1
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Lashen AG, Almalki N, Toss M, Mirza S, Malki MI, Rutland CS, Jeyapalan JN, Green AR, Mongan NP, Madhusudan S, Rakha EA. The characteristics and prognostic significance of histone H1 expression in breast cancer. Pathology 2024:S0031-3025(24)00143-0. [PMID: 38971643 DOI: 10.1016/j.pathol.2024.03.012] [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: 11/22/2023] [Revised: 03/11/2024] [Accepted: 03/25/2024] [Indexed: 07/08/2024]
Abstract
Histone H1 (H.H1) is involved in chromatin organisation and gene regulation and is overexpressed in many malignant tumours, including breast cancer (BC). This study proposed and evaluated the prognostic role of H.H1 expression in BC. H.H1 mRNA expression was evaluated in publicly available BC dataset bc-GenExMiner database (n=4421). H.H1 protein expression was assessed immunohistochemically in a well-characterised early-stage BC cohort (n=1311), and associations with clinicopathological data and survival outcomes were evaluated. At the mRNA level, there was a significant association between high H.H1 mRNA and basal-like BC subtype and with poor outcome. The association with shorter survival was observed in the whole cohort and in the basal-like class. H.H1 protein expression was detected in both tumour cells and surrounding stroma. Total expression was detected in 72% of the cases, including 28% in tumour cell nuclei and 44% in the stroma. There was strong association between high tumour H.H1 expression and triple-negative BC (TNBC) subtype (p=0.007) and with shorter survival (p=0.019), independent of other variables including tumour size, histologic tumour grade, and lymph node status. H.H1 expression is associated with poor prognosis in BC. Given poor prognostic role of H.H1 in TNBC, it may represent a potential therapeutic target for patients with this aggressive disease.
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Affiliation(s)
- Ayat G Lashen
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK; Department of Pathology, Faculty of Medicine, Menoufia University, Shebin El Kom, Egypt; Nottingham Breast Cancer Research Centre, University of Nottingham, Nottingham, UK
| | - Nabeelah Almalki
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK; Faculty of Applied Medical Science, Shaqra University, Riyadh, Saudi Arabia
| | - Michael Toss
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK; Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust Sheffield, UK
| | - Sameer Mirza
- Department of Chemistry College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohammed Imad Malki
- Pathology Unit, Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Catrin S Rutland
- School of Veterinary Medicine and Sciences, University of Nottingham, Nottingham, UK
| | - Jennie N Jeyapalan
- School of Veterinary Medicine and Sciences, University of Nottingham, Nottingham, UK
| | - Andrew R Green
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK; Nottingham Breast Cancer Research Centre, University of Nottingham, Nottingham, UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Sciences, University of Nottingham, Nottingham, UK; Department of Pharmacology, Weill Cornell Medicine, New York, USA
| | - Srinivasan Madhusudan
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK; Department of Oncology, Nottingham University Hospitals, Nottingham, UK
| | - Emad A Rakha
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK; Department of Pathology, Hamad Medical Corporation, Doha, Qatar.
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2
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D'Antona S, Porro D, Gallivanone F, Bertoli G. Characterization of cell cycle, inflammation, and oxidative stress signaling role in non-communicable diseases: Insights into genetic variants, microRNAs and pathways. Comput Biol Med 2024; 174:108346. [PMID: 38581999 DOI: 10.1016/j.compbiomed.2024.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/16/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Non-Communicable Diseases (NCDs) significantly impact global health, contributing to over 70% of premature deaths, as reported by the World Health Organization (WHO). These diseases have complex and multifactorial origins, involving genetic, epigenetic, environmental and lifestyle factors. While Genome-Wide Association Study (GWAS) is widely recognized as a valuable tool for identifying variants associated with complex phenotypes; the multifactorial nature of NCDs necessitates a more comprehensive exploration, encompassing not only the genetic but also the epigenetic aspect. For this purpose, we employed a bioinformatics-multiomics approach to examine the genetic and epigenetic characteristics of NCDs (i.e. colorectal cancer, coronary atherosclerosis, squamous cell lung cancer, psoriasis, type 2 diabetes, and multiple sclerosis), aiming to identify novel biomarkers for diagnosis and prognosis. Leveraging GWAS summary statistics, we pinpointed Single Nucleotide Polymorphisms (SNPs) independently associated with each NCD. Subsequently, we identified genes linked to cell cycle, inflammation and oxidative stress mechanisms, revealing shared genes across multiple diseases, suggesting common functional pathways. From an epigenetic perspective, we identified microRNAs (miRNAs) with regulatory functions targeting these genes of interest. Our findings underscore critical genetic pathways implicated in these diseases. In colorectal cancer, the dysregulation of the "Cytokine Signaling in Immune System" pathway, involving LAMA5 and SMAD7, regulated by Hsa-miR-21-5p, Hsa-miR-103a-3p, and Hsa-miR-195-5p, emerged as pivotal. In coronary atherosclerosis, the pathway associated with "binding of TCF/LEF:CTNNB1 to target gene promoters" displayed noteworthy implications, with the MYC factor controlled by Hsa-miR-16-5p as a potential regulatory factor. Squamous cell lung carcinoma analysis revealed significant pathways such as "PTK6 promotes HIF1A stabilization," regulated by Hsa-let-7b-5p. In psoriasis, the "Endosomal/Vacuolar pathway," involving HLA-C and Hsa-miR-148a-3p and Hsa-miR-148b-3p, was identified as crucial. Type 2 Diabetes implicated the "Regulation of TP53 Expression" pathway, controlled by Hsa-miR-106a-5p and Hsa-miR-106b-5p. In conclusion, our study elucidates the genetic framework and molecular mechanisms underlying NCDs, offering crucial insights into potential genetic/epigenetic biomarkers for diagnosis and prognosis. The specificity of pathways and related miRNAs in different pathologies highlights promising candidates for further clinical validation, with the potential to advance personalized treatments and alleviate the global burden of NCDs.
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Affiliation(s)
- Salvatore D'Antona
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Danilo Porro
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Francesca Gallivanone
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Gloria Bertoli
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy.
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3
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Yamamoto Y, Takahashi RU, Kinehara M, Yano K, Kuramoto T, Shimamoto A, Tahara H. Downregulation of Histone H3.3 Induces p53-Dependent Cellular Senescence in Human Diploid Fibroblasts. Genes (Basel) 2024; 15:543. [PMID: 38790171 PMCID: PMC11121134 DOI: 10.3390/genes15050543] [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: 03/05/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Cellular senescence is an irreversible growth arrest that acts as a barrier to cancer initiation and progression. Histone alteration is one of the major events during replicative senescence. However, little is known about the function of H3.3 in cellular senescence. Here we found that the downregulation of H3.3 induced growth suppression with senescence-like phenotypes such as senescence-associated heterochromatin foci (SAHF) and β-galactosidase (SA-β-gal) activity. Furthermore, H3.3 depletion induced senescence-like phenotypes with the p53/p21-depedent pathway. In addition, we identified miR-22-3p, tumor suppressive miRNA, as an upstream regulator of the H3F3B (H3 histone, family 3B) gene which is the histone variant H3.3 and replaces conventional H3 in active genes. Therefore, our results reveal for the first time the molecular mechanisms for cellular senescence which are regulated by H3.3 abundance. Taken together, our studies suggest that H3.3 exerts functional roles in regulating cellular senescence and is a promising target for cancer therapy.
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Affiliation(s)
- Yuki Yamamoto
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
| | - Ryou-u Takahashi
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
| | - Masaki Kinehara
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
| | - Kimiyoshi Yano
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan;
| | - Tatsuya Kuramoto
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
| | - Akira Shimamoto
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo Onoda 756-0884, Japan;
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
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4
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Zanfardino P, Amati A, Doccini S, Cox SN, Tullo A, Longo G, D'Erchia A, Picardi E, Nesti C, Santorelli FM, Petruzzella V. OPA1 mutation affects autophagy and triggers senescence in autosomal dominant optic atrophy plus fibroblasts. Hum Mol Genet 2024; 33:768-786. [PMID: 38280232 DOI: 10.1093/hmg/ddae008] [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: 11/02/2023] [Revised: 01/06/2024] [Indexed: 01/29/2024] Open
Abstract
In several cases of mitochondrial diseases, the underlying genetic and bioenergetic causes of reduced oxidative phosphorylation (OxPhos) in mitochondrial dysfunction are well understood. However, there is still limited knowledge about the specific cellular outcomes and factors involved for each gene and mutation, which contributes to the lack of effective treatments for these disorders. This study focused on fibroblasts from a patient with Autosomal Dominant Optic Atrophy (ADOA) plus syndrome harboring a mutation in the Optic Atrophy 1 (OPA1) gene. By combining functional and transcriptomic approaches, we investigated the mitochondrial function and identified cellular phenotypes associated with the disease. Our findings revealed that fibroblasts with the OPA1 mutation exhibited a disrupted mitochondrial network and function, leading to altered mitochondrial dynamics and reduced autophagic response. Additionally, we observed a premature senescence phenotype in these cells, suggesting a previously unexplored role of the OPA1 gene in inducing senescence in ADOA plus patients. This study provides novel insights into the mechanisms underlying mitochondrial dysfunction in ADOA plus and highlights the potential importance of senescence in disease progression.
