1
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Ding Q, Yang W, Xue G, Liu H, Cai Y, Que J, Jin X, Luo M, Pang F, Yang Y, Lin Y, Liu Y, Sun H, Tan R, Wang P, Xu Z, Jiang Q. Dimension reduction, cell clustering, and cell-cell communication inference for single-cell transcriptomics with DcjComm. Genome Biol 2024; 25:241. [PMID: 39252099 PMCID: PMC11382422 DOI: 10.1186/s13059-024-03385-6] [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: 01/09/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024] Open
Abstract
Advances in single-cell transcriptomics provide an unprecedented opportunity to explore complex biological processes. However, computational methods for analyzing single-cell transcriptomics still have room for improvement especially in dimension reduction, cell clustering, and cell-cell communication inference. Herein, we propose a versatile method, named DcjComm, for comprehensive analysis of single-cell transcriptomics. DcjComm detects functional modules to explore expression patterns and performs dimension reduction and clustering to discover cellular identities by the non-negative matrix factorization-based joint learning model. DcjComm then infers cell-cell communication by integrating ligand-receptor pairs, transcription factors, and target genes. DcjComm demonstrates superior performance compared to state-of-the-art methods.
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Affiliation(s)
- Qian Ding
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Wenyi Yang
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Guangfu Xue
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Hongxin Liu
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Yideng Cai
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Jinhao Que
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Xiyun Jin
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Meng Luo
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Fenglan Pang
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Yuexin Yang
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Yi Lin
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Yusong Liu
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Haoxiu Sun
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Renjie Tan
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Pingping Wang
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
| | - Zhaochun Xu
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
| | - Qinghua Jiang
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Harbin Medical University, Harbin, 150076, China.
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2
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Scanlan RL, Pease L, O'Keefe H, Martinez-Guimera A, Rasmussen L, Wordsworth J, Shanley D. Systematic transcriptomic analysis and temporal modelling of human fibroblast senescence. FRONTIERS IN AGING 2024; 5:1448543. [PMID: 39267611 PMCID: PMC11390594 DOI: 10.3389/fragi.2024.1448543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/19/2024] [Indexed: 09/15/2024]
Abstract
Cellular senescence is a diverse phenotype characterised by permanent cell cycle arrest and an associated secretory phenotype (SASP) which includes inflammatory cytokines. Typically, senescent cells are removed by the immune system, but this process becomes dysregulated with age causing senescent cells to accumulate and induce chronic inflammatory signalling. Identifying senescent cells is challenging due to senescence phenotype heterogeneity, and senotherapy often requires a combinatorial approach. Here we systematically collected 119 transcriptomic datasets related to human fibroblasts, forming an online database describing the relevant variables for each study allowing users to filter for variables and genes of interest. Our own analysis of the database identified 28 genes significantly up- or downregulated across four senescence types (DNA damage induced senescence (DDIS), oncogene induced senescence (OIS), replicative senescence, and bystander induced senescence) compared to proliferating controls. We also found gene expression patterns of conventional senescence markers were highly specific and reliable for different senescence inducers, cell lines, and timepoints. Our comprehensive data supported several observations made in existing studies using single datasets, including stronger p53 signalling in DDIS compared to OIS. However, contrary to some early observations, both p16 and p21 mRNA levels rise quickly, depending on senescence type, and persist for at least 8-11 days. Additionally, little evidence was found to support an initial TGFβ-centric SASP. To support our transcriptomic analysis, we computationally modelled temporal protein changes of select core senescence proteins during DDIS and OIS, as well as perform knockdown interventions. We conclude that while universal biomarkers of senescence are difficult to identify, conventional senescence markers follow predictable profiles and construction of a framework for studying senescence could lead to more reproducible data and understanding of senescence heterogeneity.
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Affiliation(s)
- R-L Scanlan
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - L Pease
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - H O'Keefe
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - A Martinez-Guimera
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - L Rasmussen
- Center for Healthy Aging, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - J Wordsworth
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - D Shanley
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
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3
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Mahmud S, Pitcher LE, Torbenson E, Robbins PD, Zhang L, Dong X. Developing transcriptomic signatures as a biomarker of cellular senescence. Ageing Res Rev 2024; 99:102403. [PMID: 38964507 PMCID: PMC11338099 DOI: 10.1016/j.arr.2024.102403] [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: 12/18/2023] [Revised: 06/07/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Cellular senescence is a cell fate driven by different types of stress, where damaged cells exit from the cell cycle and, in many cases, develop an inflammatory senescence-associated secretory phenotype (SASP). Senescence has often been linked to driving aging and the onset of multiple diseases conferred by the harmful SASP, which disrupts tissue homeostasis and impairs the regular function of many tissues. This phenomenon was first observed in vitro when fibroblasts halted replication after approximately 50 population doublings. In addition to replication-induced senescence, factors such as DNA damage and oncogene activation can induce cellular senescence both in culture and in vivo. Despite their contribution to aging and disease, identifying senescent cells in vivo has been challenging due to their heterogeneity. Although senescent cells can express the cell cycle inhibitors p16Ink4a and/or p21Cip1 and exhibit SA-ß-gal activity and evidence of a DNA damage response, there is no universal biomarker for these cells, regardless of inducer or cell type. Recent studies have analyzed the transcriptomic characteristics of these cells, leading to the identification of signature gene sets like CellAge, SeneQuest, and SenMayo. Advancements in single-cell and spatial RNA sequencing now allow for analyzing senescent cell heterogeneity within the same tissue and the development of machine learning algorithms, e.g., SenPred, SenSig, and SenCID, to discover cellular senescence using RNA sequencing data. Such insights not only deepen our understanding of the genetic pathways driving cellular senescence, but also promote the development of its quantifiable biomarkers. This review summarizes the current knowledge of transcriptomic signatures of cellular senescence and their potential as in vivo biomarkers.
