liu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhengyun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Ju Huang
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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Kumar NH, Kluever V, Barth E, Krautwurst S, Furlan M, Pelizzola M, Marz M, Fornasiero EF. Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain. Nucleic Acids Res 2024; 52:2865-2885. [PMID: 38471806 PMCID: PMC11014377 DOI: 10.1093/nar/gkae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/18/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive understanding of molecular changes during brain aging is essential to mitigate cognitive decline and delay neurodegenerative diseases. The interpretation of mRNA alterations during brain aging is influenced by the health and age of the animal cohorts studied. Here, we carefully consider these factors and provide an in-depth investigation of mRNA splicing and dynamics in the aging mouse brain, combining short- and long-read sequencing technologies with extensive bioinformatic analyses. Our findings encompass a spectrum of age-related changes, including differences in isoform usage, decreased mRNA dynamics and a module showing increased expression of neuronal genes. Notably, our results indicate a reduced abundance of mRNA isoforms leading to nonsense-mediated RNA decay and suggest a regulatory role for RNA-binding proteins, indicating that their regulation may be altered leading to the reshaping of the aged brain transcriptome. Collectively, our study highlights the importance of studying mRNA splicing events during brain aging.
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Affiliation(s)
- Nisha Hemandhar Kumar
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Verena Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Emanuel Barth
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
- Bioinformatics Core Facility, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Sebastian Krautwurst
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Manja Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
- Leibniz Institute for Age Research, FLI, Beutenbergstraße 11, Jena 07743, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University, Leutragraben 1, Jena 07743, Germany
- German Center for Integrative Biodiversity Research (iDiv), Puschstraße 4, Leipzig 04103, Germany
- Michael Stifel Center Jena, Friedrich Schiller University, Ernst-Abbe-Platz 2, Jena 07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fuerstengraben 1, Jena 07743, Germany
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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Koehn LM, Steele JR, Schittenhelm RB, Turner BJ, Nicolazzo JA. Sex-Dependent Changes to the Intestinal and Hepatic Abundance of Drug Transporters and Metabolizing Enzymes in the SOD1 G93A Mouse Model of Amyotrophic Lateral Sclerosis. Mol Pharm 2024; 21:1756-1767. [PMID: 38415587 DOI: 10.1021/acs.molpharmaceut.3c01089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by death and dysfunction of motor neurons that result in a rapidly progressing loss of motor function. While there are some data on alterations at the blood-brain barrier (BBB) in ALS and their potential impact on CNS trafficking of drugs, little is reported on the impact of this disease on the expression of drug-handling proteins in the small intestine and liver. This may impact the dosing of the many medicines that individuals with ALS are prescribed. In the present study, a proteomic evaluation was performed on small intestine and liver samples from postnatal day 120 SOD1G93A mice (a model of familial ALS that harbors a human mutant form of superoxide dismutase 1) and wild-type (WT) littermates (n = 7/genotype/sex). Untargeted, quantitative proteomics was undertaken using either label-based [tandem mass tag (TMT)] or label-free [data-independent acquisition (DIA)] acquisition strategies on high-resolution mass spectrometric instrumentation. Copper chaperone for superoxide dismutase (CCS) was significantly higher in SOD1G93A samples compared to the WT samples for both sexes and tissues, therefore representing a potential biomarker for ALS in this mouse model. Relative to WT mice, male SOD1G93A mice had significantly different proteins (Padj < 0.05, |fold-change|>1.2) in the small intestine (male 22, female 1) and liver (male 140, female 3). This included an up-regulation of intestinal transporters for dietary glucose [solute carrier (SLC) SLC5A1] and cholesterol (Niemann-Pick c1-like 1), as well as for several drugs (e.g., SLC15A1), in the male SOD1G93A mice. There was both an up-regulation (e.g., SLCO2A1) and down-regulation (ammonium transporter rh type b) of transporters in the male SOD1G93A liver. In addition, there was both an up-regulation (e.g., phosphoenolpyruvate carboxykinase) and down-regulation (e.g., carboxylesterase 1) of metabolizing enzymes in the male SOD1G93A liver. This proteomic data set identified male-specific changes to key small intestinal and hepatic transporters and metabolizing enzymes that may have important implications for the bioavailability of nutrients and drugs in individuals with ALS.