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Affiliation(s)
- Paola Zanfardino
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of study of Bari Aldo Moro, Piazza G. Cesare, 11, 70124 Bari, Italy
| | - Alessandro Amati
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of study of Bari Aldo Moro, Piazza G. Cesare, 11, 70124 Bari, Italy
| | - Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Viale del Tirreno, 56128 Calambrone, Pisa, Italy
| | - Sharon N Cox
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of study of Bari Aldo Moro, via Orabona 4, 70125, Bari, Italy
| | - Apollonia Tullo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via G. Amendola 122/O, 70126 Bari, Italy
| | - Giovanna Longo
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of study of Bari Aldo Moro, Piazza G. Cesare, 11, 70124 Bari, Italy
| | - Annamaria D'Erchia
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of study of Bari Aldo Moro, via Orabona 4, 70125, Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of study of Bari Aldo Moro, via Orabona 4, 70125, Bari, Italy
| | - Claudia Nesti
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Viale del Tirreno, 56128 Calambrone, Pisa, Italy
| | - Filippo M Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Viale del Tirreno, 56128 Calambrone, Pisa, Italy
| | - Vittoria Petruzzella
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of study of Bari Aldo Moro, Piazza G. Cesare, 11, 70124 Bari, Italy
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5
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Zhang Y, Lin W, Yang Y, Zhu S, Chen Y, Wang H, Teng L. MEF2D facilitates liver metastasis of gastric cancer cells through directly inducing H1X under IL-13 stimulation. Cancer Lett 2024; 591:216878. [PMID: 38609001 DOI: 10.1016/j.canlet.2024.216878] [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: 11/24/2023] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Liver metastasis is the most common metastatic occurrence in gastric cancer patients, although the precise mechanism behind it remains unclear. Through a combination of proteomics and quantitative RT-PCR, our study has revealed a significant correlation between the upregulation of myocyte enhancer factor-2D (MEF2D) and both distant metastasis and poor prognosis in gastric cancer patients. In mouse models, we observed that overexpressing or knocking down MEF2D in gastric cancer cells respectively promoted or inhibited liver metastasis. Furthermore, our research has demonstrated that MEF2D regulates the transcriptional activation of H1X by binding to the H1X promoter. This regulation leads to the upregulation of H1X, which, in turn, promotes the in vivo metastasis of gastric cancer cells along with the upregulation of the downstream gene β-CATENIN. Additionally, we found that the expression of MEF2D and H1X at both mRNA and protein levels can be induced by the inflammatory factor IL-13, and this induction exhibits a time gradient dependence. In human gastric cancer tissues, the expression of IL13RA1, the receptor for IL-13, positively correlates with the expression of MEF2D and H1X. IL13RA1 has been identified as an intermediate receptor through which IL-13 regulates MEF2D. In conclusion, our findings suggest that MEF2D plays a crucial role in promoting liver metastasis of gastric cancer by upregulating H1X and downstream target β-CATENIN in response to IL-13 stimulation. Targeting MEF2D could therefore be a promising therapeutic strategy for the clinical management of gastric cancer. STATEMENT OF SIGNIFICANCE: MEF2D promotes its transcriptional activation in gastric cancer cells by binding to the H1X promoter and is upregulated by IL-13-IL13RA1, thereby promoting distant metastasis of gastric cancer.
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Affiliation(s)
- Yingzi Zhang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China.
| | - Wu Lin
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310020, Zhejiang, China; Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China.
| | - Yan Yang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China.
| | - Songting Zhu
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China.
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China.
| | - Haiyong Wang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China.
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China.
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6
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Dubey SK, Dubey R, Kleinman ME. Unraveling Histone Loss in Aging and Senescence. Cells 2024; 13:320. [PMID: 38391933 PMCID: PMC10886805 DOI: 10.3390/cells13040320] [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: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
As the global population experiences a notable surge in aging demographics, the need to understand the intricate molecular pathways exacerbated by age-related stresses, including epigenetic dysregulation, becomes a priority. Epigenetic mechanisms play a critical role in driving age-related diseases through altered gene expression, genomic instability, and irregular chromatin remodeling. In this review, we focus on histones, a central component of the epigenome, and consolidate the key findings of histone loss and genome-wide redistribution as fundamental processes contributing to aging and senescence. The review provides insights into novel histone expression profiles, nucleosome occupancy, disruptions in higher-order chromatin architecture, and the emergence of noncanonical histone variants in the aging cellular landscape. Furthermore, we explore the current state of our understanding of the molecular mechanisms of histone deficiency in aging cells. Specific emphasis is placed on highlighting histone degradation pathways in the cell and studies that have explored potential strategies to mitigate histone loss or restore histone levels in aging cells. Finally, in addressing future perspectives, the insights gained from this review hold profound implications for advancing strategies that actively intervene in modulating histone expression profiles in the context of cellular aging and identifying potential therapeutic targets for alleviating a multitude of age-related diseases.
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Affiliation(s)
| | | | - Mark Ellsworth Kleinman
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA; (S.K.D.); (R.D.)
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7
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Hall LL, Creamer KM, Byron M, Lawrence JB. Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574742. [PMID: 38260534 PMCID: PMC10802495 DOI: 10.1101/2024.01.09.574742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The linear DNA sequence of mammalian chromosomes is organized in large blocks of DNA with similar sequence properties, producing a pattern of dark and light staining bands on mitotic chromosomes. Cytogenetic banding is essentially invariant between people and cell-types and thus may be assumed unrelated to genome regulation. We investigate whether large blocks of Alu-rich R-bands and L1-rich G-bands provide a framework upon which functional genome architecture is built. We examine two models of large-scale chromatin condensation: X-chromosome inactivation and formation of senescence-associated heterochromatin foci (SAHFs). XIST RNA triggers gene silencing but also formation of the condensed Barr Body (BB), thought to reflect cumulative gene silencing. However, we find Alu-rich regions are depleted from the L1-rich BB, supporting it is a dense core but not the entire chromosome. Alu-rich bands are also gene-rich, affirming our earlier findings that genes localize at the outer periphery of the BB. SAHFs similarly form within each territory by coalescence of syntenic L1 regions depleted for highly Alu-rich DNA. Analysis of senescent cell Hi-C data also shows large contiguous blocks of G-band and R-band DNA remodel as a segmental unit. Entire dark-bands gain distal intrachromosomal interactions as L1-rich regions form the SAHF. Most striking is that sharp Alu peaks within R-bands resist these changes in condensation. We further show that Chr19, which is exceptionally Alu rich, fails to form a SAHF. Collective results show regulation of genome architecture corresponding to large blocks of DNA and demonstrate resistance of segments with high Alu to chromosome condensation.
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Affiliation(s)
- Lisa L. Hall
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kevin M. Creamer
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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8
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Abdul-Aziz A, Devine RD, Lyberger JM, Chang H, Kovacs A, Lerma JR, Rogers AM, Byrd JC, Hertlein E, Behbehani GK. Mass Cytometry as a Tool for Investigating Senescence in Multiple Model Systems. Cells 2023; 12:2045. [PMID: 37626855 PMCID: PMC10453346 DOI: 10.3390/cells12162045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
Cellular senescence is a durable cell cycle arrest as a result of the finite proliferative capacity of cells. Senescence responds to both intrinsic and extrinsic cellular stresses, such as aging, mitochondrial dysfunction, irradiation, and chemotherapy. Here, we report on the use of mass cytometry (MC) to analyze multiple model systems and demonstrate MC as a platform for senescence analysis at the single-cell level. We demonstrate changes to p16 expression, cell cycling fraction, and histone tail modifications in several established senescent model systems and using isolated human T cells. In bone marrow mesenchymal stromal cells (BMSCs), we show increased p16 expression with subsequent passage as well as a reduction in cycling cells and open chromatin marks. In WI-38 cells, we demonstrate increased p16 expression with both culture-induced senescence and oxidative stress-induced senescence (OSIS). We also use Wanderlust, a trajectory analysis tool, to demonstrate how p16 expression changes with histone tail modifications and cell cycle proteins. Finally, we demonstrate that repetitive stimulation of human T cells with CD3/CD28 beads induces an exhausted phenotype with increased p16 expression. This p16-expressing population exhibited higher expression of exhaustion markers such as EOMES and TOX. This work demonstrates that MC is a useful platform for studying senescence at a single-cell protein level, and is capable of measuring multiple markers of senescence at once with high confidence, thereby improving our understanding of senescent pathways.
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Affiliation(s)
- Amina Abdul-Aziz
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45221, USA; (A.A.-A.)
| | - Raymond D. Devine
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Justin M. Lyberger
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Hsiaochi Chang
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Amy Kovacs
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - James R. Lerma
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45221, USA; (A.A.-A.)
| | - Andrew M. Rogers
- Maine Medical Center, Portland, ME 04102, USA
- Tufts University School of Medicine, Boston, MA 02111, USA
| | - John C. Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45221, USA; (A.A.-A.)
| | - Erin Hertlein
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45221, USA; (A.A.-A.)
| | - Gregory K. Behbehani
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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9
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Olan I, Handa T, Narita M. Beyond SAHF: An integrative view of chromatin compartmentalization during senescence. Curr Opin Cell Biol 2023; 83:102206. [PMID: 37451177 DOI: 10.1016/j.ceb.2023.102206] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/27/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023]
Abstract
Cellular senescence, a persistent form of cell cycle arrest, has been linked to the formation of heterochromatic foci, accompanied by additional concentric epigenetic layers. However, senescence is a highly heterogeneous phenotype, and the formation of these structures is context dependent. Recent developments in the understanding of the high-order chromatin organization have opened new avenues for contextualizing the nuclear and chromatin phenotypes of senescence. Oncogene-induced senescence displays prominent foci and typically exhibits increased chromatin compartmentalization, based on the chromosome conformation assays, as marked by increased transcompaction and segregation of the heterochromatin and euchromatin. However, other types of senescence (e.g., replicative senescence) exhibit comparatively lower levels of compartmentalization. Thus, a more integrative view of the global rearrangement of the chromatin architecture that occurs during senescence is emerging, with potential functional implications for the heterogeneity of the senescence phenotype.
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Affiliation(s)
- Ioana Olan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - Tetsuya Handa
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
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10
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Ceccherini E, Signore G, Tedeschi L, Vozzi F, Di Giorgi N, Michelucci E, Cecchettini A, Rocchiccioli S. Proteomic Modulation in TGF-β-Treated Cholangiocytes Induced by Curcumin Nanoparticles. Int J Mol Sci 2023; 24:10481. [PMID: 37445659 DOI: 10.3390/ijms241310481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Curcumin is a natural polyphenol that exhibits a variety of beneficial effects on health, including anti-inflammatory, antioxidant, and hepato-protective properties. Due to its poor water solubility and membrane permeability, in the present study, we prepared and characterized a water-stable, freely dispersible nanoformulation of curcumin. Although the potential of curcumin nanoformulations in the hepatic field has been studied, there are no investigations on their effect in fibrotic pathological conditions involving cholangiocytes. Exploiting an in vitro model of transforming growth factor-β (TGF-β)-stimulated cholangiocytes, we applied the Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS)-based quantitative proteomic approaches to study the proteome modulation induced by curcumin nanoformulation. Our results confirmed the well-documented anti-inflammatory properties of this nutraceutic, highlighting the induction of programmed cell death as a mechanism to counteract the cellular damages induced by TGF-β. Moreover, curcumin nanoformulation positively influenced the expression of several proteins involved in TGF-β-mediated fibrosis. Given the crucial importance of deregulated cholangiocyte functions during cholangiopathies, our results provide the basis for a better understanding of the mechanisms associated with this pathology and could represent a rationale for the development of more targeted therapies.