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Affiliation(s)
- Shamsed Mahmud
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Louise E Pitcher
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Elijah Torbenson
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Paul D Robbins
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Lei Zhang
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, 420 Washington Avenue SE, Minneapolis, MN 55455, USA.
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4
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Varghese N, Grimm A, Cader MZ, Eckert A. From Young to Old: Mimicking Neuronal Aging in Directly Converted Neurons from Young Donors. Cells 2024; 13:1260. [PMID: 39120291 PMCID: PMC11311457 DOI: 10.3390/cells13151260] [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: 06/27/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
A substantial challenge in human brain aging is to find a suitable model to mimic neuronal aging in vitro as accurately as possible. Using directly converted neurons (iNs) from human fibroblasts is considered a promising tool in human aging since it retains the aging-associated mitochondrial donor signature. Still, using iNs from aged donors can pose certain restrictions due to their lower reprogramming and conversion efficacy than those from younger individuals. To overcome these limitations, our study aimed to establish an in vitro neuronal aging model mirroring features of in vivo aging by acute exposure on young iNs to either human stress hormone cortisol or the mitochondrial stressor rotenone, considering stress as a trigger of in vivo aging. The impact of rotenone was evident in mitochondrial bioenergetic properties by showing aging-associated deficits in mitochondrial respiration, cellular ATP, and MMP and a rise in glycolysis, mitochondrial superoxide, and mitochondrial ROS; meanwhile, cortisol only partially induced an aging-associated mitochondrial dysfunction. To replicate the in vivo aging-associated mitochondrial dysfunctions, using rotenone, a mitochondrial complex I inhibitor, proved to be superior to the cortisol model. This work is the first to use stress on young iNs to recreate aging-related mitochondrial impairments.
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Affiliation(s)
- Nimmy Varghese
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, 4002 Basel, Switzerland; (N.V.); (A.G.)
- Neurobiology Lab for Brain Aging and Mental Health, University Psychiatric Clinics Basel, 4002 Basel, Switzerland
| | - Amandine Grimm
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, 4002 Basel, Switzerland; (N.V.); (A.G.)
- Neurobiology Lab for Brain Aging and Mental Health, University Psychiatric Clinics Basel, 4002 Basel, Switzerland
- Department of Biomedicine, University of Basel, 4055 Basel, Switzerland
| | - M. Zameel Cader
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DS, UK;
| | - Anne Eckert
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, 4002 Basel, Switzerland; (N.V.); (A.G.)
- Neurobiology Lab for Brain Aging and Mental Health, University Psychiatric Clinics Basel, 4002 Basel, Switzerland
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5
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Tao W, Yu Z, Han JDJ. Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators. Cell Metab 2024; 36:1126-1143.e5. [PMID: 38604170 DOI: 10.1016/j.cmet.2024.03.009] [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] [Received: 08/18/2023] [Revised: 12/15/2023] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Cellular senescence underlies many aging-related pathologies, but its heterogeneity poses challenges for studying and targeting senescent cells. We present here a machine learning program senescent cell identification (SenCID), which accurately identifies senescent cells in both bulk and single-cell transcriptome. Trained on 602 samples from 52 senescence transcriptome datasets spanning 30 cell types, SenCID identifies six major senescence identities (SIDs). Different SIDs exhibit different senescence baselines, stemness, gene functions, and responses to senolytics. SenCID enables the reconstruction of senescent trajectories under normal aging, chronic diseases, and COVID-19. Additionally, when applied to single-cell Perturb-seq data, SenCID helps reveal a hierarchy of senescence modulators. Overall, SenCID is an essential tool for precise single-cell analysis of cellular senescence, enabling targeted interventions against senescent cells.
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Affiliation(s)
- Wanyu Tao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Zhengqing Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China; Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China.