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Affiliation(s)
- Liam M Koehn
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Joel R Steele
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Bradley J Turner
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, Victoria, Australia
| | - Joseph A Nicolazzo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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Lin Y, Li Y, Liang G, Yang X, Yang J, Hu Q, Sun J, Zhang C, Fang H, Liu A. Single-cell transcriptome analysis of aging mouse liver. FASEB J 2024; 38:e23473. [PMID: 38334462 DOI: 10.1096/fj.202302282r] [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: 11/05/2023] [Revised: 12/30/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Aging has a great impact on the liver, which causes a loss of physiological integrity and an increase in susceptibility to injury, but many of the underlying molecular and cellular processes remain unclear. Here, we performed a comprehensive single-cell transcriptional profiling of the liver during aging. Our data showed that aging affected the cellular composition of the liver. The increase in inflammatory cells including neutrophils and monocyte-derived macrophages, as well as in inflammatory cytokines, could indicate an inflammatory tissue microenvironment in aged livers. Moreover, aging drove a distinct transcriptional course in each cell type. The commonly significant up-regulated genes were S100a8, S100a9, and RNA-binding motif protein 3 across all cell types. Aging-related pathways such as biosynthesis, metabolism, and oxidative stress were up-regulated in aged livers. Additionally, key ligand-receptor pairs for intercellular communication, primarily linked to macrophage migration inhibitory factor, transforming growth factor-β, and complement signaling, were also elevated. Furthermore, hepatic stellate cells (HSCs) serve as the prominent hub for intrahepatic signaling. HSCs acquired an "activated" phenotype, which may be involved in the increased intrahepatic vascular tone and fibrosis with aging. Liver sinusoidal endothelial cells derived from aged livers were pseudocapillarized and procontractile, and exhibited down-regulation of genes involved in vascular development and homeostasis. Moreover, the aging-related changes in cellular composition and gene expression were reversed by caloric restriction. Collectively, the present study suggests liver aging is linked to a significant liver sinusoidal deregulation and a moderate pro-inflammatory state, providing a potential concept for understanding the mechanism of liver aging.
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Affiliation(s)
- Yan Lin
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Ying Li
- Wuhan Fourth Hospital, Wuhan, China
| | - Guangyu Liang
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Xiao Yang
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jiankun Yang
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Qi Hu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian Sun
- Department of Biliopancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cuntai Zhang
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoshu Fang
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Anding Liu
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
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Liu M, Feng J. Association between adiposity and facial aging: results from a Mendelian randomization study. Eur J Med Res 2023; 28:350. [PMID: 37715292 PMCID: PMC10503104 DOI: 10.1186/s40001-023-01236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/16/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Skin, as a sociologically meaningful interface, has psychological implications different from other organs, particularly in the context of the global population aging. Growing evidence suggests that facial aging is associated with an increased risk of adiposity. Existing research, however, were observational, and while they may find some correlations, it is difficult to simply disentangle non-causal or reverse-causal links because these associations may be confounded or fail to accurately reflect true causative linkages. OBJECTIVES We conducted a 2-sample Mendelian randomization (MR) study to examine the potential effect of facial aging on the risk of broad obesity and its three major adiposity indicators, including body mass index (BMI), body fat percentage (BF%) and waist circumference (WC). METHODS Genetic instruments from IEU OpenGWAS project, one of the largest available genome-wide association studies (GWAS) for facial aging (423,999 samples) were used to investigate the relation to broad obesity (32,858 cases, 65,839 controls). Using the inverse-variance weighted (IVW) technique, single nucleotide polymorphisms (SNPs) associated with adiposity indicators (BMI (461,460 samples), BF% (454,633 samples), and WC (462,166 samples)) were investigated in relationship to facial aging. Further sensitivity analyses were performed, including Mendelian randomization-Egger (MR-Egger), weighted median estimates, and leave-one-out analysis, to evaluate the consistency of the results and related potential issues in MR studies. RESULTS We identified strong and significant correlations between adiposity and facial aging in the 17 broad obesity-associated SNPs (IVW estimate of odds ratio OR = 1.020, 95% CI 1.010-1.029, P = 7.303e - 05), 458 BMI-associated SNPs (IVW estimate of odds ratio OR = 1.047, 95% CI 1.0357-1.058, P = 1.154e - 16),for the 395 BF%-associated SNPs (OR = 1.056, 95%CI 1.040-1.072,P = 7.617e - 12), or for the 374 WC-associated SNPs (OR = 1.072, 95% CI 1057-1.087,P = 1.229e - 23). A range of complementary methodologies have been employed to evaluate horizontal pleiotropy and related potential caveats occurring in MR research. CONCLUSIONS Using Mendelian randomization as an alternative approach to investigate causality, we found a causal relationship between adiposity and facial aging, which was statistically strong and significant.
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Affiliation(s)
- Meiqi Liu
- Department of Plastic and Cosmetic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jingwei Feng
- Department of Plastic and Cosmetic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, Guangdong, People's Republic of China.
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Xie K, Ehninger D. Ageing-associated phenotypes in mice. Mech Ageing Dev 2023; 214:111852. [PMID: 37454704 DOI: 10.1016/j.mad.2023.111852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Ageing is a continuous process in life featuring progressive damage accumulation that leads to physiological decline, functional deterioration and ultimately death of an organism. Based on the relatively close anatomical and physiological similarity to humans, the mouse has been proven as a valuable model organism in ageing research over the last decades. In this review, we survey methods and tools currently in use to assess ageing phenotypes in mice. We summarize a range of ageing-associated alterations detectable at two major levels of analysis: (1) physiology and pathophysiology and (2) molecular biomarkers. Age-sensitive phenotypes provided in this article may serve to inform future studies targeting various aspects of organismal ageing in mice. In addition, we discuss conceptual and technical challenges faced by previous ageing studies in mice and, where possible, provide recommendations on how to resolve some of these issues.