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Affiliation(s)
- Elisa Ceccherini
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - Giovanni Signore
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
- Biochemistry Unit, Department of Biology, University of Pisa, 56123 Pisa, Italy
| | - Lorena Tedeschi
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - Federico Vozzi
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - Nicoletta Di Giorgi
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - Elena Michelucci
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
- Institute of Chemistry of Organometallic Compounds, National Research Council, 56124 Pisa, Italy
| | - Antonella Cecchettini
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Silvia Rocchiccioli
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
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11
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Kandhaya-Pillai R, Miro-Mur F, Alijotas-Reig J, Tchkonia T, Schwartz S, Kirkland JL, Oshima J. Key elements of cellular senescence involve transcriptional repression of mitotic and DNA repair genes through the p53-p16/RB-E2F-DREAM complex. Aging (Albany NY) 2023; 15:4012-4034. [PMID: 37219418 PMCID: PMC10258023 DOI: 10.18632/aging.204743] [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: 11/27/2022] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
Cellular senescence is a dynamic stress response process that contributes to aging. From initiation to maintenance, senescent cells continuously undergo complex molecular changes and develop an altered transcriptome. Understanding how the molecular architecture of these cells evolve to sustain their non-proliferative state will open new therapeutic avenues to alleviate or delay the consequences of aging. Seeking to understand these molecular changes, we studied the transcriptomic profiles of endothelial replication-induced senescence and senescence induced by the inflammatory cytokine, TNF-α. We previously reported gene expressional pattern, pathways, and the mechanisms associated with upregulated genes during TNF-α induced senescence. Here, we extend our work and find downregulated gene signatures of both replicative and TNF-α senescence were highly overlapped, involving the decreased expression of several genes associated with cell cycle regulation, DNA replication, recombination, repair, chromatin structure, cellular assembly, and organization. We identified multiple targets of p53/p16-RB-E2F-DREAM that are essential for proliferation, mitotic progression, resolving DNA damage, maintaining chromatin integrity, and DNA synthesis that were repressed in senescent cells. We show that repression of multiple target genes in the p53/p16-RB-E2F-DREAM pathway collectively contributes to the stability of the senescent arrest. Our findings show that the regulatory connection between DREAM and cellular senescence may play a potential role in the aging process.
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Affiliation(s)
- Renuka Kandhaya-Pillai
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
- Systemic Autoimmune Diseases Research Unit, Vall d’Hebron Research Institute (VHIR), Barcelona 08035, Spain
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Francesc Miro-Mur
- Systemic Autoimmune Diseases Research Unit, Vall d’Hebron Research Institute (VHIR), Barcelona 08035, Spain
| | - Jaume Alijotas-Reig
- Systemic Autoimmune Diseases Research Unit, Vall d’Hebron Research Institute (VHIR), Barcelona 08035, Spain
| | - Tamar Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physiology, Mayo Clinic, Rochester, MN 55905, USA
| | - Simo Schwartz
- Drug Delivery and Targeting Group, Clinical Biochemistry Department, Vall d’Hebron Hospital, Barcelona 08035, Spain
| | - James L. Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physiology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Junko Oshima
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
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12
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Liu Z, Liang Q, Ren Y, Guo C, Ge X, Wang L, Cheng Q, Luo P, Zhang Y, Han X. Immunosenescence: molecular mechanisms and diseases. Signal Transduct Target Ther 2023; 8:200. [PMID: 37179335 PMCID: PMC10182360 DOI: 10.1038/s41392-023-01451-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/24/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Infection susceptibility, poor vaccination efficacy, age-related disease onset, and neoplasms are linked to innate and adaptive immune dysfunction that accompanies aging (known as immunosenescence). During aging, organisms tend to develop a characteristic inflammatory state that expresses high levels of pro-inflammatory markers, termed inflammaging. This chronic inflammation is a typical phenomenon linked to immunosenescence and it is considered the major risk factor for age-related diseases. Thymic involution, naïve/memory cell ratio imbalance, dysregulated metabolism, and epigenetic alterations are striking features of immunosenescence. Disturbed T-cell pools and chronic antigen stimulation mediate premature senescence of immune cells, and senescent immune cells develop a proinflammatory senescence-associated secretory phenotype that exacerbates inflammaging. Although the underlying molecular mechanisms remain to be addressed, it is well documented that senescent T cells and inflammaging might be major driving forces in immunosenescence. Potential counteractive measures will be discussed, including intervention of cellular senescence and metabolic-epigenetic axes to mitigate immunosenescence. In recent years, immunosenescence has attracted increasing attention for its role in tumor development. As a result of the limited participation of elderly patients, the impact of immunosenescence on cancer immunotherapy is unclear. Despite some surprising results from clinical trials and drugs, it is necessary to investigate the role of immunosenescence in cancer and other age-related diseases.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China
| | - Qimeng Liang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 4500052, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Xiaoyong Ge
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China.
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13
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Abd Al-razaq MA, Freyter BM, Isermann A, Tewary G, Mangelinck A, Mann C, Rübe CE. Role of Histone Variant H2A.J in Fine-Tuning Chromatin Organization for the Establishment of Ionizing Radiation-Induced Senescence. Cells 2023; 12:916. [PMID: 36980257 PMCID: PMC10047397 DOI: 10.3390/cells12060916] [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: 02/16/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
PURPOSE Radiation-induced senescence is characterized by profound changes in chromatin organization with the formation of Senescence-Associated-Heterochromatin-Foci (SAHF) and DNA-Segments-with-Chromatin-Alterations-Reinforcing-Senescence (DNA-SCARS). Importantly, senescent cells also secrete complex combinations of pro-inflammatory factors, referred as Senescence-Associated-Secretory-Phenotype (SASP). Here, we analyzed the epigenetic mechanism of histone variant H2A.J in establishing radiation-induced senescence. EXPERIMENTAL DESIGN Primary and genetically-modified lung fibroblasts with down- or up-regulated H2A.J expression were exposed to ionizing radiation and were analyzed for the formation of SAHF and DNA-SCARS by immunofluorescence microscopy. Dynamic changes in chromatin organization and accessibility, transcription factor recruitment, and transcriptome signatures were mapped by ATAC-seq and RNA-seq analysis. The secretion of SASP factors and potential bystander effects were analyzed by ELISA and RT-PCR. Lung tissue of mice exposed to different doses were analyzed by the digital image analysis of H2A.J-immunohistochemistry. RESULTS Differential incorporation of H2A.J has profound effects on higher-order chromatin organization and on establishing the epigenetic state of senescence. Integrative analyses of ATAC-seq and RNA-seq datasets indicate that H2A.J-associated changes in chromatin accessibility of regulatory regions decisively modulates transcription factor recruitment and inflammatory gene expression, resulting in an altered SASP secretome. In lung parenchyma, pneumocytes show dose-dependent H2A.J expression in response to radiation-induced DNA damage, therefore contributing to pro-inflammatory tissue reactions. CONCLUSIONS The fine-tuned incorporation of H2A.J defines the epigenetic landscape for driving the senescence programme in response to radiation-induced DNA damage. Deregulated H2A.J deposition affects chromatin remodeling, transcription factor recruitment, and the pro-inflammatory secretome. Our findings provide new mechanistic insights into DNA-damage triggered epigenetic mechanisms governing the biological processes of radiation-induced injury.
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Affiliation(s)
- Mutaz A. Abd Al-razaq
- Department of Radiation Oncology, Saarland University Medical Center, 66421 Homburg/Saar, Germany
| | - Benjamin M. Freyter
- Department of Radiation Oncology, Saarland University Medical Center, 66421 Homburg/Saar, Germany
| | - Anna Isermann
- Department of Radiation Oncology, Saarland University Medical Center, 66421 Homburg/Saar, Germany
| | - Gargi Tewary
- Department of Radiation Oncology, Saarland University Medical Center, 66421 Homburg/Saar, Germany
| | - Adèle Mangelinck
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Carl Mann
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Claudia E. Rübe
- Department of Radiation Oncology, Saarland University Medical Center, 66421 Homburg/Saar, Germany
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14
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Gaudreau-Lapierre A, Klonisch T, Nicolas H, Thanasupawat T, Trinkle-Mulcahy L, Hombach-Klonisch S. Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling. Int J Mol Sci 2023; 24:ijms24044246. [PMID: 36835656 PMCID: PMC9966875 DOI: 10.3390/ijms24044246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
The non-histone chromatin binding protein High Mobility Group AT-hook protein 2 (HMGA2) has important functions in chromatin remodeling, and genome maintenance and protection. Expression of HMGA2 is highest in embryonic stem cells, declines during cell differentiation and cell aging, but it is re-expressed in some cancers, where high HMGA2 expression frequently coincides with a poor prognosis. The nuclear functions of HMGA2 cannot be explained by binding to chromatin alone but involve complex interactions with other proteins that are incompletely understood. The present study used biotin proximity labeling, followed by proteomic analysis, to identify the nuclear interaction partners of HMGA2. We tested two different biotin ligase HMGA2 constructs (BioID2 and miniTurbo) with similar results, and identified known and new HMGA2 interaction partners, with functionalities mainly in chromatin biology. These HMGA2 biotin ligase fusion constructs offer exciting new possibilities for interactome discovery research, enabling the monitoring of nuclear HMGA2 interactomes during drug treatments.
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Affiliation(s)
- Antoine Gaudreau-Lapierre
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Research Institute in Oncology and Hematology (RIOH), CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hannah Nicolas
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Thatchawan Thanasupawat
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Correspondence: ; Tel.: +1-204-789-3982; Fax: +1-204-789-3920
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15
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En A, Watanabe K, Ayusawa D, Fujii M. The key role of a basic domain of histone H2B N-terminal tail in the action of 5-bromodeoxyuridine to induce cellular senescence. FEBS J 2023; 290:692-711. [PMID: 35882390 DOI: 10.1111/febs.16584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 06/28/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023]
Abstract
5-Bromodeoxyuridine (BrdU), a thymidine analogue, is an interesting reagent that modulates various biological phenomena. BrdU, upon incorporation into DNA, causes destabilized nucleosome positioning which leads to changes in heterochromatin organization and gene expression in cells. We have previously shown that BrdU effectively induces cellular senescence, a phenomenon of irreversible growth arrest in mammalian cells. Identification of the mechanism of action of BrdU would provide a novel insight into the molecular mechanisms of cellular senescence. Here, we showed that a basic domain in the histone H2B N-terminal tail, termed the HBR (histone H2B repression) domain, is involved in the action of BrdU. Notably, deletion of the HBR domain causes destabilized nucleosome positioning and derepression of gene expression, as does BrdU. We also showed that the genes up-regulated by BrdU significantly overlapped with those by deletion of the HBR domain, the result of which suggested that BrdU and deletion of the HBR domain act in a similar way. Furthermore, we showed that decreased HBR domain function induced cellular senescence or facilitated the induction of cellular senescence. These findings indicated that the HBR domain is crucially involved in the action of BrdU, and also suggested that disordered nucleosome organization may be involved in the induction of cellular senescence.
