1
|
Haga M, Iida K, Okada M. Positive and negative feedback regulation of the TGF-β1 explains two equilibrium states in skin aging. iScience 2024; 27:109708. [PMID: 38706856 PMCID: PMC11066433 DOI: 10.1016/j.isci.2024.109708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 02/05/2024] [Accepted: 04/06/2024] [Indexed: 05/07/2024] Open
Abstract
During aging, skin homeostasis is essential for maintaining appearance, as well as biological defense of the human body. In this study, we identified thrombospondin-1 (THBS1) and fibromodulin (FMOD) as positive and negative regulators, respectively, of the TGF-β1-SMAD4 axis in human skin aging, based on in vitro and in vivo omics analyses and mathematical modeling. Using transcriptomic and epigenetic analyses of senescent dermal fibroblasts, TGF-β1 was identified as the key upstream regulator. Bifurcation analysis revealed a binary high-/low-TGF-β1 switch, with THBS1 as the main controller. Computational simulation of the TGF-β1 signaling pathway indicated that THBS1 expression was sensitively regulated, whereas FMOD was regulated robustly. Results of sensitivity analysis and validation showed that inhibition of SMAD4 complex formation was a promising method to control THBS1 production and senescence. Therefore, this study demonstrated the potential of combining data-driven target discovery with mathematical approaches to determine the mechanisms underlying skin aging.
Collapse
Affiliation(s)
- Masatoshi Haga
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Basic Research Development Division, ROHTO Pharmaceutical Co., Ltd, Osaka 544-8666, Japan
| | - Keita Iida
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mariko Okada
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
2
|
Sucularli C, Şimay Demir YD, Özdemir A, Ark M. Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line. Biosystems 2024; 237:105140. [PMID: 38336224 DOI: 10.1016/j.biosystems.2024.105140] [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: 12/15/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Cellular senescence is the state of permanent growth arrest. Chemotherapeutic drugs induce senescence, known as therapy-induced senescence. Although there are studies deciphering processes in senescence, more studies providing detailed information on therapy-induced senescence at the transcriptome level are needed. In order to understand temporal molecular changes of doxorubicin treatment in the course of senescence formation, two data sets from HeLa cells at 16 h and 72 h doxorubicin treatment were analyzed. GO BP enrichment, KEGG pathways and hub genes specific to or shared between 16 h and 72 h doxorubicin treated HeLa cells were identified. Genes functioning in p53 signaling were upregulated only in 16 h, while genes functioning in extracellular matrix organization were upregulated only in 72 h doxorubicin treated HeLa cells. Wound healing genes were gradually upregulated from 16 h to 72 h doxorubicin treatment and metabolic pathways were downregulated at both. ncRNA processing and ribosome biogenesis GO BP terms were enriched in upregulated genes at 16 h, while these terms were enriched in downregulated genes at 72 h senescent HeLa cells. According to our results, genes functioning in p53 signaling may be involved in the induction of senescence, but may not be required to maintain senescence in HeLa cells.
Collapse
Affiliation(s)
- Ceren Sucularli
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, 06100, Ankara, Turkey.
| | | | - Aysun Özdemir
- Department of Pharmacology, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | - Mustafa Ark
- Department of Pharmacology, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| |
Collapse
|
3
|
Hattangady NG, Carter K, Maroni-Rana B, Wang T, Ayers JL, Yu M, Grady WM. Mapping the core senescence phenotype of primary human colon fibroblasts. Aging (Albany NY) 2024; 16:3068-3087. [PMID: 38385965 DOI: 10.18632/aging.205577] [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: 05/16/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Advanced age is the largest risk factor for many diseases and several types of cancer, including colorectal cancer (CRC). Senescent cells are known to accumulate with age in various tissues, where they can modulate the surrounding tissue microenvironment through their senescence associated secretory phenotype (SASP). Recently, we showed that there is an increased number of senescent cells in the colons of CRC patients and demonstrated that senescent fibroblasts and their SASP create microniches in the colon that are conducive to CRC onset and progression. However, the composition of the SASP is heterogenous and cell-specific, and the precise senescence profile of colon fibroblasts has not been well-defined. To generate a SASP atlas of human colon fibroblasts, we induced senescence in primary human colon fibroblasts using various in vitro methods and assessed the resulting transcriptome. Using RNASequencing and further validation by quantitative RT-PCR and Luminex assays, we define and validate a 'core senescent profile' that might play a significant role in shaping the colon microenvironment. We also performed KEGG analysis and GO analyses to identify key pathways and biological processes that are differentially regulated in colon fibroblast senescence. These studies provide insights into potential driver proteins involved in senescence-associated diseases, like CRC, which may lead to therapies to improve overall health in the elderly and to prevent CRC.