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Affiliation(s)
- Kan Xie
- Translational Biogerontology Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1/99, 53127 Bonn, Germany
| | - Dan Ehninger
- Translational Biogerontology Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1/99, 53127 Bonn, Germany.
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陈 梓, 李 胜, 张 祐, 杨 婉, 王 婷. [Lipocalin 2 induces self-limited inhibition of osteoblast differentiation of mesenchymal stem cells]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:1339-1344. [PMID: 37712270 PMCID: PMC10505573 DOI: 10.12122/j.issn.1673-4254.2023.08.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Indexed: 09/16/2023]
Abstract
OBJECTIVE To explore the role of lipocalin 2 (Lcn2) in bone development and senile osteoporosis. METHODS Chromatin immunoprecipitation with H3K27AC and H3K9Me3 antibodies coupled with massively parallel sequencing (ChIP-Seq) was performed to analyze the changes in binding of modified histones at the Lcn2 gene locus in C3H10T1/2 mesenchymal stem cells (MSCs) induced with osteogenic induction medium for 3 days. ITRAQ-MS/MS and ELISA were used to compare Lcn2 protein expressions in the cancellous bone and the serum between 16- and 3-month-old male mice. The effect of treatment with recombinant Lcn2 protein on osteogenic differentiation of C3H10T1/2 cells was evaluated by detecting changes in ALP expression, and Western blotting was performed to examine the changes in OSX and OCN expression. RESULTS The expression of Lcn2 protein in the cancellous bone and its serum levels were significantly higher in 16-month-old than in 3-month-old male mice (P < 0.01). In C3H10T1/2 cells, ALP expression level decreased significantly after treatment with recombinant Lcn2 protein (P < 0.05) accompanied by lowered protein expressions of OSX and OCN (P < 0.05). Analysis with ROSE software revealed a super enhancer in the Lcn2 gene region of C3H10T1/2 cells after osteogenesis induction. RNA-seq results confirmed that Lcn2 was among the top 4 up-regulated genes in C3H10T1/2 cells following osteogenic induction, and a super enhancer was also detected in Zbtb16 gene, which showed the highest up- regulation after osteogenic induction. Real- time quantitative PCR further confirmed that the mRNA level of Lcn2 increased sharply in C3H10T1/2 cells after osteogenic induction (P < 0.001). CONCLUSION Lcn2 is essential for normal osteogenic differentiation of MSCs, but its overexpression and excessive secretion in aging induce self-limited inhibition of osteogenic differentiation of MSCs.
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Affiliation(s)
- 梓锋 陈
- 广州市番禺区中心医院创伤骨科,广东 广州 511400Department of Orthopedics, Panyu Central Hospital, Guangzhou 511400, China
- 南方医科大学基础医学院细胞生物学,广东 广州 510515Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - 胜发 李
- 南方医科大学珠江医院临床研究中心,广东 广州 510260Department of Clinical Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou 510260, China
| | - 祐鸣 张
- 南方医科大学基础医学院细胞生物学,广东 广州 510515Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - 婉雯 杨
- 南方医科大学基础医学院细胞生物学,广东 广州 510515Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - 婷 王
- 南方医科大学基础医学院细胞生物学,广东 广州 510515Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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Zheng XQ, Lin JL, Huang J, Wu T, Song CL. Targeting aging with the healthy skeletal system: The endocrine role of bone. Rev Endocr Metab Disord 2023; 24:695-711. [PMID: 37402956 DOI: 10.1007/s11154-023-09812-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2023] [Indexed: 07/06/2023]
Abstract
Aging is an inevitable biological process, and longevity may be related to bone health. Maintaining strong bone health can extend one's lifespan, but the exact mechanism is unclear. Bone and extraosseous organs, including the heart and brain, have complex and precise communication mechanisms. In addition to its load bearing capacity, the skeletal system secretes cytokines, which play a role in bone regulation of extraosseous organs. FGF23, OCN, and LCN2 are three representative bone-derived cytokines involved in energy metabolism, endocrine homeostasis and systemic chronic inflammation levels. Today, advanced research methods provide new understandings of bone as a crucial endocrine organ. For example, gene editing technology enables bone-specific conditional gene knockout models, which allows the study of bone-derived cytokines to be more precise. We systematically evaluated the various effects of bone-derived cytokines on extraosseous organs and their possible antiaging mechanism. Targeting aging with the current knowledge of the healthy skeletal system is a potential therapeutic strategy. Therefore, we present a comprehensive review that summarizes the current knowledge and provides insights for futures studies.
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Affiliation(s)
- Xuan-Qi Zheng
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
| | - Jia-Liang Lin
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
| | - Jie Huang
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
| | - Tong Wu
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
| | - Chun-Li Song
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China.