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Affiliation(s)
- Atsuki En
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Kazuaki Watanabe
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Dai Ayusawa
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Michihiko Fujii
- Graduate School of Nanobioscience, Yokohama City University, Japan
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16
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Abstract
Cellular senescence is implicated in a wide range of physiological and pathological conditions throughout an organism's entire lifetime. In particular, it has become evident that senescence plays a causative role in aging and age-associated disorders. This is not due simply to the loss of function of senescent cells. Instead, the substantial alterations of the cellular activities of senescent cells, especially the array of secretory factors, impact the surrounding tissues or even entire organisms. Such non-cell-autonomous functionality is largely coordinated by tissue-specific genes, constituting a cell fate-determining state. Senescence can be viewed as a gain-of-function phenotype or a process of cell identity shift. Cellular functionality or lineage-specific gene expression is tightly linked to the cell type-specific epigenetic landscape, reinforcing the heterogeneity of senescence across cell types. Here, we aim to define the senescence cellular functionality and epigenetic features that may contribute to the gain-of-function phenotype.
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Affiliation(s)
- Ioana Olan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom; ,
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom; ,
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17
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Sikder S, Arunkumar G, Melters DP, Dalal Y. Breaking the aging epigenetic barrier. Front Cell Dev Biol 2022; 10:943519. [PMID: 35966762 PMCID: PMC9366916 DOI: 10.3389/fcell.2022.943519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Aging is an inexorable event occurring universally for all organisms characterized by the progressive loss of cell function. However, less is known about the key events occurring inside the nucleus in the process of aging. The advent of chromosome capture techniques and extensive modern sequencing technologies have illuminated a rather dynamic structure of chromatin inside the nucleus. As cells advance along their life cycle, chromatin condensation states alter which leads to a different epigenetic landscape, correlated with modified gene expression. The exact factors mediating these changes in the chromatin structure and function remain elusive in the context of aging cells. The accumulation of DNA damage, reactive oxygen species and loss of genomic integrity as cells cease to divide can contribute to a tumor stimulating environment. In this review, we focus on genomic and epigenomic changes occurring in an aged cell which can contribute to age-related tumor formation.
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18
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Zheng X, Liu Z, Zhong J, Zhou L, Chen J, Zheng L, Li Z, Zhang R, Pan J, Wu Y, Liu Z, Kang T. Downregulation of HINFP induces senescence-associated secretory phenotype to promote metastasis in a non-cell-autonomous manner in bladder cancer. Oncogene 2022; 41:3587-3598. [PMID: 35668172 DOI: 10.1038/s41388-022-02371-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/09/2022]
Abstract
Transcription dysregulation is a salient characteristic of bladder cancer (BC), but no appropriate therapeutic target for it has been established. Here, we found that heterogeneous downregulation of histone H4 transcription factor (HINFP) was associated with senescence in BC tissues and that lower HINFP expression could predict an unfavorable outcome in BC patients. Knockout of HINFP transcriptionally inhibited H1F0 and H1FX to trigger DNA damage, consequently inducing cell senescence to repress the proliferation and growth of BC cells. However, the senescence-associated secretory phenotype, characterized by increases in MMP1/3, enhances the invasion and metastasis of non-senescent BC cells. Histone deacetylase inhibitors (HDACis) could efficiently eliminate the senescent cells induced by HINFP knockout to suppress the invasion and metastasis of BC cells. Our study suggests that HDACis, widely used in multiple cancer types in a clinical context, may also benefit BC patients with metastases induced by cell senescence.
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Affiliation(s)
- Xianchong Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zefu Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jianliang Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Liwen Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiawei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhiyong Li
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jingxuan Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Zhuowei Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
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19
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Tan SYX, Zhang J, Tee WW. Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer. Front Cell Dev Biol 2022; 10:931493. [PMID: 35757000 PMCID: PMC9213816 DOI: 10.3389/fcell.2022.931493] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Epigenetics comprise a diverse array of reversible and dynamic modifications to the cell’s genome without implicating any DNA sequence alterations. Both the external environment surrounding the organism, as well as the internal microenvironment of cells and tissues, contribute to these epigenetic processes that play critical roles in cell fate specification and organismal development. On the other hand, dysregulation of epigenetic activities can initiate and sustain carcinogenesis, which is often augmented by inflammation. Chronic inflammation, one of the major hallmarks of cancer, stems from proinflammatory cytokines that are secreted by tumor and tumor-associated cells in the tumor microenvironment. At the same time, inflammatory signaling can establish positive and negative feedback circuits with chromatin to modulate changes in the global epigenetic landscape. In this review, we provide an in-depth discussion of the interconnected crosstalk between epigenetics and inflammation, specifically how epigenetic mechanisms at different hierarchical levels of the genome control inflammatory gene transcription, which in turn enact changes within the cell’s epigenomic profile, especially in the context of inflammation-induced cancer.
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Affiliation(s)
- Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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20
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Wang X, Xu X, Mao G, Guo Y, Wang G, Sun X, Xu N, Zhang Z. Structural Characterization of Gracilariopsis lemaneiformis Polysaccharide and Its Property in Delaying Cellular Senescence. Front Nutr 2022; 9:876992. [PMID: 35651509 PMCID: PMC9149564 DOI: 10.3389/fnut.2022.876992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/19/2022] [Indexed: 01/10/2023] Open
Abstract
The sulfated polysaccharide was isolated from the purified G. lemaneiformis polysaccharide (PGP), and its property in delaying H2O2-induced 2BS cellular senescence was studied. The results showed that PGP was a linear polysaccharide containing alternating α-(1 → 3)- and β-(1 → 4)-galactopyranose units. Most of the sulfate groups are at C6 of the -(1 → 4)-α-D-Galp, and a small part of them are at C3 and C6. PGP pretreatment could decrease SA-β-gal-positive cells and prevent the formation of senescence-associated heterochromatic foci (SAHF) induced by H2O2 in a dose-dependent manner. It is speculated that PGP may delay aging by downregulating the expression of p21 and p53 genes. The finding provides new insights into the beneficial role of G. lemaneiformis polysaccharide (GP) on retarding senescence process.
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Affiliation(s)
- Xiaomei Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, China
| | - Xiaogang Xu
- Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou, China
| | - Genxiang Mao
- Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou, China
| | - Yue Guo
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, China
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xue Sun
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Key Laboratory of Aquacultural Biotechnology, Ministry of Education, Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Nianjun Xu
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Key Laboratory of Aquacultural Biotechnology, Ministry of Education, Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Zhongshan Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, China
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21
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Lejart A, Zentout S, Chapuis C, D'Augustin O, Smith R, Salbert G, Huet S. The N-terminal domain of TET1 promotes the formation of dense chromatin regions refractory to transcription. Chromosoma 2022; 131:47-58. [PMID: 35235010 DOI: 10.1007/s00412-022-00769-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/03/2022]
Abstract
TET (ten-eleven translocation) enzymes initiate active cytosine demethylation via the oxidation of 5-methylcytosine. TET1 is composed of a C-terminal domain, which bears the catalytic activity of the enzyme, and a N-terminal region that is less well characterized except for the CXXC domain responsible for the targeting to CpG islands. While cytosine demethylation induced by TET1 promotes transcription, this protein also interacts with chromatin-regulating factors that rather silence this process, the coordination between these two opposite functions of TET1 being unclear. In the present work, we uncover a new function of the N-terminal part of the TET1 protein in the regulation of the chromatin architecture. This domain of the protein promotes the establishment of a compact chromatin architecture displaying reduced exchange rate of core histones and partial dissociation of the histone linker. This chromatin reorganization process, which does not rely on the CXXC domain, is associated with a global shutdown of transcription and an increase in heterochromatin-associated histone epigenetic marks. Based on these findings, we propose that the dense chromatin organization generated by the N-terminal domain of TET1 could contribute to restraining the transcription enhancement induced by the DNA demethylation activity of this enzyme.
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Affiliation(s)
- Audrey Lejart
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Ostiane D'Augustin
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 92265, Fontenay-aux-Roses, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Gilles Salbert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France.
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France.
- Institut Universitaire de France, Paris, France.
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22
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Crouch J, Shvedova M, Thanapaul RJRS, Botchkarev V, Roh D. Epigenetic Regulation of Cellular Senescence. Cells 2022; 11:672. [PMID: 35203320 PMCID: PMC8870565 DOI: 10.3390/cells11040672] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Senescence is a complex cellular stress response that abolishes proliferative capacity and generates a unique secretory pattern that is implicated in organismal aging and age-related disease. How a cell transitions to a senescent state is multifactorial and often requires transcriptional regulation of multiple genes. Epigenetic alterations to DNA and chromatin are powerful regulators of genome architecture and gene expression, and they play a crucial role in mediating the induction and maintenance of senescence. This review will highlight the changes in chromatin, DNA methylation, and histone alterations that establish and maintain cellular senescence, alongside the specific epigenetic regulation of the senescence-associated secretory phenotype (SASP).
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Affiliation(s)
- Jack Crouch
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Maria Shvedova
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Rex Jeya Rajkumar Samdavid Thanapaul
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Vladimir Botchkarev
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Daniel Roh
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
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23
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Lynch SM, Guo G, Gibson DS, Bjourson AJ, Rai TS. Role of Senescence and Aging in SARS-CoV-2 Infection and COVID-19 Disease. Cells 2021; 10:3367. [PMID: 34943875 PMCID: PMC8699414 DOI: 10.3390/cells10123367] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a global pandemic associated with substantial morbidity and mortality worldwide, with particular risk for severe disease and mortality in the elderly population. SARS-CoV-2 infection is driven by a pathological hyperinflammatory response which results in a dysregulated immune response. Current advancements in aging research indicates that aging pathways have fundamental roles in dictating healthspan in addition to lifespan. Our review discusses the aging immune system and highlights that senescence and aging together, play a central role in COVID-19 pathogenesis. In our review, we primarily focus on the immune system response to SARS-CoV-2 infection, the interconnection between severe COVID-19, immunosenescence, aging, vaccination, and the emerging problem of Long-COVID. We hope to highlight the importance of identifying specific senescent endotypes (or "sendotypes"), which can used as determinants of COVID-19 severity and mortality. Indeed, identified sendotypes could be therapeutically exploited for therapeutic intervention. We highlight that senolytics, which eliminate senescent cells, can target aging-associated pathways and therefore are proving attractive as potential therapeutic options to alleviate symptoms, prevent severe infection, and reduce mortality burden in COVID-19 and thus ultimately enhance healthspan.