Collapse
Affiliation(s)
- Namita Ganesh Hattangady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kelly Carter
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Brett Maroni-Rana
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ting Wang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jessica Lee Ayers
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - William M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA 98195, USA
| |
Collapse
|
4
|
Kim S, Morgunova E, Naqvi S, Goovaerts S, Bader M, Koska M, Popov A, Luong C, Pogson A, Swigut T, Claes P, Taipale J, Wysocka J. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. Cell 2024; 187:692-711.e26. [PMID: 38262408 PMCID: PMC10872279 DOI: 10.1016/j.cell.2023.12.032] [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: 04/20/2023] [Revised: 10/23/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024]
Abstract
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest that it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how "Coordinator," a long DNA motif composed of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines the regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, whereas HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in the shared regulation of genes involved in cell-type and positional identities and ultimately shapes facial morphology and evolution.
Collapse
Affiliation(s)
- Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Seppe Goovaerts
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christy Luong
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Angela Pogson
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Peter Claes
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium; Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, University of Cambridge, Cambridge, UK; Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
| |
Collapse
|
5
|
Caldas P, Luz M, Baseggio S, Andrade R, Sobral D, Grosso AR. Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features. Commun Biol 2024; 7:100. [PMID: 38225287 PMCID: PMC10789751 DOI: 10.1038/s42003-024-05779-5] [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: 03/27/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Transcription termination is a crucial step in the production of conforming mRNAs and functional proteins. Under cellular stress conditions, the transcription machinery fails to identify the termination site and continues transcribing beyond gene boundaries, a phenomenon designated as transcription readthrough. However, the prevalence and impact of this phenomenon in healthy human tissues remain unexplored. Here, we assessed transcription readthrough in almost 3000 transcriptome profiles representing 23 human tissues and found that 34% of the expressed protein-coding genes produced readthrough transcripts. The production of readthrough transcripts was restricted in genomic regions with high transcriptional activity and was associated with inefficient splicing and increased chromatin accessibility in terminal regions. In addition, we showed that these transcripts contained several binding sites for the same miRNA, unravelling a potential role as miRNA sponges. Overall, this work provides evidence that transcription readthrough is pervasive and non-stochastic, not only in abnormal conditions but also in healthy tissues. This suggests a potential role for such transcripts in modulating normal cellular functions.
Collapse
Affiliation(s)
- Paulo Caldas
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Mariana Luz
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Simone Baseggio
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Rita Andrade
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Daniel Sobral
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Ana Rita Grosso
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Huang Y, Ge MX, Li YH, Li JL, Yu Q, Xiao FH, Ao HS, Yang LQ, Li J, He Y, Kong QP. Longevity-Associated Transcription Factor ATF7 Promotes Healthspan by Suppressing Cellular Senescence and Systematic Inflammation. Aging Dis 2023:AD.2022.1217. [PMID: 37163432 PMCID: PMC10389835 DOI: 10.14336/ad.2022.1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/17/2022] [Indexed: 05/12/2023] Open
Abstract
Aging is characterized by persistent low-grade systematic inflammation, which is largely responsible for the occurrence of various age-associated diseases. We and others have previously reported that long-lived people (such as centenarians) can delay the onset of or even escape certain major age-related diseases. Here, by screening blood transcriptome and inflammatory profiles, we found that long-lived individuals had a relatively lower inflammation level (IL6, TNFα), accompanied by up-regulation of activating transcription factor 7 (ATF7). Interestingly, ATF7 expression was gradually reduced during cellular senescence. Loss of ATF7 induced cellular senescence, while overexpression delayed senescence progress and senescence-associated secretory phenotype (SASP) secretion. We showed that the anti-senescence effects of ATF7 were achieved by inhibiting nuclear factor kappa B (NF-κB) signaling and increasing histone H3K9 dimethylation (H3K9me2). In Caenorhabditis elegans, ATF7 overexpression significantly suppressed aging biomarkers and extended lifespan. Our findings suggest that ATF7 is a longevity-promoting factor that lowers cellular senescence and inflammation in long-lived individuals.