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China.
- Engineering Research Center of Bone and Joint Precision Medicine, Beijing, China.
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Yu X, Wang Y, Song Y, Gao X, Deng H. AP-1 is a regulatory transcription factor of inflammaging in the murine kidney and liver. Aging Cell 2023; 22:e13858. [PMID: 37154113 PMCID: PMC10352569 DOI: 10.1111/acel.13858] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/07/2023] [Indexed: 05/10/2023] Open
Abstract
Aging is characterized by chronic low-grade inflammation in multiple tissues, also termed "inflammaging", which represents a significant risk factor for many aging-related chronic diseases. However, the mechanisms and regulatory networks underlying inflammaging across different tissues have not yet been fully elucidated. Here, we profiled the transcriptomes and epigenomes of the kidney and liver from young and aged mice and found that activation of the inflammatory response is a conserved signature in both tissues. Moreover, we revealed links between transcriptome changes and chromatin dynamics through integrative analysis and identified AP-1 and ETS family transcription factors (TFs) as potential regulators of inflammaging. Further in situ validation showed that c-JUN (a member of the AP-1 family) was mainly activated in aged renal and hepatic cells, while increased SPI1 (a member of the ETS family) was mostly induced by elevated infiltration of macrophages, indicating that these TFs have different mechanisms in inflammaging. Functional data demonstrated that genetic knockdown of Fos, a major member of the AP-1 family, significantly attenuated the inflammatory response in aged kidneys and livers. Taken together, our results revealed conserved signatures and regulatory TFs of inflammaging in the kidney and liver, providing novel targets for the development of anti-aging interventions.
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Affiliation(s)
- Xiaojie Yu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Yuting Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Yifan Song
- The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Xianda Gao
- School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijingChina
| | - Hongkui Deng
- The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
- School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijingChina
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10
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Porukala M, Vinod PK. Network-level analysis of ageing and its relationship with diseases and tissue regeneration in the mouse liver. Sci Rep 2023; 13:4632. [PMID: 36944690 PMCID: PMC10030664 DOI: 10.1038/s41598-023-31315-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
The liver plays a vital role in maintaining whole-body metabolic homeostasis, compound detoxification and has the unique ability to regenerate itself post-injury. Ageing leads to functional impairment of the liver and predisposes the liver to non-alcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC). Mapping the molecular changes of the liver with ageing may help to understand the crosstalk of ageing with different liver diseases. A systems-level analysis of the ageing-induced liver changes and its crosstalk with liver-associated conditions is lacking. In the present study, we performed network-level analyses of the ageing liver using mouse transcriptomic data and a protein-protein interaction (PPI) network. A sample-wise analysis using network entropy measure was performed, which showed an increasing trend with ageing and helped to identify ageing genes based on local entropy changes. To gain further insights, we also integrated the differentially expressed genes (DEGs) between young and different age groups with the PPI network and identified core modules and nodes associated with ageing. Finally, we computed the network proximity of the ageing network with different networks of liver diseases and regeneration to quantify the effect of ageing. Our analysis revealed the complex interplay of immune, cancer signalling, and metabolic genes in the ageing liver. We found significant network proximities between ageing and NAFLD, HCC, liver damage conditions, and the early phase of liver regeneration with common nodes including NLRP12, TRP53, GSK3B, CTNNB1, MAT1 and FASN. Overall, our study maps the network-level changes of ageing and their interconnections with the physiology and pathology of the liver.
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Affiliation(s)
- Manisri Porukala
- Centre for Computational Natural Sciences and Bioinformatics, IIIT, Hyderabad, 500032, India
| | - P K Vinod
- Centre for Computational Natural Sciences and Bioinformatics, IIIT, Hyderabad, 500032, India.
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Salnikov L, Goldberg S, Rijhwani H, Shi Y, Pinsky E. The RNA-Seq data analysis shows how the ontogenesis defines aging. FRONTIERS IN AGING 2023; 4:1143334. [PMID: 36999000 PMCID: PMC10046809 DOI: 10.3389/fragi.2023.1143334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/03/2023] [Indexed: 03/15/2023]
Abstract
This paper presents a global statistical analysis of the RNA-Seq results of the entire Mus musculus genome. We explain aging by a gradual redistribution of limited resources between two major tasks of the organism: its self-sustenance based on the function of the housekeeping gene group (HG) and functional differentiation provided by the integrative gene group (IntG). All known disorders associated with aging are the result of a deficiency in the repair processes provided by the cellular infrastructure. Understanding exactly how this deficiency arises is our primary goal. Analysis of RNA production data of 35,630 genes, from which 5,101 were identified as HG genes, showed that RNA production levels in the HG and IntG genes had statistically significant differences (p-value <0.0001) throughout the entire observation period. In the reproductive period of life, which has the lowest actual mortality risk for Mus musculus, changes in the age dynamics of RNA production occur. The statistically significant dynamics of the decrease of RNA production in the HG group in contrast to the IntG group was determined (p-value = 0.0045). The trend toward significant shift in the HG/IntG ratio occurs after the end of the reproductive period, coinciding with the beginning of the mortality rate increase in Mus musculus indirectly supports our hypothesis. The results demonstrate a different orientation of the impact of ontogenesis regulatory mechanisms on the groups of genes representing cell infrastructures and their organismal functions, making the chosen direction promising for further research and understanding the mechanisms of aging.