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Affiliation(s)
| | | | | | | | - Taranjit Singh Rai
- Northern Ireland Centre for Stratified Medicine, School of Biomedical Sciences, Ulster University, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry BT47 6SB, UK; (S.M.L.); (G.G.); (D.S.G.); (A.J.B.)
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24
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Lund PJ, Lopes M, Sidoli S, Coradin M, Vitorino FNDL, da Cunha JPC, Garcia BA. FGF-2 induces a failure of cell cycle progression in cells harboring amplified K-Ras, revealing new insights into oncogene-induced senescence. Mol Omics 2021; 17:725-739. [PMID: 34636387 PMCID: PMC8511509 DOI: 10.1039/d1mo00019e] [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] [Indexed: 11/21/2022]
Abstract
Paradoxically, oncogenes that drive cell cycle progression may also trigger pathways leading to senescence, thereby inhibiting the growth of tumorigenic cells. Knowledge of how these pathways operate, and how tumor cells may evade these pathways, is important for understanding tumorigenesis. The Y1 cell line, which harbors an amplification of the proto-oncogene Ras, rapidly senesces in response to the mitogen fibroblast growth factor-2 (FGF-2). To gain a more complete picture of how FGF-2 promotes senescence, we employed a multi-omics approach to analyze histone modifications, mRNA and protein expression, and protein phosphorylation in Y1 cells treated with FGF-2. Compared to control cells treated with serum alone, FGF-2 caused a delayed accumulation of acetylation on histone H4 and higher levels of H3K27me3. Sequencing analysis revealed decreased expression of cell cycle-related genes with concomitant loss of H3K27ac. At the same time, FGF-2 promoted the expression of p21, various cytokines, and MAPK-related genes. Nuclear envelope proteins, particularly lamin B1, displayed increased phosphorylation in response to FGF-2. Proteome analysis suggested alterations in cellular metabolism, as evident by modulated expression of enzymes involved in purine biosynthesis, tRNA aminoacylation, and the TCA cycle. We propose that Y1 cells senesce due to an inability to progress through the cell cycle, which may stem from DNA damage or TGFb signaling. Altogether, the phenotype of Y1 cells is consistent with rapidly established oncogene-induced senescence, demonstrating the synergy between growth factors and oncogenes in driving senescence and bringing additional insight into this tumor suppressor mechanism.
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Affiliation(s)
- Peder J Lund
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Mariana Lopes
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Mariel Coradin
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Francisca Nathália de Luna Vitorino
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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25
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Sams E. Oligodendrocytes in the aging brain. Neuronal Signal 2021; 5:NS20210008. [PMID: 34290887 PMCID: PMC8264650 DOI: 10.1042/ns20210008] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/22/2022] Open
Abstract
More than half of the human brain volume is made up of white matter: regions where axons are coated in myelin, which primarily functions to increase the conduction speed of axon potentials. White matter volume significantly decreases with age, correlating with cognitive decline. Much research in the field of non-pathological brain aging mechanisms has taken a neuron-centric approach, with relatively little attention paid to other neural cells. This review discusses white matter changes, with focus on oligodendrocyte lineage cells and their ability to produce and maintain myelin to support normal brain homoeostasis. Improved understanding of intrinsic cellular changes, general senescence mechanisms, intercellular interactions and alterations in extracellular environment which occur with aging and impact oligodendrocyte cells is paramount. This may lead to strategies to support oligodendrocytes in aging, for example by supporting myelin synthesis, protecting against oxidative stress and promoting the rejuvenation of the intrinsic regenerative potential of progenitor cells. Ultimately, this will enable the protection of white matter integrity thus protecting cognitive function into the later years of life.
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Affiliation(s)
- Eleanor Catherine Sams
- Blizard Institute, Barts and The London School of Medicine and Dentistry Centre for Neuroscience, Surgery and Trauma, Blizard Institute, 4 Newark Street, Whitechapel E1 2AT, London
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26
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Mechanisms of Ataxia Telangiectasia Mutated (ATM) Control in the DNA Damage Response to Oxidative Stress, Epigenetic Regulation, and Persistent Innate Immune Suppression Following Sepsis. Antioxidants (Basel) 2021; 10:antiox10071146. [PMID: 34356379 PMCID: PMC8301080 DOI: 10.3390/antiox10071146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
Cells have evolved extensive signaling mechanisms to maintain redox homeostasis. While basal levels of oxidants are critical for normal signaling, a tipping point is reached when the level of oxidant species exceed cellular antioxidant capabilities. Myriad pathological conditions are characterized by elevated oxidative stress, which can cause alterations in cellular operations and damage to cellular components including nucleic acids. Maintenance of nuclear chromatin are critically important for host survival and eukaryotic organisms possess an elaborately orchestrated response to initiate repair of such DNA damage. Recent evidence indicates links between the cellular antioxidant response, the DNA damage response (DDR), and the epigenetic status of the cell under conditions of elevated oxidative stress. In this emerging model, the cellular response to excessive oxidants may include redox sensors that regulate both the DDR and an orchestrated change to the epigenome in a tightly controlled program that both protects and regulates the nuclear genome. Herein we use sepsis as a model of an inflammatory pathophysiological condition that results in elevated oxidative stress, upregulation of the DDR, and epigenetic reprogramming of hematopoietic stem cells (HSCs) to discuss new evidence for interplay between the antioxidant response, the DNA damage response, and epigenetic status.
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27
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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28
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Changes in Chromatin Organization Eradicate Cellular Stress Resilience to UVA/B Light and Induce Premature Aging. Cells 2021; 10:cells10071755. [PMID: 34359924 PMCID: PMC8304177 DOI: 10.3390/cells10071755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/10/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Complex interactions among DNA and nuclear proteins maintain genome organization and stability. The nuclear proteins, particularly the histones, organize, compact, and preserve the stability of DNA, but also allow its dynamic reorganization whenever the nuclear processes require access to it. Five histone classes exist and they are evolutionarily conserved among eukaryotes. The linker histones are the fifth class and over time, their role in chromatin has been neglected. Linker histones interact with DNA and the other histones and thus sustain genome stability and nuclear organization. Saccharomyces cerevisiae is a brilliant model for studying linker histones as the gene for it is a single-copy and is non-essential. We, therefore, created a linker histone-free yeast strain using a knockout of the relevant gene and traced the way cells age chronologically. Here we present our results demonstrating that the altered chromatin dynamics during the chronological lifespan of the yeast cells with a mutation in ARP4 (the actin-related protein 4) and without the gene HHO1 for the linker histone leads to strong alterations in the gene expression profiles of a subset of genes involved in DNA repair and autophagy. The obtained results further prove that the yeast mutants have reduced survival upon UVA/B irradiation possibly due to the accelerated decompaction of chromatin and impaired proliferation. Our hypothesis posits that the higher-order chromatin structure and the interactions among chromatin proteins are crucial for the maintenance of chromatin organization during chronological aging under optimal and UVA-B stress conditions.
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29
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Di Giorgio E, Paluvai H, Dalla E, Ranzino L, Renzini A, Moresi V, Minisini M, Picco R, Brancolini C. HDAC4 degradation during senescence unleashes an epigenetic program driven by AP-1/p300 at selected enhancers and super-enhancers. Genome Biol 2021; 22:129. [PMID: 33966634 PMCID: PMC8108360 DOI: 10.1186/s13059-021-02340-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/06/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cellular senescence is a permanent state of replicative arrest defined by a specific pattern of gene expression. The epigenome in senescent cells is sculptured in order to sustain the new transcriptional requirements, particularly at enhancers and super-enhancers. How these distal regulatory elements are dynamically modulated is not completely defined. RESULTS Enhancer regions are defined by the presence of H3K27 acetylation marks, which can be modulated by class IIa HDACs, as part of multi-protein complexes. Here, we explore the regulation of class IIa HDACs in different models of senescence. We find that HDAC4 is polyubiquitylated and degraded during all types of senescence and it selectively binds and monitors H3K27ac levels at specific enhancers and super-enhancers that supervise the senescent transcriptome. Frequently, these HDAC4-modulated elements are also monitored by AP-1/p300. The deletion of HDAC4 in transformed cells which have bypassed oncogene-induced senescence is coupled to the re-appearance of senescence and the execution of the AP-1/p300 epigenetic program. CONCLUSIONS Overall, our manuscript highlights a role of HDAC4 as an epigenetic reader and controller of enhancers and super-enhancers that supervise the senescence program. More generally, we unveil an epigenetic checkpoint that has important consequences in aging and cancer.
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Affiliation(s)
- Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | | | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Liliana Ranzino
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Alessandra Renzini
- DAHFMO Unit of Histology and Medical Embryology, Sapienza University of Rome, via Antonio Scarpa 16, 00161, Rome, Italy
| | - Viviana Moresi
- DAHFMO Unit of Histology and Medical Embryology, Sapienza University of Rome, via Antonio Scarpa 16, 00161, Rome, Italy
| | - Martina Minisini
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Raffaella Picco
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy.
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30
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Pathak RU, Soujanya M, Mishra RK. Deterioration of nuclear morphology and architecture: A hallmark of senescence and aging. Ageing Res Rev 2021; 67:101264. [PMID: 33540043 DOI: 10.1016/j.arr.2021.101264] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/04/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
The metazoan nucleus is a highly structured organelle containing several well-defined sub-organelles. It is the largest organelle inside a cell taking up from one tenth to half of entire cell volume. This makes it one of the easiest organelles to identify and study under the microscope. Abnormalities in the nuclear morphology and architecture are commonly observed in an aged and senescent cell. For example, the nuclei enlarge, loose their shape, appear lobulated, harbour nuclear membrane invaginations, carry enlarged/fragmented nucleolus, loose heterochromatin, etc. In this review we discuss about the age-related changes in nuclear features and elaborate upon the molecular reasons driving the change. Many of these changes can be easily imaged under a microscope and analysed in silico. Thus, computational image analysis of nuclear features appears to be a promising tool to evaluate physiological age of a cell and offers to be a legitimate biomarker. It can be used to examine progression of age-related diseases and evaluate therapies.