Collapse
Affiliation(s)
- Yaqun Huang
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Xia Ge
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Hong Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jing-Lin Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong-Shun Ao
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ji Li
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Yonghan He
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
8
|
Alexakou E, Bakopoulou A, Apatzidou DA, Kritis A, Malousi A, Anastassiadou V. Biological Effects of "Inflammageing" on Human Oral Cells: Insights into a Potential Confounder of Age-Related Diseases. Int J Mol Sci 2023; 25:5. [PMID: 38203178 PMCID: PMC10778866 DOI: 10.3390/ijms25010005] [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: 11/19/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
OBJECTIVES The term "inflammageing" describes the process of inflammation-induced aging that leads living cells to a state of permanent cell cycle arrest due to chronic antigenic irritation. This in vitro study aimed to shed light on the mechanisms of "inflammageing" on human oral cells. METHODS Primary cultures of human gingival fibroblasts (hGFs) were exposed to variable pro-inflammatory stimuli, including lipopolysaccharide (LPS), Tumor Necrosis Factor-alpha (TNFa), and gingival crevicular fluid (GCF) collected from active periodontal pockets of systemically healthy patients. Inflammageing was studied through two experimental models, employing either late-passage ("aged") cells (p. 10) that were exposed to the pro-inflammatory stimuli or early-passage ("young") cells (p. 1) continuously exposed during a period of several passages (up to p. 10) to the above-mentioned stimuli. Cells were evaluated for the expression of beta-galactosidase activity (histochemical staining), senescence-associated genes (qPCR analysis), and biomarkers related to a Senescence-Associated Secretory Phenotype (SASP), through proteome profile analysis and bioinformatics. RESULTS A significant increase (p < 0.05) in beta-galactosidase-positive cells was observed after exposure to each pro-inflammatory stimulus. The senescence-associated gene expression included upregulation for CCND1 and downregulation for SUSD6, and STAG1, a profile typical for cellular senescence. Overall, pro-inflammatory priming of late-passage cells caused more pronounced effects in terms of senescence than long-term exposure of early-passage cells to these stimuli. Proteomic analysis showed induction of SASP, evidenced by upregulation of several pro-inflammatory proteins (IL-6, IL-10, IL-16, IP-10, MCP-1, MCP-2, M-CSF, MIP-1a, MIP-1b, TNFb, sTNF-RI, sTNF-RII, TIMP-2) implicated in cellular aging and immune responses. The least potent impact on the induction of SASP was provoked by LPS and the most pronounced by GCF. CONCLUSION This study demonstrates that long-term exposure of hGFs to various pro-inflammatory signals induced or accelerated cellular senescence with the most pronounced impact noted for the late-passage cells. The outcome of these analyses provides insights into oral chronic inflammation as a potential confounder of age-related diseases.
Collapse
Affiliation(s)
- Elli Alexakou
- Department of Prosthodontics, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki (A.U.TH.), 54124 Thessaloniki, Greece; (E.A.); (V.A.)
| | - Athina Bakopoulou
- Department of Prosthodontics, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki (A.U.TH.), 54124 Thessaloniki, Greece; (E.A.); (V.A.)
| | - Danae A. Apatzidou
- Department of Preventive Dentistry, Periodontology & Implant Biology, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki (A.U.TH.), 54124 Thessaloniki, Greece;
| | - Aristeidis Kritis
- Department of Physiology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki (A.U.TH.), 54124 Thessaloniki, Greece;
- Regenerative Medicine Center, Basic and Translational Research Unit (BTRU) of Special Unit for Biomedical Research and Education (BRESU), Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Andigoni Malousi
- Department of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki (A.U.TH.), 54124 Thessaloniki, Greece;
| | - Vassiliki Anastassiadou
- Department of Prosthodontics, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki (A.U.TH.), 54124 Thessaloniki, Greece; (E.A.); (V.A.)
| |
Collapse
|
9
|
Li Y, Zhang W, Ye Y, Sun Y, Yang L, Chen G, Chen K, Smith S, Zhou J. Atg4b Overexpression Extends Lifespan and Healthspan in Drosophila melanogaster. Int J Mol Sci 2023; 24:9893. [PMID: 37373039 PMCID: PMC10298381 DOI: 10.3390/ijms24129893] [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: 04/27/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Autophagy plays important but complex roles in aging, affecting health and longevity. We found that, in the general population, the levels of ATG4B and ATG4D decreased during aging, yet they are upregulated in centenarians, suggesting that overexpression of ATG4 members could be positive for healthspan and lifespan. We therefore analyzed the effect of overexpressing Atg4b (a homolog of human ATG4D) in Drosophila, and found that, indeed, Atg4b overexpression increased resistance to oxidative stress, desiccation stress and fitness as measured by climbing ability. The overexpression induced since mid-life increased lifespan. Transcriptome analysis of Drosophila subjected to desiccation stress revealed that Atg4b overexpression increased stress response pathways. In addition, overexpression of ATG4B delayed cellular senescence, and improved cell proliferation. These results suggest that ATG4B have contributed to a slowdown in cellular senescence, and in Drosophila, Atg4b overexpression may have led to improved healthspan and lifespan by promoting a stronger stress response. Overall, our study suggests that ATG4D and ATG4B have the potential to become targets for health and lifespan interventions.
Collapse
Affiliation(s)
- Yongxuan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Kunming 650223, China; (Y.L.); (W.Z.); (Y.Y.); (Y.S.); (L.Y.); (G.C.); (K.C.)