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Affiliation(s)
- Lev Salnikov
- AntiCA Biomed, San Diego, CA, United States
- *Correspondence: Lev Salnikov,
| | - Saveli Goldberg
- Department of Radiation Oncology, Mass General Hospital, Boston, MA, United Kingdom
| | - Heena Rijhwani
- Department of Computer Science, Met College, Boston University, Boston, MA, United Kingdom
| | - Yuran Shi
- Department of Computer Science, Brandeis University, Waltham, MA, United Kingdom
| | - Eugene Pinsky
- Department of Computer Science, Met College, Boston University, Boston, MA, United Kingdom
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12
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Alonso-Alvarez C, Andrade P, Cantarero A, Morales J, Carneiro M. Relocation to avoid costs: A hypothesis on red carotenoid-based signals based on recent CYP2J19 gene expression data. Bioessays 2022; 44:e2200037. [PMID: 36209392 DOI: 10.1002/bies.202200037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/25/2022] [Accepted: 09/22/2022] [Indexed: 11/11/2022]
Abstract
In many vertebrates, the enzymatic oxidation of dietary yellow carotenoids generates red keto-carotenoids giving color to ornaments. The oxidase CYP2J19 is here a key effector. Its purported intracellular location suggests a shared biochemical pathway between trait expression and cell functioning. This might guarantee the reliability of red colorations as individual quality signals independent of production costs. We hypothesize that the ornament type (feathers vs. bare parts) and production costs (probably CYP2J19 activity compromising vital functions) could have promoted tissue-specific gene relocation. We review current avian tissue-specific CYP2J19 expression data. Among the ten red-billed species showing CYP2J19 bill expression, only one showed strong hepatic expression. Moreover, a phylogenetically-controlled analysis of 25 red-colored species shows that those producing red bare parts are less likely to have strong hepatic CYP2J19 expression than species with only red plumages. Thus, both production costs and shared pathways might have contributed to the evolution of red signals.
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Affiliation(s)
- Carlos Alonso-Alvarez
- Department of Evolutionary Ecology, National Museum of Natural Sciences - CSIC. C/ José Gutiérrez Abascal 2, Madrid, Spain
| | - Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Alejandro Cantarero
- Department of Evolutionary Ecology, National Museum of Natural Sciences - CSIC. C/ José Gutiérrez Abascal 2, Madrid, Spain.,Department of Physiology, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Judith Morales
- Department of Evolutionary Ecology, National Museum of Natural Sciences - CSIC. C/ José Gutiérrez Abascal 2, Madrid, Spain
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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13
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Liu JF, Wu Y, Yang YH, Wu SF, Liu S, Xu P, Yang JT. Phosphoproteome profiling of mouse liver during normal aging. Proteome Sci 2022; 20:12. [PMID: 35932011 PMCID: PMC9354360 DOI: 10.1186/s12953-022-00194-2] [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: 10/19/2021] [Accepted: 07/24/2022] [Indexed: 08/30/2023] Open
Abstract
Background Aging is a complex biological process accompanied by a time-dependent functional decline that affects most living organisms. Omics studies help to comprehensively understand the mechanism of aging and discover potential intervention methods. Old mice are frequently obese with a fatty liver. Methods We applied mass spectrometry-based phosphoproteomics to obtain a global phosphorylation profile of the liver in mice aged 2 or 18 months. MaxQuant was used for quantitative analysis and PCA was used for unsupervised clustering. Results Through phosphoproteome analysis, a total of 5,685 phosphosites in 2,335 proteins were filtered for quantitative analysis. PCA analysis of both the phosphoproteome and transcriptome data could distinguish young and old mice. However, from kinase prediction, kinase-substrate interaction analysis, and KEGG functional enrichment analysis done with phosphoproteome data, we observed high phosphorylation of fatty acid biosynthesis, β-oxidation, and potential secretory processes, together with low phosphorylation of the Egfr-Sos1-Araf/Braf-Map2k1-Mapk1 pathway and Ctnnb1 during aging. Proteins with differentially expressed phosphosites seemed more directly related to the aging-associated fatty liver phenotype than the differentially expressed transcripts. The phosphoproteome may reveal distinctive biological functions that are lost in the transcriptome. Conclusions In summary, we constructed a phosphorylation-associated network in the mouse liver during normal aging, which may help to discover novel antiaging strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-022-00194-2. The first phosphoproteome profiling of mouse livers during normal aging. A total of 5,685 phosphosites in 2,335 proteins were quantified in this study. A phosphorylation-regulated pathway network was constructed. Metabolism, secretion, and the cell cycle might be dysregulated during normal aging.