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6
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Esterly AT, Zapata HJ. The quest to define senescence. Front Genet 2024; 15:1396535. [PMID: 38660674 PMCID: PMC11039885 DOI: 10.3389/fgene.2024.1396535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Affiliation(s)
| | - Heidi J. Zapata
- Department of Internal Medicine, Yale School of Medicine, Section of Infectious Diseases, New Haven, CT, United States
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7
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Huang Y, Ge MX, Li YH, Li JL, Yu Q, Xiao FH, Ao HS, Yang LQ, Li J, He Y, Kong QP. Longevity-Associated Transcription Factor ATF7 Promotes Healthspan by Suppressing Cellular Senescence and Systematic Inflammation. Aging Dis 2023:AD.2022.1217. [PMID: 37163432 PMCID: PMC10389835 DOI: 10.14336/ad.2022.1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/17/2022] [Indexed: 05/12/2023] Open
Abstract
Aging is characterized by persistent low-grade systematic inflammation, which is largely responsible for the occurrence of various age-associated diseases. We and others have previously reported that long-lived people (such as centenarians) can delay the onset of or even escape certain major age-related diseases. Here, by screening blood transcriptome and inflammatory profiles, we found that long-lived individuals had a relatively lower inflammation level (IL6, TNFα), accompanied by up-regulation of activating transcription factor 7 (ATF7). Interestingly, ATF7 expression was gradually reduced during cellular senescence. Loss of ATF7 induced cellular senescence, while overexpression delayed senescence progress and senescence-associated secretory phenotype (SASP) secretion. We showed that the anti-senescence effects of ATF7 were achieved by inhibiting nuclear factor kappa B (NF-κB) signaling and increasing histone H3K9 dimethylation (H3K9me2). In Caenorhabditis elegans, ATF7 overexpression significantly suppressed aging biomarkers and extended lifespan. Our findings suggest that ATF7 is a longevity-promoting factor that lowers cellular senescence and inflammation in long-lived individuals.
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Affiliation(s)
- Yaqun Huang
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Xia Ge
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Hong Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jing-Lin Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong-Shun Ao
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ji Li
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Yonghan He
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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8
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da Cruz IBM, de Afonso Bonotto NC, Turra BO, Teixeira CF, Azzolin VF, Ribeiro EAM, Piccoli JDCE, Barbisan F. Rotenone-exposure as cytofunctional aging model of human dermal fibroblast prior replicative senescence. Toxicol In Vitro 2023:105637. [PMID: 37394047 DOI: 10.1016/j.tiv.2023.105637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
Rotenone (Ro), causes superoxide imbalance by inhibiting complex I of the mitochondrial electron transport chain, being able to serve as a model for functional skin aging by inducing cytofunctional changes in dermal fibroblasts prior to proliferative senescence. To test this hypothesis, we conducted an initial protocol to select a concentration of Ro (0.5, 1, 1.5, 2, 2.5, and 3 μM) that would induce the highest levels of the aging marker beta-galactosidase (β-gal) in human dermal HFF-1 fibroblasts after 72 h of culture, as well as a moderate increase in apoptosis and partial G1 arrestment. We evaluated whether the selected concentration (1 μM) differentially modulated oxidative and cytofunctional markers of fibroblasts. Ro 1.0 μM increased β-gal levels and apoptosis frequency, decreased the frequency of S/G2 cells, induced higher levels of oxidative markers, and presented a genotoxic effect. Fibroblasts exposed to Ro showed lower mitochondrial activity, extracellular collagen deposition, and fewer fibroblast cytoplasmic connections than controls. Ro triggered overexpression of the gene associated with aging (MMP-1), downregulation genes of collagen production (COL1A, FGF-2), and cellular growth/regeneration (FGF-7). The 1 μM concentration of Ro could serve as an experimental model for functional aging fibroblasts prior to replicative senescence. It could be used to identify causal aging mechanisms and strategies to delay skin aging events.
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Affiliation(s)
- Ivana Beatrice Mânica da Cruz
- Postgraduate Program of Pharmacology, Federal University of Santa Maria, Santa Maria, RS, Brazil; Postgraduate Program of em Gerontology, Federal University of Santa Maria, Santa Maria, RS, Brazil; Santa Maria, RS, Brazil d Open University of the Third Age, State University of Amazonas, Manaus, AM, Brazil
| | - Nathália Cardoso de Afonso Bonotto
- Postgraduate Program of Pharmacology, Federal University of Santa Maria, Santa Maria, RS, Brazil; Postgraduate Program of em Gerontology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Bárbara Osmarin Turra
- Postgraduate Program of Pharmacology, Federal University of Santa Maria, Santa Maria, RS, Brazil; Santa Maria, RS, Brazil d Open University of the Third Age, State University of Amazonas, Manaus, AM, Brazil
| | - Cibele Ferreira Teixeira
- Postgraduate Program of Pharmacology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Verônica Farina Azzolin
- Postgraduate Program of em Gerontology, Federal University of Santa Maria, Santa Maria, RS, Brazil; Santa Maria, RS, Brazil d Open University of the Third Age, State University of Amazonas, Manaus, AM, Brazil
| | - Ednea Aguiar Maia Ribeiro
- Santa Maria, RS, Brazil d Open University of the Third Age, State University of Amazonas, Manaus, AM, Brazil
| | | | - Fernanda Barbisan
- Postgraduate Program of Pharmacology, Federal University of Santa Maria, Santa Maria, RS, Brazil; Postgraduate Program of em Gerontology, Federal University of Santa Maria, Santa Maria, RS, Brazil; Santa Maria, RS, Brazil d Open University of the Third Age, State University of Amazonas, Manaus, AM, Brazil.