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Affiliation(s)
| | - Mamilla Soujanya
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India
| | - Rakesh Kumar Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India.
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31
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Kumari R, Jat P. Mechanisms of Cellular Senescence: Cell Cycle Arrest and Senescence Associated Secretory Phenotype. Front Cell Dev Biol 2021; 9:645593. [PMID: 33855023 PMCID: PMC8039141 DOI: 10.3389/fcell.2021.645593] [Citation(s) in RCA: 603] [Impact Index Per Article: 201.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a stable cell cycle arrest that can be triggered in normal cells in response to various intrinsic and extrinsic stimuli, as well as developmental signals. Senescence is considered to be a highly dynamic, multi-step process, during which the properties of senescent cells continuously evolve and diversify in a context dependent manner. It is associated with multiple cellular and molecular changes and distinct phenotypic alterations, including a stable proliferation arrest unresponsive to mitogenic stimuli. Senescent cells remain viable, have alterations in metabolic activity and undergo dramatic changes in gene expression and develop a complex senescence-associated secretory phenotype. Cellular senescence can compromise tissue repair and regeneration, thereby contributing toward aging. Removal of senescent cells can attenuate age-related tissue dysfunction and extend health span. Senescence can also act as a potent anti-tumor mechanism, by preventing proliferation of potentially cancerous cells. It is a cellular program which acts as a double-edged sword, with both beneficial and detrimental effects on the health of the organism, and considered to be an example of evolutionary antagonistic pleiotropy. Activation of the p53/p21WAF1/CIP1 and p16INK4A/pRB tumor suppressor pathways play a central role in regulating senescence. Several other pathways have recently been implicated in mediating senescence and the senescent phenotype. Herein we review the molecular mechanisms that underlie cellular senescence and the senescence associated growth arrest with a particular focus on why cells stop dividing, the stability of the growth arrest, the hypersecretory phenotype and how the different pathways are all integrated.
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Affiliation(s)
- Ruchi Kumari
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, United Kingdom
| | - Parmjit Jat
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, United Kingdom
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32
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Rocha A, Dalgarno A, Neretti N. The functional impact of nuclear reorganization in cellular senescence. Brief Funct Genomics 2021; 21:24-34. [PMID: 33755107 PMCID: PMC8789270 DOI: 10.1093/bfgp/elab012] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is the irreversible cell cycle arrest in response to DNA damage. Because senescent cells accumulate with age and contribute to chronic inflammation, they are promising therapeutic targets for healthspan extension. The senescent phenotype can vary depending on cell type and on the specific insults that induce senescence. This variability is also reflected in the extensive remodeling of the genome organization within the nucleus of senescent cells. Here, we give an overview of the nuclear changes that occur in different forms of senescence, including changes to chromatin state and composition and to the three-dimensional organization of the genome, as well as alterations to the nuclear envelope and to the accessibility of repetitive genomic regions. Many of these changes are shared across all forms of senescence, implicating nuclear organization as a fundamental driver of the senescent state and of how senescent cells interact with the surrounding tissue.
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Affiliation(s)
- Azucena Rocha
- Molecular Biology, Cell Biology and Biochemistry program at Brown University
| | - Audrey Dalgarno
- Molecular Biology, Cell Biology and Biochemistry program at Brown University
| | - Nicola Neretti
- Associate Professor in the Department of Molecular Biology, Cell Biology and Biochemistry at Brown University
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33
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Stabell M, Sæther T, Røhr ÅK, Gabrielsen OS, Myklebost O. Methylation-dependent SUMOylation of the architectural transcription factor HMGA2. Biochem Biophys Res Commun 2021; 552:91-97. [PMID: 33744765 DOI: 10.1016/j.bbrc.2021.02.099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/19/2021] [Indexed: 11/26/2022]
Abstract
High mobility group A2 (HMGA2) is a chromatin-associated protein involved in the regulation of stem cell function, embryogenesis and cancer development. Although the protein does not contain a consensus SUMOylation site, it is shown to be SUMOylated. In this study, we demonstrate that the first lysine residue in the reported K66KAE SUMOylation motif in HMGA2 can be methylated in vitro and in vivo by the Set7/9 methyltransferase. By editing the lysine, the increased hydrophobicity of the resulting 6-N-methyl-lysine transforms the sequence into a consensus SUMO motif. This post-translational editing dramatically increases the subsequent SUMOylation of this site. Furthermore, similar putative methylation-dependent SUMO motifs are found in a number of other chromatin factors, and we confirm methylation-dependent SUMOylation of a site in one such protein, the Polyhomeotic complex 1 homolog (PHC1). Together, these results suggest that crosstalk between methylation and SUMOylation is a general mode for regulation of chromatin function.
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Affiliation(s)
- Marianne Stabell
- Department of Tumor Biology, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, PO Box 4953 Nydalen, N-0424, Oslo, Norway; Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Thomas Sæther
- Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Åsmund K Røhr
- Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Odd S Gabrielsen
- Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, PO Box 4953 Nydalen, N-0424, Oslo, Norway; Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway.
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34
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Sławińska N, Krupa R. Molecular Aspects of Senescence and Organismal Ageing-DNA Damage Response, Telomeres, Inflammation and Chromatin. Int J Mol Sci 2021; 22:ijms22020590. [PMID: 33435578 PMCID: PMC7827783 DOI: 10.3390/ijms22020590] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 02/07/2023] Open
Abstract
Cells can become senescent in response to stress. Senescence is a process characterised by a stable proliferative arrest. Sometimes it can be beneficial—for example, it can suppress tumour development or take part in tissue repair. On the other hand, studies show that it is also involved in the ageing process. DNA damage response (DDR) is triggered by DNA damage or telomere shortening during cell division. When left unresolved, it may lead to the activation of senescence. Senescent cells secrete certain proteins in larger quantities. This phenomenon is referred to as senescence-associated secretory phenotype (SASP). SASP can induce senescence in other cells; evidence suggests that overabundance of senescent cells contributes to ageing. SASP proteins include proinflammatory cytokines and metalloproteinases, which degrade the extracellular matrix. Shortening of telomeres is another feature associated with organismal ageing. Older organisms have shorter telomeres. Restoring telomerase activity in mice not only slowed but also partially reversed the symptoms of ageing. Changes in chromatin structure during senescence include heterochromatin formation or decondensation and loss of H1 histones. During organismal ageing, cells can experience heterochromatin loss, DNA demethylation and global histone loss. Cellular and organismal ageing are both complex processes with many aspects that are often related. The purpose of this review is to bring some of these aspects forward and provide details regarding them.
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35
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Corpet A, Kleijwegt C, Roubille S, Juillard F, Jacquet K, Texier P, Lomonte P. PML nuclear bodies and chromatin dynamics: catch me if you can! Nucleic Acids Res 2020; 48:11890-11912. [PMID: 33068409 PMCID: PMC7708061 DOI: 10.1093/nar/gkaa828] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic cells compartmentalize their internal milieu in order to achieve specific reactions in time and space. This organization in distinct compartments is essential to allow subcellular processing of regulatory signals and generate specific cellular responses. In the nucleus, genetic information is packaged in the form of chromatin, an organized and repeated nucleoprotein structure that is a source of epigenetic information. In addition, cells organize the distribution of macromolecules via various membrane-less nuclear organelles, which have gathered considerable attention in the last few years. The macromolecular multiprotein complexes known as Promyelocytic Leukemia Nuclear Bodies (PML NBs) are an archetype for nuclear membrane-less organelles. Chromatin interactions with nuclear bodies are important to regulate genome function. In this review, we will focus on the dynamic interplay between PML NBs and chromatin. We report how the structure and formation of PML NBs, which may involve phase separation mechanisms, might impact their functions in the regulation of chromatin dynamics. In particular, we will discuss how PML NBs participate in the chromatinization of viral genomes, as well as in the control of specific cellular chromatin assembly pathways which govern physiological mechanisms such as senescence or telomere maintenance.
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Affiliation(s)
- Armelle Corpet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Constance Kleijwegt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Simon Roubille
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Franceline Juillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Karine Jacquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Pascale Texier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
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36
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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Martins F, Sousa J, Pereira CD, Cruz e Silva OAB, Rebelo S. Nuclear envelope dysfunction and its contribution to the aging process. Aging Cell 2020; 19:e13143. [PMID: 32291910 PMCID: PMC7253059 DOI: 10.1111/acel.13143] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022] Open
Abstract
The nuclear envelope (NE) is the central organizing unit of the eukaryotic cell serving as a genome protective barrier and mechanotransduction interface between the cytoplasm and the nucleus. The NE is mainly composed of a nuclear lamina and a double membrane connected at specific points where the nuclear pore complexes (NPCs) form. Physiological aging might be generically defined as a functional decline across lifespan observed from the cellular to organismal level. Therefore, during aging and premature aging, several cellular alterations occur, including nuclear‐specific changes, particularly, altered nuclear transport, increased genomic instability induced by DNA damage, and telomere attrition. Here, we highlight and discuss proteins associated with nuclear transport dysfunction induced by aging, particularly nucleoporins, nuclear transport factors, and lamins. Moreover, changes in the structure of chromatin and consequent heterochromatin rearrangement upon aging are discussed. These alterations correlate with NE dysfunction, particularly lamins’ alterations. Finally, telomere attrition is addressed and correlated with altered levels of nuclear lamins and nuclear lamina‐associated proteins. Overall, the identification of molecular mechanisms underlying NE dysfunction, including upstream and downstream events, which have yet to be unraveled, will be determinant not only to our understanding of several pathologies, but as here discussed, in the aging process.