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Affiliation(s)
- Jiang-Feng Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yue Wu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,School of Statistics and Data Science, Nankai University, Tianjin, 300071, China
| | - Ye-Hong Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Song-Feng Wu
- State Key Laboratory of ProteomicsResearch Unit of Proteomics & ResearchDevelopment of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Shu Liu
- State Key Laboratory of ProteomicsResearch Unit of Proteomics & ResearchDevelopment of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Ping Xu
- State Key Laboratory of ProteomicsResearch Unit of Proteomics & ResearchDevelopment of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China.
| | - Jun-Tao Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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14
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Savina A, Jaffredo T, Saldmann F, Faulkes CG, Moguelet P, Leroy C, Marmol DD, Codogno P, Foucher L, Zalc A, Viltard M, Friedlander G, Aractingi S, Fontaine RH. Single-cell transcriptomics reveals age-resistant maintenance of cell identities, stem cell compartments and differentiation trajectories in long-lived naked mole-rats skin. Aging (Albany NY) 2022; 14:3728-3756. [PMID: 35507806 PMCID: PMC9134947 DOI: 10.18632/aging.204054] [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: 12/01/2021] [Accepted: 04/25/2022] [Indexed: 11/25/2022]
Abstract
Naked mole-rats (NMR) are subterranean rodents characterized by an unusual longevity coupled with an unexplained resistance to aging. In the present study, we performed extensive in situ analysis and single-cell RNA-sequencing comparing young and older animals. At variance with other species, NMR exhibited a striking stability of skin compartments and cell types, which remained stable over time without aging-associated changes. Remarkably, the number of stem cells was constant throughout aging. We found three classical cellular states defining a unique keratinocyte differentiation trajectory that were not altered after pseudo-temporal reconstruction. Epidermal gene expression did not change with aging either. Langerhans cell clusters were conserved, and only a higher basal stem cell expression of Igfbp3 was found in aged animals. In accordance, NMR skin healing closure was similar in young and older animals. Altogether, these results indicate that NMR skin is characterized by peculiar genetic and cellular features, different from those previously demonstrated for mice and humans. The remarkable stability of the aging NMR skin transcriptome likely reflects unaltered homeostasis and resilience.
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Affiliation(s)
| | - Thierry Jaffredo
- Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, INSERM, Paris, France
| | | | - Chris G Faulkes
- Queen Mary University of London, School of Biological and Chemical Sciences, London, United Kingdom
| | - Philippe Moguelet
- Service d'Anatomie et Cytologie Pathologiques, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Christine Leroy
- Université Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, Paris, France
| | | | - Patrice Codogno
- Université Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, Paris, France
| | - Lucy Foucher
- Ecole Nationale Vétérinaire d'Alfort, Centre de Recherche Biomédicale, Maisons-Alfort, France
| | - Antoine Zalc
- Université Paris Cité, CNRS, INSERM, Institut Cochin, Paris, France
| | - Mélanie Viltard
- Fondation pour la Recherche en Physiologie, Brussels, Belgium
| | - Gérard Friedlander
- Université Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, Paris, France
| | - Selim Aractingi
- Université Paris Cité, CNRS, INSERM, Institut Cochin, Paris, France.,Service de Dermatologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, France
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15
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Somers HM, Fuqua JH, Bonnet FX, Rollins JA. Quantification of tissue-specific protein translation in whole C. elegans using O-propargyl-puromycin labeling and fluorescence microscopy. CELL REPORTS METHODS 2022; 2:100203. [PMID: 35497499 PMCID: PMC9046455 DOI: 10.1016/j.crmeth.2022.100203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/01/2021] [Accepted: 03/29/2022] [Indexed: 01/23/2023]
Abstract
The regulation of gene expression via protein translation is critical for growth, development, and stress response. While puromycin-based techniques have been used to quantify protein translation in C. elegans, they have been limited to using lysate from whole worms. To achieve tissue-specific quantification of ribosome activity in intact C. elegans, we report the application of O-propargyl-puromycin in a cuticle defective mutant followed by conjugation of an azide fluorophore for detection using fluorescent confocal microscopy. We apply this technique to quantify translation in response to heat shock, cycloheximide, or knockdown of translation factors. Furthermore, we demonstrate that O-propargyl-puromycin can be used to quantify translation between tissues or within a tissue like the germline. This technique is expected to have a broad range of applications in determining how protein translation is altered in different tissues in response to stress or gene knockdowns or with age.