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9
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Mitochondria and Antibiotics: For Good or for Evil? Biomolecules 2021; 11:biom11071050. [PMID: 34356674 PMCID: PMC8301944 DOI: 10.3390/biom11071050] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 01/16/2023] Open
Abstract
The discovery and application of antibiotics in the common clinical practice has undeniably been one of the major medical advances in our times. Their use meant a drastic drop in infectious diseases-related mortality and contributed to prolonging human life expectancy worldwide. Nevertheless, antibiotics are considered by many a double-edged sword. Their extensive use in the past few years has given rise to a global problem: antibiotic resistance. This factor and the increasing evidence that a wide range of antibiotics can damage mammalian mitochondria, have driven a significant sector of the medical and scientific communities to advise against the use of antibiotics for purposes other to treating severe infections. Notwithstanding, a notorious number of recent studies support the use of these drugs to treat very diverse conditions, ranging from cancer to neurodegenerative or mitochondrial diseases. In this context, there is great controversy on whether the risks associated to antibiotics outweigh their promising beneficial features. The aim of this review is to provide insight in the topic, purpose for which the most relevant findings regarding antibiotic therapies have been discussed.
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10
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Re-analysis of herbal extracts data reveals that inflammatory processes are mediated by hormetic mechanisms. Chem Biol Interact 2019; 314:108844. [PMID: 31600484 DOI: 10.1016/j.cbi.2019.108844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 12/25/2022]
Abstract
Using data from Schink et al. (2018), a large number of herbal extracts were assessed for their capacity to induce pro- and anti-inflammatory effects based on TLR4 expression normalized for cell viability in two immune cell models (i.e., HeLa-TLR4 transfected reporter cell line, and THP-1 monocytes) applying seven concentrations (0.01-3.0%). The analysis revealed that 70-80% of the extracts satisfying the a priori entry criteria also satisfied a priori evaluative criteria for hormetic concentration responses. These findings demonstrate that a large proportion of herbal extracts display hormetic dose responses in immune cells, indicating that hormetic mechanisms mediate pro- and anti-inflammatory processes and may provide a means to guide optimal dosing strategies. The identification of doses eliciting only anti-inflammatory therapeutic activity as well as the use of dose-variable herbal extracts in the treatment of inflammatory diseases will be challenging.
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11
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Palmeira CM, Teodoro JS, Amorim JA, Steegborn C, Sinclair DA, Rolo AP. Mitohormesis and metabolic health: The interplay between ROS, cAMP and sirtuins. Free Radic Biol Med 2019; 141:483-491. [PMID: 31349039 PMCID: PMC6718302 DOI: 10.1016/j.freeradbiomed.2019.07.017] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 02/07/2023]
Abstract
The key role of mitochondria in oxidative metabolism and redox homeostasis explains the link between mitochondrial dysfunction and the development of metabolic disorders. Mitochondria's highly dynamic nature, based on alterations in biogenesis, mitophagy, fusion and fission, allows adjusting sequential redox reactions of the electron transport chain (ETC) and dissipation of the membrane potential by ATP synthase, to different environmental cues. With reactive oxygen species being an inevitable by-product of oxidative phosphorylation (OXPHOS), alterations on mitochondrial oxidative rate with a consequent excessive load of reactive oxygen species have been traditionally associated with pathological conditions. However, reactive oxygen species have also been suggested as promoters of mitohormesis, a process in which low, non-cytotoxic concentrations of reactive oxygen species promote mitochondrial homeostasis. Therefore, signaling systems involved in the regulation of mitochondrial homeostasis are attractive candidates for drug development for metabolic diseases triggered by mitochondrial dysfunction. Reversible phosphorylation downstream the cyclic AMP (cAMP) signaling cascade and deacetylation mediated by sirtuins are recognized as major mitochondrial regulators.
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Affiliation(s)
- Carlos Marques Palmeira
- Department of Life Sciences, University of Coimbra, Portugal; Center for Neurosciences and Cell Biology, University of Coimbra, Portugal
| | - João Soeiro Teodoro
- Department of Life Sciences, University of Coimbra, Portugal; Center for Neurosciences and Cell Biology, University of Coimbra, Portugal
| | - João Alves Amorim
- Center for Neurosciences and Cell Biology, University of Coimbra, Portugal; IIIUC - Institute of Interdisciplinary Research, University of Coimbra, Portugal; Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA, USA
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, 95440, Bayreuth, Germany
| | - David A Sinclair
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA, USA; Laboratory for Ageing Research, Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Anabela Pinto Rolo
- Department of Life Sciences, University of Coimbra, Portugal; Center for Neurosciences and Cell Biology, University of Coimbra, Portugal.
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12
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Branco CS, Duong A, Machado AK, Wu A, Scola G, Andreazza AC, Salvador M. Araucaria angustifolia (Bertol.) Kuntze has neuroprotective action through mitochondrial modulation in dopaminergic SH-SY5Y cells. Mol Biol Rep 2019; 46:6013-6025. [PMID: 31452047 DOI: 10.1007/s11033-019-05037-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Brain disorders (BD) including neuropsychiatric and neurodegenerative diseases, are often associated with impairments in mitochondrial function and oxidative damage that can lead to neuronal injury. The mitochondrial complex I enzyme is one of the main sites of ROS generation and is implicated in many BD pathophysiologies. Despite advances in therapeutics for BD management, conventional pharmacotherapy still cannot efficiently control neuronal redox imbalance and mitochondrial dysfunction. Araucaria angustifolia is one of the main pine species in South America and presents a notable therapeutic history in folk medicine. A. angustifolia extract (AAE), obtained from the natural waste named bracts, is rich in flavonoids; molecules able to regulate cell redox metabolism. We examined the effects of AAE on rotenone-induced mitochondrial complex I dysfunction in human dopaminergic SH-SY5Y cells. AAE restored complex I assembly and activity mainly through overexpression of NDUFS7 protein and NDUFV2 gene levels. These findings were accompanied by a reduction in the generation of neuronal reactive oxygen species and lipid peroxidation. Our data demonstrates, for the first time, that AAE exerts in vitro neuroprotective effects, thus making it an interesting source for future drug development in BD-associated mitochondrial dysfunctions.