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Kunming 650223, China; (Y.L.); (W.Z.); (Y.Y.); (Y.S.); (L.Y.); (G.C.); (K.C.)
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunshuang Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Kunming 650223, China; (Y.L.); (W.Z.); (Y.Y.); (Y.S.); (L.Y.); (G.C.); (K.C.)
| | - Yinan Sun
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Kunming 650223, China; (Y.L.); (W.Z.); (Y.Y.); (Y.S.); (L.Y.); (G.C.); (K.C.)
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Kunming 650223, China; (Y.L.); (W.Z.); (Y.Y.); (Y.S.); (L.Y.); (G.C.); (K.C.)
| | - Guijun Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Kunming 650223, China; (Y.L.); (W.Z.); (Y.Y.); (Y.S.); (L.Y.); (G.C.); (K.C.)
| | - Kangning Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Kunming 650223, China; (Y.L.); (W.Z.); (Y.Y.); (Y.S.); (L.Y.); (G.C.); (K.C.)
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheryl Smith
- Biology Department, Arcadia University, Philadelphia, PA 19104, USA;
| | - Jumin Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Kunming 650223, China; (Y.L.); (W.Z.); (Y.Y.); (Y.S.); (L.Y.); (G.C.); (K.C.)
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| |
Collapse
|
10
|
Kim S, Morgunova E, Naqvi S, Bader M, Koska M, Popov A, Luong C, Pogson A, Claes P, Taipale J, Wysocka J. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.541540. [PMID: 37398193 PMCID: PMC10312427 DOI: 10.1101/2023.05.29.541540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how 'Coordinator', a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.
Collapse
Affiliation(s)
- Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Mervenaz Koska
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | | | - Christy Luong
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
| | - Angela Pogson
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| |
Collapse
|
11
|
Alicea GM, Portuallo ME, Patel P, Fane ME, Carey AE, Speicher D, Tang HY, Kossenkov AV, Rebecca VW, Wirtz DG, Weeraratna AT. Age-related increases in IGFBP2 increase melanoma cell invasion and lipid synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539059. [PMID: 37205503 PMCID: PMC10187234 DOI: 10.1101/2023.05.02.539059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Aged melanoma patients (>65 years old) have more aggressive disease relative to young patients (<55 years old) for reasons that are not completely understood. Analysis of the young and aged secretome from human dermal fibroblasts identified >5-fold levels of insulin-like growth factor binding protein 2 (IGFBP2) in the aged fibroblast secretome. IGFBP2 functionally triggers upregulation of the PI3K-dependent fatty acid biosynthesis program in melanoma cells through increases in FASN. Melanoma cells co-cultured with aged dermal fibroblasts have higher levels of lipids relative to young dermal fibroblasts, which can be lowered by silencing IGFBP2 expression in fibroblasts, prior to treating with conditioned media. Conversely, ectopically treating melanoma cells with recombinant IGFBP2 in the presence of conditioned media from young fibroblasts, promoted lipid synthesis and accumulation in the melanoma cells. Neutralizing IGFBP2 in vitro reduces migration and invasion in melanoma cells, and in vivo studies demonstrate that neutralizing IGFBP2 in syngeneic aged mice, ablates tumor growth as well as metastasis. Conversely, ectopic treatment of young mice with IGFBP2 in young mice increases tumor growth and metastasis. Our data reveal that aged dermal fibroblasts increase melanoma cell aggressiveness through increased secretion of IGFBP2, stressing the importance of considering age when designing studies and treatment. Significance The aged microenvironment drives metastasis in melanoma cells. This study reports that IGFBP2 secretion by aged fibroblasts induces FASN in melanoma cells and drives metastasis. Neutralizing IGFBP2 decreases melanoma tumor growth and metastasis.
Collapse
|
12
|
Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A. Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells. Aging Cell 2023:e13809. [PMID: 37082798 DOI: 10.1111/acel.13809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 04/22/2023] Open
Abstract
To prioritize gene and protein candidates that may enable the selective identification and removal of senescent cells, we compared gene expression signatures from replicative senescent cells to transcriptomics and proteomics atlases of normal human tissues and cell types. RNA-seq samples from in vitro senescent cells (6 studies, 13 conditions) were analyzed for identifying targets at the gene and transcript levels that are highly expressed in senescent cells compared to their expression in normal human tissues and cell types. A gene set made of 301 genes called SenoRanger was established based on consensus analysis across studies and backgrounds. Of the identified senescence-associated targets, 29% of the genes in SenoRanger are also highly differentially expressed in aged tissues from GTEx. The SenoRanger gene set includes previously known as well as novel senescence-associated genes. Pathway analysis that connected the SenoRanger genes to their functional annotations confirms their potential role in several aging and senescence-related processes. Overall, SenoRanger provides solid hypotheses about potentially useful targets for identifying and removing senescence cells.