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Affiliation(s)
- Hannah M. Somers
- Mount Desert Island Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME 04609, USA
| | - Jeremy H. Fuqua
- Mount Desert Island Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME 04609, USA
| | - Frédéric X.A. Bonnet
- Mount Desert Island Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME 04609, USA
| | - Jarod A. Rollins
- Mount Desert Island Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME 04609, USA
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16
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Wang MD, Tian J, Zhang JH, Zhao SY, Song MJ, Wang ZX. Human Galectin-7 Gene LGALS7 Promoter Sequence Polymorphisms and Risk of Spontaneous Intracerebral Hemorrhage: A Prospective Study. Front Mol Neurosci 2022; 15:840340. [PMID: 35401111 PMCID: PMC8984465 DOI: 10.3389/fnmol.2022.840340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background and purposeDespite evidence for the role of genetic factors in stroke, only a small proportion of strokes have been clearly attributed to monogenic factors, due to phenotypic heterogeneity. The goal of this study was to determine whether a significant relationship exists between human galectin-7 gene LGALS7 promoter region polymorphisms and the risk of stroke due to non-traumatic intracerebral hemorrhage (ICH).MethodsThis two-stage genetic association study included an initial exploratory stage followed by a discovery stage. During the exploratory stage, transgenic galectin-7 mice or transgenic mice with the scrambled sequence of the hairpin structure –silenced down gene LGALS7—were generated and then expressed differentially expressed proteins and galectin-7-interacting proteins were identified through proteomic analysis. During the discovery stage, a single-nucleotide polymorphism (SNP) genotyping approach was used to determine associations between 2 LGALS7 SNPs and ICH stroke risk for a cohort of 24 patients with stroke of the Chinese Han population and 70 controls.ResultsDuring the exploratory phase, LGALS7 expression was found to be decreased in TGLGALS–DOWN mice as compared to its expression in TGLGALS mice. During the discovery phase, analysis of LGALS7 sequences of 24 non-traumatic ICH cases and 70 controls led to the identification of 2 ICH susceptibility loci: a genomic region on 19q13.2 containing two LGALS7 SNPs, rs567785577 and rs138945880, whereby the A allele of rs567785577 and the T allele of rs138945880 were associated with greater risk of contracting ICH [for T and A vs. C and G, unadjusted odds ratio (OR) = 13.5; 95% CI = 2.249–146.5; p = 0.002]. This is the first study to genotype the galectin-7 promoter in patients with hemorrhagic stroke. Genotype and allele association tests and preliminary analysis of patients with stroke revealed that a single locus may be a genetic risk factor for hemorrhagic stroke.ConclusionA and T alleles of two novel SNP loci of 19q13.2, rs567785577 and rs138945880, respectively, were evaluated for associations with susceptibility to ICH. Further studies with expanded case numbers that include subjects of other ethnic populations are needed to elucidate mechanisms underlying associations between these SNPs and ICH risk.
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Affiliation(s)
- Ming-Dong Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jing Tian
- Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, China National Clinical Research Center of Respiratory Disease, Beijing, China
| | - John H. Zhang
- Physiology Program, Department of Anesthesiology, Neurosurgery, Neurology, and Physiology, Center for Neuroscience Research, Loma Linda University School of Medicine, Loma Linda, CA, United States
| | - Shun-Ying Zhao
- Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, China National Clinical Research Center of Respiratory Disease, Beijing, China
- *Correspondence: Shun-Ying Zhao,
| | - Ming-Jing Song
- Medical School, Huanghe Science and Technology University, Zhengzhou, China
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
- Ming-Jing Song,
| | - Zhan-Xiang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Zhan-Xiang Wang,
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17
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Barth E, Srivastava A, Wengerodt D, Stojiljkovic M, Axer H, Witte OW, Kretz A, Marz M. Age-dependent expression changes of circadian system-related genes reveal a potentially conserved link to aging. Aging (Albany NY) 2021; 13:25694-25716. [PMID: 34923482 PMCID: PMC8751596 DOI: 10.18632/aging.203788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022]
Abstract
The circadian clock system influences the biology of life by establishing circadian rhythms in organisms, tissues, and cells, thus regulating essential biological processes based on the day/night cycle. Circadian rhythms change over a lifetime due to maturation and aging, and disturbances in the control of the circadian system are associated with several age-related pathologies. However, the impact of chronobiology and the circadian system on healthy organ and tissue aging remains largely unknown. Whether aging-related changes of the circadian system’s regulation follow a conserved pattern across different species and tissues, hence representing a common driving force of aging, is unclear. Based on a cross-sectional transcriptome analysis covering 329 RNA-Seq libraries, we provide indications that the circadian system is subjected to aging-related gene alterations shared between evolutionarily distinct species, such as Homo sapiens, Mus musculus, Danio rerio, and Nothobranchius furzeri. We discovered differentially expressed genes by comparing tissue-specific transcriptional profiles of mature, aged, and old-age individuals and report on six genes (per2, dec2, cirp, klf10, nfil3, and dbp) of the circadian system, which show conserved aging-related expression patterns in four organs of the species examined. Our results illustrate how the circadian system and aging might influence each other in various tissues over a long lifespan and conceptually complement previous studies tracking short-term diurnal and nocturnal gene expression oscillations.