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Affiliation(s)
- Catia Santos Branco
- Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, RS, 95070 560, Brazil.
| | - Angela Duong
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | | | - Abbie Wu
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Gustavo Scola
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Centre for Addiction and Mental Health - CAMH, Toronto, ON, Canada
| | - Ana Cristina Andreazza
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Centre for Addiction and Mental Health - CAMH, Toronto, ON, Canada
| | - Mirian Salvador
- Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, RS, 95070 560, Brazil
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13
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Hernandez-Segura A, Rubingh R, Demaria M. Identification of stable senescence-associated reference genes. Aging Cell 2019; 18:e12911. [PMID: 30710410 PMCID: PMC6413663 DOI: 10.1111/acel.12911] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/10/2018] [Accepted: 12/23/2018] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a state of permanent cell cycle arrest activated in response to damaging stimuli. Many hallmarks associated with senescent cells are measured by quantitative real-time PCR (qPCR). As the selection of stable reference genes for interpretation of qPCR data is often overlooked, we performed a systematic review to understand normalization strategies entailed in experiments involving senescent cells. We found that, in violation of the Minimum Information for publication of qPCR Experiments (MIQE) guidelines, most reports used only one reference gene to normalize qPCR data, and that stability of the reference genes was either not tested or not reported. To identify new and more stable reference genes in senescent fibroblasts, we analyzed the Shapiro-Wilk normality test and the coefficient of variation per gene using in public RNAseq datasets. We then compared the new reference gene candidates with commonly used ones by using both RNAseq and qPCR data. Finally, we defined the best reference genes to be used universally or in a strain-dependent manner. This study intends to raise awareness of the instability of classical reference genes in senescent cells and to serve as a first attempt to define guidelines for the selection of more reliable normalization methods.
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Affiliation(s)
- Alejandra Hernandez-Segura
- European Research Institute for the Biology of Ageing, University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - Richard Rubingh
- European Research Institute for the Biology of Ageing, University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - Marco Demaria
- European Research Institute for the Biology of Ageing, University Medical Center Groningen; University of Groningen; Groningen The Netherlands
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14
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Kurz S, Thieme R, Amberg R, Groth M, Jahnke HG, Pieroh P, Horn LC, Kolb M, Huse K, Platzer M, Volke D, Dehghani F, Buzdin A, Engel K, Robitzki A, Hoffmann R, Gockel I, Birkenmeier G. The anti-tumorigenic activity of A2M-A lesson from the naked mole-rat. PLoS One 2017; 12:e0189514. [PMID: 29281661 PMCID: PMC5744951 DOI: 10.1371/journal.pone.0189514] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/28/2017] [Indexed: 12/30/2022] Open
Abstract
Cancer resistance is a major cause for longevity of the naked mole-rat. Recent liver transcriptome analysis in this animal compared to wild-derived mice revealed higher expression of alpha2-macroglobulin (A2M) and cell adhesion molecules, which contribute to the naked mole-rat’s cancer resistance. Notably, A2M is known to dramatically decrease with age in humans. We hypothesize that this might facilitate tumour development. Here we found that A2M modulates tumour cell adhesion, migration and growth by inhibition of tumour promoting signalling pathways, e.g. PI3K / AKT, SMAD and up-regulated PTEN via down-regulation of miR-21, in vitro and in tumour xenografts. A2M increases the expression of CD29 and CD44 but did not evoke EMT. Transcriptome analysis of A2M-treated tumour cells, xenografts and mouse liver demonstrated a multifaceted regulation of tumour promoting signalling pathways indicating a less tumorigenic environment mediated by A2M. By virtue of these multiple actions the naturally occurring A2M has strong potential as a novel therapeutic agent.