Collapse
Affiliation(s)
- Eden Z Deng
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Reid H Fleishman
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zhuorui Xie
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
13
|
Chibaya L, Snyder J, Ruscetti M. Senescence and the tumor-immune landscape: Implications for cancer immunotherapy. Semin Cancer Biol 2022; 86:827-845. [PMID: 35143990 PMCID: PMC9357237 DOI: 10.1016/j.semcancer.2022.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/03/2022] [Indexed: 01/27/2023]
Abstract
Cancer therapies, including conventional chemotherapy, radiation, and molecularly targeted agents, can lead to tumor eradication through a variety of mechanisms. In addition to their effects on tumor cell growth and survival, these regimens can also influence the surrounding tumor-immune microenvironment in ways that ultimately impact therapy responses. A unique biological outcome of cancer therapy is induction of cellular senescence. Senescence is a damage-induced stress program that leads to both the durable arrest of tumor cells and remodeling the tumor-immune microenvironment through activation of a collection pleiotropic cytokines, chemokines, growth factors, and proteinases known as the senescence-associated secretory phenotype (SASP). Depending on the cancer context and the mechanism of action of the therapy, the SASP produced following therapy-induced senescence (TIS) can promote anti-tumor immunity that enhances therapeutic efficacy, or alternatively chronic inflammation that leads to therapy failure and tumor relapse. Thus, a deeper understanding of the mechanisms regulating the SASP and components necessary for robust anti-tumor immune surveillance in different cancer and therapy contexts are key to harnessing senescence for tumor control. Here we draw a roadmap to modulate TIS and its immune-stimulating features for cancer immunotherapy.
Collapse
Affiliation(s)
- Loretah Chibaya
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jarin Snyder
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marcus Ruscetti
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA; Immunology and Microbiology Program, University of Massachusetts Chan Medical School, Worcester, MA, USA; Cancer Center, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| |
Collapse
|
14
|
Suzuki M, Tezuka K, Handa T, Sato R, Takeuchi H, Takao M, Tano M, Uchida Y. Upregulation of ribosome complexes at the blood-brain barrier in Alzheimer's disease patients. J Cereb Blood Flow Metab 2022; 42:2134-2150. [PMID: 35766008 PMCID: PMC9580172 DOI: 10.1177/0271678x221111602] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The cerebrovascular-specific molecular mechanism in Alzheimer's disease (AD) was investigated by employing comprehensive and accurate quantitative proteomics. Highly purified brain capillaries were isolated from cerebral gray and white matter of four AD and three control donors, and examined by SWATH (sequential window acquisition of all theoretical fragment ion spectra) proteomics. Of the 29 ribosomal proteins that were quantified, 28 (RPLP0, RPL4, RPL6, RPL7A, RPL8, RPL10A, RPL11, RPL12, RPL14, RPL15, RPL18, RPL23, RPL27, RPL27A, RPL31, RPL35A, RPS2, RPS3, RPS3A, RPS4X, RPS7, RPS8, RPS14, RPS16, RPS20, RPS24, RPS25, and RPSA) were significantly upregulated in AD patients. This upregulation of ribosomal protein expression occurred only in brain capillaries and not in brain parenchyma. The protein expression of protein processing and N-glycosylation-related proteins in the endoplasmic reticulum (DDOST, STT3A, MOGS, GANAB, RPN1, RPN2, SEC61B, UGGT1, LMAN2, and SSR4) were also upregulated in AD brain capillaries and was correlated with the expression of ribosomal proteins. The findings reported herein indicate that the ribosome complex, the subsequent protein processing and N-glycosylation-related processes are significantly and specifically upregulated in the brain capillaries of AD patients.
Collapse
Affiliation(s)
- Masayoshi Suzuki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kenta Tezuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Takumi Handa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Risa Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hina Takeuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Masaki Takao
- Department of Neurology and Brain Bank, Mihara Memorial Hospital, Isesaki, Japan.,Department of Clinical Laboratory, National Center of Neurology and Psychiatry, National Center Hospital, Kodaira, Japan
| | - Mitsutoshi Tano
- Department of Neurology and Brain Bank, Mihara Memorial Hospital, Isesaki, Japan
| | - Yasuo Uchida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| |
Collapse
|
15
|
Song Q, Hou Y, Zhang Y, Liu J, Wang Y, Fu J, Zhang C, Cao M, Cui Y, Zhang X, Wang X, Zhang J, Liu C, Zhang Y, Wang P. Integrated multi-omics approach revealed cellular senescence landscape. Nucleic Acids Res 2022; 50:10947-10963. [PMID: 36243980 PMCID: PMC9638896 DOI: 10.1093/nar/gkac885] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/27/2022] [Accepted: 10/01/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular senescence is a complex multifactorial biological phenomenon that plays essential roles in aging, and aging-related diseases. During this process, the senescent cells undergo gene expression altering and chromatin structure remodeling. However, studies on the epigenetic landscape of senescence using integrated multi-omics approaches are limited. In this research, we performed ATAC-seq, RNA-seq and ChIP-seq on different senescent types to reveal the landscape of senescence and identify the prime regulatory elements. We also obtained 34 key genes and deduced that NAT1, PBX1 and RRM2, which interacted with each other, could be the potential markers of aging and aging-related diseases. In summary, our work provides the landscape to study accessibility dynamics and transcriptional regulations in cellular senescence. The application of this technique in different types of senescence allows us to identify the regulatory elements responsible for the substantial regulation of transcription, providing the insights into molecular mechanisms of senescence.