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Affiliation(s)
- Filipa Martins
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Jéssica Sousa
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Cátia D. Pereira
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Odete A. B. Cruz e Silva
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
- The Discoveries CTR Aveiro Portugal
| | - Sandra Rebelo
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
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38
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Blanco-Luquin I, Acha B, Urdánoz-Casado A, Sánchez-Ruiz De Gordoa J, Vicuña-Urriza J, Roldán M, Labarga A, Zelaya MV, Cabello C, Méndez-López I, Mendioroz M. Early epigenetic changes of Alzheimer's disease in the human hippocampus. Epigenetics 2020; 15:1083-1092. [PMID: 32233750 DOI: 10.1080/15592294.2020.1748917] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The discovery of new biomarkers would be very valuable to improve the detection of early Alzheimer's disease (AD). DNA methylation marks may serve as epigenetic biomarkers of early AD. Here we identified epigenetic marks that are present in the human hippocampus from the earliest stages of AD. A previous methylome dataset of the human AD hippocampus was used to select a set of eight differentially methylated positions (DMPs) since early AD stages. Next, bisulphite pyrosequencing was performed in an expanded homogeneous cohort of 18 pure controls and 35 hippocampal samples with neuropathological changes of pure AD. Correlation between DNA methylation levels in DMPs and phospho-tau protein burden assessed by immunohistochemistry in the hippocampus was also determined. We found four DMPs showing higher levels of DNA methylation at early AD stages compared to controls, involving ELOVL2, GIT1/TP53I13 and the histone gene locus at chromosome 6. DNA methylation levels assessed by bisulphite pyrosequencing correlated with phospho-tau protein burden for ELOVL2 and HIST1H3E/HIST1H3 F genes. In this discovery study, a set of four epigenetic marks of early AD stages have been identified in the human hippocampus. It would be worth studying in-depth the specific pathways related to these epigenetic marks. These early alterations in DNA methylation in the AD hippocampus could be regarded as candidate biomarkers to be explored in future translational studies. ABBREVIATIONS AD: Alzheimer's disease; DMPs: Differentially methylated positions; CSF: Cerebrospinal fluid; βA42: β-amyloid 42; PET: positron emission tomography; 5mC: 5-methyl cytosine; CpG: cytosine-guanine dinucleotides; ANK1: ankyrin-1; BIN1: amphiphysin II; p-tau: hyperphosphorylated tau; CERAD: Consortium to Establish A Registry for Alzheimer's Disease; SD: standard deviation; ANOVA: one-way analysis of variance; VLCFAs: very long-chain fatty acids; DHA: docosahexaenoic acid; mTOR: mechanistic target of rapamycin.
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Affiliation(s)
- Idoia Blanco-Luquin
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario De Navarra, Universidad Pública De Navarra (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - Blanca Acha
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario De Navarra, Universidad Pública De Navarra (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - Amaya Urdánoz-Casado
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario De Navarra, Universidad Pública De Navarra (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - Javier Sánchez-Ruiz De Gordoa
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario De Navarra, Universidad Pública De Navarra (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain.,Department of Neurology, Complejo Hospitalario De Navarra- IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - Janire Vicuña-Urriza
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario De Navarra, Universidad Pública De Navarra (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - Miren Roldán
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario De Navarra, Universidad Pública De Navarra (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - Alberto Labarga
- Bioinformatics Unit, Navarrabiomed, Public University of Navarre (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - María Victoria Zelaya
- Department of Pathology, Complejo Hospitalario De Navarra- IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - Carolina Cabello
- Department of Neurology, Complejo Hospitalario De Navarra- IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
| | - Iván Méndez-López
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario De Navarra, Universidad Pública De Navarra (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain.,Department of Internal Medicine, Hospital García-Orcoyen , Estella, Spain
| | - Maite Mendioroz
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario De Navarra, Universidad Pública De Navarra (UPNA), IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain.,Department of Neurology, Complejo Hospitalario De Navarra- IdiSNA (Navarra Institute for Health Research) , Pamplona, Spain
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39
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Paluvai H, Di Giorgio E, Brancolini C. The Histone Code of Senescence. Cells 2020; 9:cells9020466. [PMID: 32085582 PMCID: PMC7072776 DOI: 10.3390/cells9020466] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Senescence is the end point of a complex cellular response that proceeds through a set of highly regulated steps. Initially, the permanent cell-cycle arrest that characterizes senescence is a pro-survival response to irreparable DNA damage. The maintenance of this prolonged condition requires the adaptation of the cells to an unfavorable, demanding and stressful microenvironment. This adaptation is orchestrated through a deep epigenetic resetting. A first wave of epigenetic changes builds a dam on irreparable DNA damage and sustains the pro-survival response and the cell-cycle arrest. Later on, a second wave of epigenetic modifications allows the genomic reorganization to sustain the transcription of pro-inflammatory genes. The balanced epigenetic dynamism of senescent cells influences physiological processes, such as differentiation, embryogenesis and aging, while its alteration leads to cancer, neurodegeneration and premature aging. Here we provide an overview of the most relevant histone modifications, which characterize senescence, aging and the activation of a prolonged DNA damage response.
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40
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Casella G, Munk R, Kim KM, Piao Y, De S, Abdelmohsen K, Gorospe M. Transcriptome signature of cellular senescence. Nucleic Acids Res 2019; 47:7294-7305. [PMID: 31251810 DOI: 10.1093/nar/gkz555] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023] Open
Abstract
Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage and signaling from activated oncogenes. At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated protein expression and secretion, DNA damage and β-galactosidase activity; unfortunately, these traits are neither exclusively nor universally present in senescent cells. To identify robust shared markers of senescence, we have performed RNA-sequencing analysis across eight diverse models of senescence triggered in human diploid fibroblasts (WI-38, IMR-90) and endothelial cells (HUVEC, HAEC) by replicative exhaustion, exposure to ionizing radiation or doxorubicin, and expression of the oncogene HRASG12V. The intersection of the altered transcriptomes revealed 50 RNAs consistently elevated and 18 RNAs consistently reduced across all senescence models, including many protein-coding mRNAs and some non-coding RNAs. We propose that these shared transcriptome profiles will enable the identification of senescent cells in vivo, the investigation of their roles in aging and malignancy and the development of strategies to target senescent cells therapeutically.
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Affiliation(s)
- Gabriel Casella
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, Maryland 21224, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, Maryland 21224, USA
| | - Kyoung Mi Kim
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, Maryland 21224, USA
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, Maryland 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, Maryland 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, Maryland 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, Baltimore, Maryland 21224, USA
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41
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Gorgoulis V, Adams PD, Alimonti A, Bennett DC, Bischof O, Bishop C, Campisi J, Collado M, Evangelou K, Ferbeyre G, Gil J, Hara E, Krizhanovsky V, Jurk D, Maier AB, Narita M, Niedernhofer L, Passos JF, Robbins PD, Schmitt CA, Sedivy J, Vougas K, von Zglinicki T, Zhou D, Serrano M, Demaria M. Cellular Senescence: Defining a Path Forward. Cell 2019; 179:813-827. [PMID: 31675495 DOI: 10.1016/j.cell.2019.10.005] [Citation(s) in RCA: 1461] [Impact Index Per Article: 292.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/20/2019] [Accepted: 10/03/2019] [Indexed: 01/10/2023]
Abstract
Cellular senescence is a cell state implicated in various physiological processes and a wide spectrum of age-related diseases. Recently, interest in therapeutically targeting senescence to improve healthy aging and age-related disease, otherwise known as senotherapy, has been growing rapidly. Thus, the accurate detection of senescent cells, especially in vivo, is essential. Here, we present a consensus from the International Cell Senescence Association (ICSA), defining and discussing key cellular and molecular features of senescence and offering recommendations on how to use them as biomarkers. We also present a resource tool to facilitate the identification of genes linked with senescence, SeneQuest (available at http://Senequest.net). Lastly, we propose an algorithm to accurately assess and quantify senescence, both in cultured cells and in vivo.
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Affiliation(s)
- Vassilis Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Biomedical Research Foundation, Academy of Athens, Athens, Greece; Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - Peter D Adams
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK; CRUK Beatson Institute, Glasgow G61 1BD, UK; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrea Alimonti
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland, Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, Lugano, Switzerland; Department of Medicine, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine, Padova, Italy
| | - Dorothy C Bennett
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London SW17 0RE, UK
| | - Oliver Bischof
- Laboratory of Nuclear Organization and Oncogenesis, Department of Cell Biology and Infection, Inserm U993, Institute Pasteur, Paris, France
| | - Cleo Bishop
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St, London E1 2AT, UK
| | | | - Manuel Collado
- Health Research Institute of Santiago de Compostela (IDIS), Clinical University Hospital (CHUS), Santiago de Compostela, Spain
| | - Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Gerardo Ferbeyre
- Faculty of Medicine, Department of Biochemistry, Université de Montréal and CRCHUM, Montreal, QC, Canada
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Eiji Hara
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Valery Krizhanovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Jurk
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Andrea B Maier
- Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Amsterdam Movement Sciences, Vrije Universiteit, Amsterdam, the Netherlands; Department of Medicine and Aged Care, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Laura Niedernhofer
- Institute on the Biology of Aging and Metabolism, University of Minnesota, MN, USA
| | - João F Passos
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Paul D Robbins
- Institute on the Biology of Aging and Metabolism, University of Minnesota, MN, USA
| | - Clemens A Schmitt
- Charité - University Medical Center, Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Kepler University Hospital, Department of Hematology and Oncology, Johannes Kepler University, Linz, Austria
| | - John Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, and Center for the Biology of Aging, Brown University, Providence, RI, USA
| | | | - Thomas von Zglinicki
- Newcastle University Institute for Ageing, Institute for Cell and Molecular Biology, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Manuel Serrano
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Marco Demaria
- University of Groningen (RUG), European Research Institute for the Biology of Aging (ERIBA), University Medical Center Groningen (UMCG), Groningen, the Netherlands.
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42
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Pack LR, Daigh LH, Meyer T. Putting the brakes on the cell cycle: mechanisms of cellular growth arrest. Curr Opin Cell Biol 2019; 60:106-113. [PMID: 31252282 PMCID: PMC7187785 DOI: 10.1016/j.ceb.2019.05.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/15/2019] [Accepted: 05/18/2019] [Indexed: 02/06/2023]
Abstract
Precise regulation of cellular proliferation is critical to tissue homeostasis and development, but misregulation leads to diseases of excess proliferation or cell loss. To achieve precise control, cells utilize distinct mechanisms of growth arrest such as quiescence and senescence. The decision to enter these growth-arrested states or proliferate is mediated by the core cell-cycle machinery that responds to diverse external and internal signals. Recent advances have revealed the molecular underpinnings of these cell-cycle decisions, highlighting the unique nature of cell-cycle entry from quiescence, identifying endogenous DNA damage as a quiescence-inducing signal, and establishing how persistent arrest is achieved in senescence.
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Affiliation(s)
- Lindsey R Pack
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leighton H Daigh
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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43
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Tümpel S, Rudolph KL. Quiescence: Good and Bad of Stem Cell Aging. Trends Cell Biol 2019; 29:672-685. [PMID: 31248787 DOI: 10.1016/j.tcb.2019.05.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 12/25/2022]
Abstract
Stem cells are required for lifelong homeostasis and regeneration of tissues and organs in mammals, but the function of stem cells declines during aging. To preserve stem cells during life, they are kept in a quiescent state with low metabolic and low proliferative activity. However, activation of quiescent stem cells - an essential process for organ homeostasis/regeneration - requires concerted and faithful regulation of multiple molecular circuits controlling biosynthetic processes, repair mechanisms, and metabolic activity. Thus, while protecting stem cell maintenance, quiescence comes at the cost of vulnerability during the process of stem cell activation. Here we discuss molecular and biochemical processes regulating stem cells' maintenance in and exit from quiescence and how age-related failures of these circuits can contribute to organism aging.