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Affiliation(s)
- Susanne Kurz
- Institute of Biochemistry, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - René Thieme
- Department of Visceral, Transplantation, Thoracic and Vascular Surgery, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - Ronny Amberg
- Institute of Biochemistry, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - Marco Groth
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Heinz-Georg Jahnke
- Centre for Biotechnology and Biomedicine, Molecular Biological-Biochemical Processing Technology, University of Leipzig, Germany
| | - Philipp Pieroh
- Department of Anatomy and Cell Biology, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, Halle (Saale), Germany
| | - Lars-Christian Horn
- Institute of Pathology, Division of Breast, Gynaecological and Perinatal Pathology, University of Leipzig, Leipzig, Germany
| | - Marlen Kolb
- Institute of Biochemistry, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - Klaus Huse
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Daniela Volke
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Faramarz Dehghani
- Department of Anatomy and Cell Biology, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, Halle (Saale), Germany
| | - Anton Buzdin
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, Baltimore, Maryland, United States of America
- Department of Pathway Engineering for Cancer Research, OmicsWay Corp., Walnut, CA, United States of America
- National Research Centre “Kurchatov Institute”, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, 1, Akademika Kurchatova sq., Moscow, Russia
| | - Kathrin Engel
- Institute of Biochemistry, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - Andrea Robitzki
- Centre for Biotechnology and Biomedicine, Molecular Biological-Biochemical Processing Technology, University of Leipzig, Germany
| | - Ralf Hoffmann
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Ines Gockel
- Department of Visceral, Transplantation, Thoracic and Vascular Surgery, University of Leipzig, Medical Faculty, Leipzig, Germany
| | - Gerd Birkenmeier
- Institute of Biochemistry, University of Leipzig, Medical Faculty, Leipzig, Germany
- * E-mail:
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15
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Egea J, Fabregat I, Frapart YM, Ghezzi P, Görlach A, Kietzmann T, Kubaichuk K, Knaus UG, Lopez MG, Olaso-Gonzalez G, Petry A, Schulz R, Vina J, Winyard P, Abbas K, Ademowo OS, Afonso CB, Andreadou I, Antelmann H, Antunes F, Aslan M, Bachschmid MM, Barbosa RM, Belousov V, Berndt C, Bernlohr D, Bertrán E, Bindoli A, Bottari SP, Brito PM, Carrara G, Casas AI, Chatzi A, Chondrogianni N, Conrad M, Cooke MS, Costa JG, Cuadrado A, My-Chan Dang P, De Smet B, Debelec-Butuner B, Dias IHK, Dunn JD, Edson AJ, El Assar M, El-Benna J, Ferdinandy P, Fernandes AS, Fladmark KE, Förstermann U, Giniatullin R, Giricz Z, Görbe A, Griffiths H, Hampl V, Hanf A, Herget J, Hernansanz-Agustín P, Hillion M, Huang J, Ilikay S, Jansen-Dürr P, Jaquet V, Joles JA, Kalyanaraman B, Kaminskyy D, Karbaschi M, Kleanthous M, Klotz LO, Korac B, Korkmaz KS, Koziel R, Kračun D, Krause KH, Křen V, Krieg T, Laranjinha J, Lazou A, Li H, Martínez-Ruiz A, Matsui R, McBean GJ, Meredith SP, Messens J, Miguel V, Mikhed Y, Milisav I, Milković L, Miranda-Vizuete A, Mojović M, Monsalve M, Mouthuy PA, Mulvey J, Münzel T, Muzykantov V, Nguyen ITN, Oelze M, Oliveira NG, Palmeira CM, Papaevgeniou N, Pavićević A, Pedre B, Peyrot F, Phylactides M, Pircalabioru GG, Pitt AR, Poulsen HE, Prieto I, Rigobello MP, Robledinos-Antón N, Rodríguez-Mañas L, Rolo AP, Rousset F, Ruskovska T, Saraiva N, Sasson S, Schröder K, Semen K, Seredenina T, Shakirzyanova A, Smith GL, Soldati T, Sousa BC, Spickett CM, Stancic A, Stasia MJ, Steinbrenner H, Stepanić V, Steven S, Tokatlidis K, Tuncay E, Turan B, Ursini F, Vacek J, Vajnerova O, Valentová K, Van Breusegem F, Varisli L, Veal EA, Yalçın AS, Yelisyeyeva O, Žarković N, Zatloukalová M, Zielonka J, Touyz RM, Papapetropoulos A, Grune T, Lamas S, Schmidt HHHW, Di Lisa F, Daiber A. European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS). Redox Biol 2017; 13:94-162. [PMID: 28577489 PMCID: PMC5458069 DOI: 10.1016/j.redox.2017.05.007] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 12/12/2022] Open
Abstract
The European Cooperation in Science and Technology (COST) provides an ideal framework to establish multi-disciplinary research networks. COST Action BM1203 (EU-ROS) represents a consortium of researchers from different disciplines who are dedicated to providing new insights and tools for better understanding redox biology and medicine and, in the long run, to finding new therapeutic strategies to target dysregulated redox processes in various diseases. This report highlights the major achievements of EU-ROS as well as research updates and new perspectives arising from its members. The EU-ROS consortium comprised more than 140 active members who worked together for four years on the topics briefly described below. The formation of reactive oxygen and nitrogen species (RONS) is an established hallmark of our aerobic environment and metabolism but RONS also act as messengers via redox regulation of essential cellular processes. The fact that many diseases have been found to be associated with oxidative stress established the theory of oxidative stress as a trigger of diseases that can be corrected by antioxidant therapy. However, while experimental studies support this thesis, clinical studies still generate controversial results, due to complex pathophysiology of oxidative stress in humans. For future improvement of antioxidant therapy and better understanding of redox-associated disease progression detailed knowledge on the sources and targets of RONS formation and discrimination of their detrimental or beneficial roles is required. In order to advance this important area of biology and medicine, highly synergistic approaches combining a variety of diverse and contrasting disciplines are needed.