Collapse
Affiliation(s)
- Qiao Song
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yuli Hou
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yiyin Zhang
- Shanghai Jiayin Biotechnology, Shanghai 200092, PR China
| | - Jing Liu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yaqi Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Jingxuan Fu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Chi Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Min Cao
- Department of Clinical Laboratory, Beijing Huairou Hospital, Beijing 101400, PR China
| | - Yuting Cui
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Xiaomin Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Xiaoling Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Jingjing Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Congcong Liu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yingzhen Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Peichang Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| |
Collapse
|
16
|
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.
Collapse
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; ,
| |
Collapse
|
17
|
Caliskan A, Crouch SAW, Giddins S, Dandekar T, Dangwal S. Progeria and Aging-Omics Based Comparative Analysis. Biomedicines 2022; 10:2440. [PMID: 36289702 PMCID: PMC9599154 DOI: 10.3390/biomedicines10102440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 10/21/2023] Open
Abstract
Since ancient times aging has also been regarded as a disease, and humankind has always strived to extend the natural lifespan. Analyzing the genes involved in aging and disease allows for finding important indicators and biological markers for pathologies and possible therapeutic targets. An example of the use of omics technologies is the research regarding aging and the rare and fatal premature aging syndrome progeria (Hutchinson-Gilford progeria syndrome, HGPS). In our study, we focused on the in silico analysis of differentially expressed genes (DEGs) in progeria and aging, using a publicly available RNA-Seq dataset (GEO dataset GSE113957) and a variety of bioinformatics tools. Despite the GSE113957 RNA-Seq dataset being well-known and frequently analyzed, the RNA-Seq data shared by Fleischer et al. is far from exhausted and reusing and repurposing the data still reveals new insights. By analyzing the literature citing the use of the dataset and subsequently conducting a comparative analysis comparing the RNA-Seq data analyses of different subsets of the dataset (healthy children, nonagenarians and progeria patients), we identified several genes involved in both natural aging and progeria (KRT8, KRT18, ACKR4, CCL2, UCP2, ADAMTS15, ACTN4P1, WNT16, IGFBP2). Further analyzing these genes and the pathways involved indicated their possible roles in aging, suggesting the need for further in vitro and in vivo research. In this paper, we (1) compare "normal aging" (nonagenarians vs. healthy children) and progeria (HGPS patients vs. healthy children), (2) enlist genes possibly involved in both the natural aging process and progeria, including the first mention of IGFBP2 in progeria, (3) predict miRNAs and interactomes for WNT16 (hsa-mir-181a-5p), UCP2 (hsa-mir-26a-5p and hsa-mir-124-3p), and IGFBP2 (hsa-mir-124-3p, hsa-mir-126-3p, and hsa-mir-27b-3p), (4) demonstrate the compatibility of well-established R packages for RNA-Seq analysis for researchers interested but not yet familiar with this kind of analysis, and (5) present comparative proteomics analyses to show an association between our RNA-Seq data analyses and corresponding changes in protein expression.
Collapse
Affiliation(s)
- Aylin Caliskan
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Samantha A. W. Crouch
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sara Giddins
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Seema Dangwal
- Stanford Cardiovascular Institute, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
18
|
Takaya K, Asou T, Kishi K. Downregulation of senescence-associated secretory phenotype by knockdown of secreted frizzled-related protein 4 contributes to the prevention of skin aging. Aging (Albany NY) 2022; 14:8167-8178. [PMID: 36084952 DOI: 10.18632/aging.204273] [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: 05/20/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022]
Abstract
There is growing evidence that the appearance and texture of the skin that is altered during the aging process are considerably enhanced by the accumulation of senescent dermal fibroblasts. These senescent cells magnify aging via an inflammatory, histolytic, and senescence-associated secretory phenotype (SASP). Secreted frizzled-related protein 4 (SFRP4) was previously determined to be expressed in dermal fibroblasts of aging skin, and its increased expression has been shown to promote cellular senescence. However, its role in the SASP remains unknown. We found that SFRP4 was significantly expressed in p16ink4a-positive human skin fibroblasts and that treatment with recombinant SFRP4 promoted SASP and senescence, whereas siRNA knockdown of SFRP4 suppressed SASP. Furthermore, we found that knockdown of SFRP4 in mouse skin ameliorates age-related reduction of subcutaneous adipose tissue, panniculus carnosus muscle layer, and thinning and dispersion of collagen fibers. These findings suggest a potential candidate for the development of new skin rejuvenation therapies that suppress SASP.