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Affiliation(s)
- Stefan Tümpel
- Research Group on Stem Cell Aging, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany
| | - K Lenhard Rudolph
- Research Group on Stem Cell Aging, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany.
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44
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Pignolo RJ, Samsonraj RM, Law SF, Wang H, Chandra A. Targeting Cell Senescence for the Treatment of Age-Related Bone Loss. Curr Osteoporos Rep 2019; 17:70-85. [PMID: 30806947 DOI: 10.1007/s11914-019-00504-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We review cell senescence in the context of age-related bone loss by broadly discussing aging mechanisms in bone, currently known inducers and markers of senescence, the senescence-associated secretory phenotype (SASP), and the emerging roles of senescence in bone homeostasis and pathology. RECENT FINDINGS Cellular senescence is a state of irreversible cell cycle arrest induced by insults or stressors including telomere attrition, oxidative stress, DNA damage, oncogene activation, and other intrinsic or extrinsic triggers and there is mounting evidence for the role of senescence in aging bone. Cellular aging also instigates a SASP that exerts detrimental paracrine and likely systemic effects. With aging, multiple cell types in the bone microenvironment become senescent, with osteocytes and myeloid cells as primary contributors to the SASP. Targeting undesired senescent cells may be a favorable strategy to promote bone anabolic and anti-resorptive functions in aging bone, with the possibility of improving bone quality and function with normal aging and/or disease.
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Affiliation(s)
- Robert J Pignolo
- Department of Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.
- Division of Geriatric Medicine & Gerontology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA.
| | | | - Susan F Law
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Haitao Wang
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Division of Geriatric Medicine & Gerontology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Abhishek Chandra
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Division of Geriatric Medicine & Gerontology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
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45
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Abstract
Originally thought of as a stress response end point, the view of cellular senescence has since evolved into one encompassing a wide range of physiological and pathological functions, including both protumorignic and antitumorigenic features. It has also become evident that senescence is a highly dynamic and heterogenous process. Efforts to reconcile the beneficial and detrimental features of senescence suggest that physiological functions require the transient presence of senescent cells in the tissue microenvironment. Here, we propose the concept of a physiological "senescence life cycle," which has pathological consequences if not executed in its entirety.
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Affiliation(s)
- Adelyne Sue Li Chan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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46
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Xia X, Jiang Q, McDermott J, Han JDJ. Aging and Alzheimer's disease: Comparison and associations from molecular to system level. Aging Cell 2018; 17:e12802. [PMID: 29963744 PMCID: PMC6156542 DOI: 10.1111/acel.12802] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/15/2018] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease is the most prevalent cause of dementia, which is defined by the combined presence of amyloid and tau, but researchers are gradually moving away from the simple assumption of linear causality proposed by the original amyloid hypothesis. Aging is the main risk factor for Alzheimer's disease that cannot be explained by amyloid hypothesis. To evaluate how aging and Alzheimer's disease are intrinsically interwoven with each other, we review and summarize evidence from molecular, cellular, and system level. In particular, we focus on study designs, treatments, or interventions in Alzheimer's disease that could also be insightful in aging and vice versa.
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Affiliation(s)
- Xian Xia
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences; Chinese Academy of Sciences ; Shanghai China
| | - Quanlong Jiang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences; Chinese Academy of Sciences ; Shanghai China
| | - Joseph McDermott
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences; Chinese Academy of Sciences ; Shanghai China
| | - Jing-Dong J. Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences; Chinese Academy of Sciences ; Shanghai China
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47
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Vinatier C, Domínguez E, Guicheux J, Caramés B. Role of the Inflammation-Autophagy-Senescence Integrative Network in Osteoarthritis. Front Physiol 2018; 9:706. [PMID: 29988615 PMCID: PMC6026810 DOI: 10.3389/fphys.2018.00706] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
Osteoarthritis is the most common musculoskeletal disease causing chronic disability in adults. Studying cartilage aging, chondrocyte senescence, inflammation, and autophagy mechanisms have identified promising targets and pathways with clinical translatability potential. In this review, we highlight the most recent mechanistic and therapeutic preclinical models of aging with particular relevance in the context of articular cartilage and OA. Evidence supporting the role of metabolism, nuclear receptors and transcription factors, cell senescence, and circadian rhythms in the development of musculoskeletal system degeneration assure further translational efforts. This information might be useful not only to propose hypothesis and advanced models to study the molecular mechanisms underlying joint degeneration, but also to translate our knowledge into novel disease-modifying therapies for OA.
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Affiliation(s)
- Claire Vinatier
- INSERM, UMR 1229, Regenerative Medicine and Skeleton, University of Nantes, ONIRIS, Nantes, France.,University of Nantes, UFR Odontologie, Nantes, France
| | - Eduardo Domínguez
- Biofarma Research Group, Center for Research in Molecular Medicine and Chronic Diseases, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Jerome Guicheux
- INSERM, UMR 1229, Regenerative Medicine and Skeleton, University of Nantes, ONIRIS, Nantes, France.,University of Nantes, UFR Odontologie, Nantes, France.,CHU Nantes, PHU4 OTONN, Nantes, France
| | - Beatriz Caramés
- Grupo de Biología del Cartílago, Servicio de Reumatología. Instituto de Investigación Biomédica de A Coruña, Complexo Hospitalario Universitario de A Coruña, Sergas, A Coruña, Spain
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48
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Zheng H, Huang Q, Huang S, Yang X, Zhu T, Wang W, Wang H, He S, Ji L, Wang Y, Qi X, Liu Z, Lu L. Senescence Inducer Shikonin ROS-Dependently Suppressed Lung Cancer Progression. Front Pharmacol 2018; 9:519. [PMID: 29875661 PMCID: PMC5974149 DOI: 10.3389/fphar.2018.00519] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/30/2018] [Indexed: 01/03/2023] Open
Abstract
Lung adenocarcinoma (LAC), predominant subclassfication of lung cancer, leads high incidence and mortality annually worldwide. During the premalignant transition from lung adenomas to LAC, cellular senescence is regard as a critical physiological barrier against tumor progression. Nevertheless, the role of senescence in tumorigenesis is controversial and few senescence inducers are extensively determined. In this study, we used two classical cell lines A549 and H1299 and two NSCLC xenograft models on Balb/c-nude mice to reveal the pro-senescence effects of shikonin and the corresponding underlying mechanism in LAC. Shikonin, a pure compound isolated from the herbal medicine Lithospermum erythrorhizon, remarkably stimulated cellular senescence including increased SAHF formation, enlarged cellular morphology, and induced SA-β-Gal positive staining. Further mechanism study revealed that the pro-senescence effect of shikonin was dependent on the increased intercellular ROS generation, which subsequently triggered DNA damage-p53/p21waf axis without activating oncogenes such as Ras and MEK-1. Meanwhile, Kdm2b, an H3K36me2-specific demethylase effectively suppressed ROS generation, was also notably suppressed by shikonin treatment. Moreover, shikonin at 10 mg/kg significantly inhibited tumor weights by 55.84% and 50.98% in A549 and H1299 xenograft model, respectively (P < 0.05) through activating cellular senescence. Our study suggested that shikonin, a ROS-dependent senescence inducer, could serve as a promising agent for further lung cancer treatment.
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Affiliation(s)
- Hongming Zheng
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiuju Huang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Suchao Huang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xia Yang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ting Zhu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wensheng Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haojia Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shugui He
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liyan Ji
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoxiao Qi
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau
| | - Linlin Lu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau
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49
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McManus FP, Bourdeau V, Acevedo M, Lopes-Paciencia S, Mignacca L, Lamoliatte F, Rojas Pino JW, Ferbeyre G, Thibault P. Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated proteins and an anti-senescence function of UBC9. Sci Rep 2018; 8:7754. [PMID: 29773808 PMCID: PMC5958138 DOI: 10.1038/s41598-018-25150-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/28/2018] [Indexed: 12/13/2022] Open
Abstract
Several regulators of SUMOylation have been previously linked to senescence but most targets of this modification in senescent cells remain unidentified. Using a two-step purification of a modified SUMO3, we profiled the SUMO proteome of senescent cells in a site-specific manner. We identified 25 SUMO sites on 23 proteins that were significantly regulated during senescence. Of note, most of these proteins were PML nuclear body (PML-NB) associated, which correlates with the increased number and size of PML-NBs observed in senescent cells. Interestingly, the sole SUMO E2 enzyme, UBC9, was more SUMOylated during senescence on its Lys-49. Functional studies of a UBC9 mutant at Lys-49 showed a decreased association to PML-NBs and the loss of UBC9’s ability to delay senescence. We thus propose both pro- and anti-senescence functions of protein SUMOylation.
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Affiliation(s)
- Francis P McManus
- Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Véronique Bourdeau
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Mariana Acevedo
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Stéphane Lopes-Paciencia
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Lian Mignacca
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Frédéric Lamoliatte
- Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - John W Rojas Pino
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
| | - Pierre Thibault
- Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada. .,Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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50
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Song S, Johnson FB. Epigenetic Mechanisms Impacting Aging: A Focus on Histone Levels and Telomeres. Genes (Basel) 2018; 9:genes9040201. [PMID: 29642537 PMCID: PMC5924543 DOI: 10.3390/genes9040201] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/13/2022] Open
Abstract
Aging and age-related diseases pose some of the most significant and difficult challenges to modern society as well as to the scientific and medical communities. Biological aging is a complex, and, under normal circumstances, seemingly irreversible collection of processes that involves numerous underlying mechanisms. Among these, chromatin-based processes have emerged as major regulators of cellular and organismal aging. These include DNA methylation, histone modifications, nucleosome positioning, and telomere regulation, including how these are influenced by environmental factors such as diet. Here we focus on two interconnected categories of chromatin-based mechanisms impacting aging: those involving changes in the levels of histones or in the functions of telomeres.
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Affiliation(s)
- Shufei Song
- Biochemistry and Molecular Biophysics Graduate Group, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Pathology and Laboratory Medicine, and Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - F Brad Johnson
- Department of Pathology and Laboratory Medicine, and Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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