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Affiliation(s)
- Javier Egea
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine. Univerisdad Autonoma de Madrid, Spain
| | - Isabel Fabregat
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | - Yves M Frapart
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | | | - Agnes Görlach
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Kateryna Kubaichuk
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ulla G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Manuela G Lopez
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine. Univerisdad Autonoma de Madrid, Spain
| | | | - Andreas Petry
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - Rainer Schulz
- Institute of Physiology, JLU Giessen, Giessen, Germany
| | - Jose Vina
- Department of Physiology, University of Valencia, Spain
| | - Paul Winyard
- University of Exeter Medical School, St Luke's Campus, Exeter EX1 2LU, UK
| | - Kahina Abbas
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - Opeyemi S Ademowo
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Catarina B Afonso
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Ioanna Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Haike Antelmann
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Fernando Antunes
- Departamento de Química e Bioquímica and Centro de Química e Bioquímica, Faculdade de Ciências, Portugal
| | - Mutay Aslan
- Department of Medical Biochemistry, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Markus M Bachschmid
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Rui M Barbosa
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Vsevolod Belousov
- Molecular technologies laboratory, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - David Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, USA
| | - Esther Bertrán
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | | | - Serge P Bottari
- GETI, Institute for Advanced Biosciences, INSERM U1029, CNRS UMR 5309, Grenoble-Alpes University and Radio-analysis Laboratory, CHU de Grenoble, Grenoble, France
| | - Paula M Brito
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; Faculdade de Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Guia Carrara
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ana I Casas
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Afroditi Chatzi
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - Niki Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Marcus Conrad
- Helmholtz Center Munich, Institute of Developmental Genetics, Neuherberg, Germany
| | - Marcus S Cooke
- Oxidative Stress Group, Dept. Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA
| | - João G Costa
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid. Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Pham My-Chan Dang
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - Barbara De Smet
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy; Pharmahungary Group, Szeged, Hungary
| | - Bilge Debelec-Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir 35100, Turkey
| | - Irundika H K Dias
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Joe Dan Dunn
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - Amanda J Edson
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Mariam El Assar
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain
| | - Jamel El-Benna
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Ana S Fernandes
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Kari E Fladmark
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Ulrich Förstermann
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Rashid Giniatullin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Zoltán Giricz
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Anikó Görbe
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Helen Griffiths
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK; Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Vaclav Hampl
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Alina Hanf
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Jan Herget
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pablo Hernansanz-Agustín
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Melanie Hillion
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Jingjing Huang
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Serap Ilikay
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - Pidder Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Vincent Jaquet
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Jaap A Joles
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | | | | | - Mahsa Karbaschi
- Oxidative Stress Group, Dept. Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Lars-Oliver Klotz
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - Bato Korac
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - Kemal Sami Korkmaz
- Department of Bioengineering, Cancer Biology Laboratory, Faculty of Engineering, Ege University, Bornova, 35100 Izmir, Turkey
| | - Rafal Koziel
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Damir Kračun
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - Karl-Heinz Krause
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Vladimír Křen
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, UK
| | - João Laranjinha
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Antigone Lazou
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Huige Li
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Antonio Martínez-Ruiz
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Reiko Matsui
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Gethin J McBean
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Stuart P Meredith
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Verónica Miguel
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Yuliya Mikhed
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Irina Milisav
- University of Ljubljana, Faculty of Medicine, Institute of Pathophysiology and Faculty of Health Sciences, Ljubljana, Slovenia
| | - Lidija Milković
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Miloš Mojović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - María Monsalve
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Pierre-Alexis Mouthuy
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - John Mulvey
- Department of Medicine, University of Cambridge, UK
| | - Thomas Münzel
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Vladimir Muzykantov
- Department of Pharmacology, Center for Targeted Therapeutics & Translational Nanomedicine, ITMAT/CTSA Translational Research Center University of Pennsylvania The Perelman School of Medicine, Philadelphia, PA, USA
| | - Isabel T N Nguyen
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | - Matthias Oelze
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Nuno G Oliveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos M Palmeira
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - Nikoletta Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Aleksandra Pavićević
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Brandán Pedre
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Fabienne Peyrot
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France; ESPE of Paris, Paris Sorbonne University, Paris, France
| | - Marios Phylactides
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Henrik E Poulsen
- Laboratory of Clinical Pharmacology, Rigshospitalet, University Hospital Copenhagen, Denmark; Department of Clinical Pharmacology, Bispebjerg Frederiksberg Hospital, University Hospital Copenhagen, Denmark; Department Q7642, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Ignacio Prieto
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Maria Pia Rigobello
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Natalia Robledinos-Antón
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid. Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Leocadio Rodríguez-Mañas
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain; Servicio de Geriatría, Hospital Universitario de Getafe, Getafe, Spain
| | - Anabela P Rolo
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - Francis Rousset
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, Stip, Republic of Macedonia
| | - Nuno Saraiva
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Shlomo Sasson
- Institute for Drug Research, Section of Pharmacology, Diabetes Research Unit, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Katrin Schröder
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany
| | - Khrystyna Semen
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Tamara Seredenina
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Anastasia Shakirzyanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Thierry Soldati
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - Bebiana C Sousa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Corinne M Spickett
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Ana Stancic
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - Marie José Stasia
- Université Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, F38000 Grenoble, France; CDiReC, Pôle Biologie, CHU de Grenoble, Grenoble, F-38043, France
| | - Holger Steinbrenner
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - Višnja Stepanić
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Sebastian Steven
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - Erkan Tuncay
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - Belma Turan
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - Fulvio Ursini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | - Olga Vajnerova
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Valentová
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lokman Varisli
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - Elizabeth A Veal
- Institute for Cell and Molecular Biosciences, and Institute for Ageing, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - A Suha Yalçın
- Department of Biochemistry, School of Medicine, Marmara University, İstanbul, Turkey
| | | | - Neven Žarković
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | | | - Rhian M Touyz
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - Andreas Papapetropoulos
- Laboratoty of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Tilman Grune
- German Institute of Human Nutrition, Department of Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Santiago Lamas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Harald H H W Schmidt
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Fabio Di Lisa
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy.
| | - Andreas Daiber
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany.