Collapse
Affiliation(s)
- Kento Takaya
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Toru Asou
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Kazuo Kishi
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| |
Collapse
|
19
|
Ge MX, Yu Q, Li GH, Yang LQ, He Y, Li J, Kong QP. Multiple time-series expression trajectories imply dynamic functional changes during cellular senescence. Comput Struct Biotechnol J 2022; 20:4131-4137. [PMID: 36016715 PMCID: PMC9379982 DOI: 10.1016/j.csbj.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
Cellular senescence is a dynamic process driven by epigenetic and genetic changes. Although some transcriptomic signatures of senescent cells have been discovered, how these senescence-related signals change over time remains largely unclear. Here, we profiled the transcriptome dynamics of human dermal fibroblast (HDF) cells in successive stages of growth from proliferation to senescence. Based on time-series expression profile analysis, we discovered four trajectories (C1, C2, C3, C4) that are dynamically expressed as senescence progresses. While some genes were continuously up-regulated (C4) or down-regulated (C2) with aging, other genes did not change linearly with cell proliferation, but remained stable until entering the senescent state (C1, C3). Further analysis revealed that the four modes were enriched in different biological pathways, including regulation of cellular senescence. These findings provide a new perspective on understanding the dynamic regulatory mechanism of cellular senescence.
Collapse
|
20
|
Spinelli R, Florese P, Parrillo L, Zatterale F, Longo M, D’Esposito V, Desiderio A, Nerstedt A, Gustafson B, Formisano P, Miele C, Raciti GA, Napoli R, Smith U, Beguinot F. ZMAT3 hypomethylation contributes to early senescence of preadipocytes from healthy first-degree relatives of type 2 diabetics. Aging Cell 2022; 21:e13557. [PMID: 35146866 PMCID: PMC8920444 DOI: 10.1111/acel.13557] [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: 08/10/2021] [Revised: 12/16/2021] [Accepted: 01/09/2022] [Indexed: 12/18/2022] Open
Abstract
Senescence of adipose precursor cells (APC) impairs adipogenesis, contributes to the age-related subcutaneous adipose tissue (SAT) dysfunction, and increases risk of type 2 diabetes (T2D). First-degree relatives of T2D individuals (FDR) feature restricted adipogenesis, reflecting the detrimental effects of APC senescence earlier in life and rendering FDR more vulnerable to T2D. Epigenetics may contribute to these abnormalities but the underlying mechanisms remain unclear. In previous methylome comparison in APC from FDR and individuals with no diabetes familiarity (CTRL), ZMAT3 emerged as one of the top-ranked senescence-related genes featuring hypomethylation in FDR and associated with T2D risk. Here, we investigated whether and how DNA methylation changes at ZMAT3 promote early APC senescence. APC from FDR individuals revealed increases in multiple senescence markers compared to CTRL. Senescence in these cells was accompanied by ZMAT3 hypomethylation, which caused ZMAT3 upregulation. Demethylation at this gene in CTRL APC led to increased ZMAT3 expression and premature senescence, which were reverted by ZMAT3 siRNA. Furthermore, ZMAT3 overexpression in APC determined senescence and activation of the p53/p21 pathway, as observed in FDR APC. Adipogenesis was also inhibited in ZMAT3-overexpressing APC. In FDR APC, rescue of ZMAT3 methylation through senolytic exposure simultaneously downregulated ZMAT3 expression and improved adipogenesis. Interestingly, in human SAT, aging and T2D were associated with significantly increased expression of both ZMAT3 and the P53 senescence marker. Thus, DNA hypomethylation causes ZMAT3 upregulation in FDR APC accompanied by acquisition of the senescence phenotype and impaired adipogenesis, which may contribute to FDR predisposition for T2D.