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Affiliation(s)
- Emanuel Barth
- Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - Akash Srivastava
- Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.,FLI Leibniz Institute for Age Research, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Diane Wengerodt
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Milan Stojiljkovic
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Hubertus Axer
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Otto W Witte
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Alexandra Kretz
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Manja Marz
- Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.,FLI Leibniz Institute for Age Research, Jena, Germany.,German Center for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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18
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Uraguchi K, Maeda Y, Takahara J, Omichi R, Fujimoto S, Kariya S, Nishizaki K, Ando M. Upregulation of a nuclear factor-kappa B-interacting immune gene network in mice cochleae with age-related hearing loss. PLoS One 2021; 16:e0258977. [PMID: 34679122 PMCID: PMC8535356 DOI: 10.1371/journal.pone.0258977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/09/2021] [Indexed: 12/15/2022] Open
Abstract
Epidemiological data suggest that inflammation and innate immunity play significant roles in the pathogenesis of age-related hearing loss (ARHL) in humans. In this mouse study, real-time RT-PCR array targeting 84 immune-related genes revealed that the expressions of 40 genes (47.6%) were differentially regulated with greater than a twofold change in 12-month-old cochleae with ARHL relative to young control mice, 33 (39.3%) of which were upregulated. These differentially regulated genes (DEGs) were involved in functional pathways for cytokine–cytokine receptor interaction, chemokine signaling, TNF signaling, and Toll-like receptor signaling. An NF-κB subunit, Nfkb1, was upregulated in aged cochleae, and bioinformatic analyses predicted that NF-κB would interact with the genomic regulatory regions of eight upregulated DEGs, including Tnf and Ptgs2. In aging cochleae, major proinflammatory molecules, IL1B and IL18rap, were upregulated by 6 months of age and thereafter. Remarkable upregulations of seven immune-related genes (Casp1, IL18r1, IL1B, Card9, Clec4e, Ifit1, and Tlr9) occurred at an advanced stage (between 9 and 12 months of age) of ARHL. Immunohistochemistry analysis of cochlear sections from the 12-month-old mice indicated that IL-18r1 and IL-1B were localized to the spiral ligament, spiral limbus, and organ of Corti. The two NF-κB-interacting inflammatory molecules, TNFα and PTGS2, immunolocalized ubiquitously in cochlear structures, including the lateral wall (the stria vascularis and spiral ligament), in the histological sections of aged cochleae. IBA1-positive macrophages were observed in the stria vascularis and spiral ligament in aged mice. Therefore, inflammatory and immune reactions are modulated in aged cochlear tissues with ARHL.
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Affiliation(s)
- Kensuke Uraguchi
- Department of Otolaryngology- Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yukihide Maeda
- Department of Otolaryngology- Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- * E-mail:
| | - Junko Takahara
- Department of Otolaryngology- Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Ryotaro Omichi
- Department of Otolaryngology- Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Shohei Fujimoto
- Department of Otolaryngology- Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Shin Kariya
- Department of Otolaryngology- Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kazunori Nishizaki
- Department of Otolaryngology- Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Mizuo Ando
- Department of Otolaryngology- Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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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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20
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Harper JM, Holmes DJ. New Perspectives on Avian Models for Studies of Basic Aging Processes. Biomedicines 2021; 9:biomedicines9060649. [PMID: 34200297 PMCID: PMC8230007 DOI: 10.3390/biomedicines9060649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/18/2022] Open
Abstract
Avian models have the potential to elucidate basic cellular and molecular mechanisms underlying the slow aging rates and exceptional longevity typical of this group of vertebrates. To date, most studies of avian aging have focused on relatively few of the phenomena now thought to be intrinsic to the aging process, but primarily on responses to oxidative stress and telomere dynamics. But a variety of whole-animal and cell-based approaches to avian aging and stress resistance have been developed-especially the use of primary cell lines and isolated erythrocytes-which permit other processes to be investigated. In this review, we highlight newer studies using these approaches. We also discuss recent research on age-related changes in neural function in birds in the context of sensory changes relevant to homing and navigation, as well as the maintenance of song. More recently, with the advent of "-omic" methodologies, including whole-genome studies, new approaches have gained momentum for investigating the mechanistic basis of aging in birds. Overall, current research suggests that birds exhibit an enhanced resistance to the detrimental effects of oxidative damage and maintain higher than expected levels of cellular function as they age. There is also evidence that genetic signatures associated with cellular defenses, as well as metabolic and immune function, are enhanced in birds but data are still lacking relative to that available from more conventional model organisms. We are optimistic that continued development of avian models in geroscience, especially under controlled laboratory conditions, will provide novel insights into the exceptional longevity of this animal taxon.
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Affiliation(s)
- James M. Harper
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77341, USA
- Correspondence: ; Tel.: +1-936-294-1543
| | - Donna J. Holmes
- Department of Biological Sciences and WWAMI Medical Education Program, University of Idaho, Moscow, ID 83844, USA;
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