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16
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Marthandan S, Menzel U, Priebe S, Groth M, Guthke R, Platzer M, Hemmerich P, Kaether C, Diekmann S. Conserved genes and pathways in primary human fibroblast strains undergoing replicative and radiation induced senescence. Biol Res 2016; 49:34. [PMID: 27464526 PMCID: PMC4963952 DOI: 10.1186/s40659-016-0095-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023] Open
Abstract
Background Cellular senescence is induced either internally, for example by replication exhaustion and cell division, or externally, for example by irradiation. In both cases, cellular damages accumulate which, if not successfully repaired, can result in senescence induction. Recently, we determined the transcriptional changes combined with the transition into replicative senescence in primary human fibroblast strains. Here, by γ-irradiation we induced premature cellular senescence in the fibroblast cell strains (HFF and MRC-5) and determined the corresponding transcriptional changes by high-throughput RNA sequencing. Results Comparing the transcriptomes, we found a high degree of similarity in differential gene expression in replicative as well as in irradiation induced senescence for both cell strains suggesting, in each cell strain, a common cellular response to error accumulation. On the functional pathway level, “Cell cycle” was the only pathway commonly down-regulated in replicative and irradiation-induced senescence in both fibroblast strains, confirming the tight link between DNA repair and cell cycle regulation. However, “DNA repair” and “replication” pathways were down-regulated more strongly in fibroblasts undergoing replicative exhaustion. We also retrieved genes and pathways in each of the cell strains specific for irradiation induced senescence. Conclusion We found the pathways associated with “DNA repair” and “replication” less stringently regulated in irradiation induced compared to replicative senescence. The strong regulation of these pathways in replicative senescence highlights the importance of replication errors for its induction. Electronic supplementary material The online version of this article (doi:10.1186/s40659-016-0095-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiva Marthandan
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
| | - Uwe Menzel
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Steffen Priebe
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Marco Groth
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Matthias Platzer
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Peter Hemmerich
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaether
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Stephan Diekmann
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
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17
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Marthandan S, Baumgart M, Priebe S, Groth M, Schaer J, Kaether C, Guthke R, Cellerino A, Platzer M, Diekmann S, Hemmerich P. Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq. PLoS One 2016; 11:e0154531. [PMID: 27140416 PMCID: PMC4854426 DOI: 10.1371/journal.pone.0154531] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/14/2016] [Indexed: 12/15/2022] Open
Abstract
Cellular senescence correlates with changes in the transcriptome. To obtain a complete view on senescence-associated transcription networks and pathways, we assessed by deep RNA sequencing the transcriptomes of five of the most commonly used laboratory strains of human fibroblasts during their transition into senescence. In a number of cases, we verified the RNA-seq data by real-time PCR. By determining cellular protein levels we observed that the age-related expression of most but not all genes is regulated at the transcriptional level. We found that 78% of the age-affected differentially expressed genes were commonly regulated in the same direction (either up- or down-regulated) in all five fibroblast strains, indicating a strong conservation of age-associated changes in the transcriptome. KEGG pathway analyses confirmed up-regulation of the senescence-associated secretory phenotype and down-regulation of DNA synthesis/repair and most cell cycle pathways common in all five cell strains. Newly identified senescence-induced pathways include up-regulation of endocytotic/phagocytic pathways and down-regulation of the mRNA metabolism and the mRNA splicing pathways. Our results provide an unprecedented comprehensive and deep view into the individual and common transcriptome and pathway changes during the transition into of senescence of five human fibroblast cell strains.
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Affiliation(s)
- S. Marthandan
- Leibniz-Institute on Aging—Fritz Lipmann Institute e.V. (FLI), Jena, Germany
- * E-mail:
| | - M. Baumgart
- Leibniz-Institute on Aging—Fritz Lipmann Institute e.V. (FLI), Jena, Germany
| | - S. Priebe
- Leibniz Institute for Natural Product Research and Infection Biology—Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - M. Groth
- Leibniz-Institute on Aging—Fritz Lipmann Institute e.V. (FLI), Jena, Germany
| | - J. Schaer
- Leibniz Institute for Natural Product Research and Infection Biology—Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - C. Kaether
- Leibniz-Institute on Aging—Fritz Lipmann Institute e.V. (FLI), Jena, Germany
| | - R. Guthke
- Leibniz Institute for Natural Product Research and Infection Biology—Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - A. Cellerino
- Leibniz-Institute on Aging—Fritz Lipmann Institute e.V. (FLI), Jena, Germany
- Laboratory of NeuroBiology, Scuola Normale Superiore, Pisa, Italy
| | - M. Platzer
- Leibniz-Institute on Aging—Fritz Lipmann Institute e.V. (FLI), Jena, Germany
| | - S. Diekmann
- Leibniz-Institute on Aging—Fritz Lipmann Institute e.V. (FLI), Jena, Germany
| | - P. Hemmerich
- Leibniz-Institute on Aging—Fritz Lipmann Institute e.V. (FLI), Jena, Germany
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