Collapse
Affiliation(s)
- Rosa Spinelli
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Pasqualina Florese
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Luca Parrillo
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Federica Zatterale
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Michele Longo
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Vittoria D’Esposito
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Antonella Desiderio
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Annika Nerstedt
- Lundberg Laboratory for Diabetes Research Department of Molecular and Clinical Medicine Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Birgit Gustafson
- Lundberg Laboratory for Diabetes Research Department of Molecular and Clinical Medicine Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Pietro Formisano
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Claudia Miele
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Gregory Alexander Raciti
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| | - Raffaele Napoli
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
| | - Ulf Smith
- Lundberg Laboratory for Diabetes Research Department of Molecular and Clinical Medicine Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Francesco Beguinot
- Department of Translational Medical Sciences Federico II University of Naples Naples Italy
- URT Genomics of Diabetes Institute of Experimental Endocrinology and Oncology National Research Council Naples Italy
| |
Collapse
|
21
|
BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes. Commun Biol 2022; 5:146. [PMID: 35177756 PMCID: PMC8854590 DOI: 10.1038/s42003-022-03087-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Genomic imprinting and X chromosome inactivation (XCI) are two prototypical epigenetic mechanisms whereby a set of genes is expressed mono-allelically in order to fine-tune their expression levels. Defects in genomic imprinting have been observed in several neurodevelopmental disorders, in a wide range of tumours and in induced pluripotent stem cells (iPSCs). Single Nucleotide Variants (SNVs) are readily detectable by RNA-sequencing allowing the determination of whether imprinted or X-linked genes are aberrantly expressed from both alleles, although standardised analysis methods are still missing. We have developed a tool, named BrewerIX, that provides comprehensive information about the allelic expression of a large, manually-curated set of imprinted and X-linked genes. BrewerIX does not require programming skills, runs on a standard personal computer, and can analyze both bulk and single-cell transcriptomes of human and mouse cells directly from raw sequencing data. BrewerIX confirmed previous observations regarding the bi-allelic expression of some imprinted genes in naive pluripotent cells and extended them to preimplantation embryos. BrewerIX also identified misregulated imprinted genes in breast cancer cells and in human organoids and identified genes escaping XCI in human somatic cells. We believe BrewerIX will be useful for the study of genomic imprinting and XCI during development and reprogramming, and for detecting aberrations in cancer, iPSCs and organoids. Due to its ease of use to non-computational biologists, its implementation could become standard practice during sample assessment, thus raising the robustness and reproducibility of future studies. BrewerIX is an easy-to-use computational tool that can assess bi-allelic expression of imprinted and X-linked genes from RNA-seq data.
Collapse
|
22
|
Jo HR, Jeong JH. MicroRNA-Mediated Downregulation of HMGB2 Contributes to Cellular Senescence in Microvascular Endothelial Cells. Cells 2022; 11:cells11030584. [PMID: 35159393 PMCID: PMC8834370 DOI: 10.3390/cells11030584] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/29/2022] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
High mobility group box 2 (HMGB2) is a non-histone chromosomal protein involved in various biological processes, including cellular senescence. However, its role in cellular senescence has not been evaluated extensively. To determine the regulatory role and mechanism of HMGB2 in cellular senescence, we performed gene expression analysis, senescence staining, and tube formation assays using young and senescent microvascular endothelial cells (MVECs) after small RNA treatment or HMGB2 overexpression. HMGB2 expression decreased with age and was regulated at the transcriptional level. siRNA-mediated downregulation inhibited cell proliferation and accelerated cellular senescence. In contrast, ectopic overexpression delayed senescence and maintained relatively higher tube-forming activity. To determine the HMGB2 downregulation mechanism, we screened miRNAs that were significantly upregulated in senescent MVECs and selected HMGB2-targeting miRNAs. Six miRNAs, miR-23a-3p, 23b-3p, -181a-5p, -181b-5p, -221-3p, and -222-3p, were overexpressed in senescent MVECs. Ectopic introduction of miR-23a-3p, -23b-3p, -181a-5p, -181b-5p, and -221-3p, with the exception of miR-222-3p, led to the downregulation of HMGB2, upregulation of senescence-associated markers, and decreased tube formation activity. Inhibition of miR-23a-3p, -181a-5p, -181b-5p, and -221-3p delayed cellular senescence. Restoration of HMGB2 expression using miRNA inhibitors represents a potential strategy to overcome the detrimental effects of cellular senescence in endothelial cells.
Collapse
Affiliation(s)
- Hye-Ram Jo
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Science, Seoul 01812, Korea;
- Radiological and Medico-Oncological Sciences, University of Science and Technology, Daejeon 34113, Korea
| | - Jae-Hoon Jeong
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Science, Seoul 01812, Korea;
- Radiological and Medico-Oncological Sciences, University of Science and Technology, Daejeon 34113, Korea
- Correspondence: ; Tel.: +82-2970-1386
| |
Collapse
|
23
|
Angstadt S, Zhu Q, Jaffee EM, Robinson DN, Anders RA. Pancreatic Ductal Adenocarcinoma Cortical Mechanics and Clinical Implications. Front Oncol 2022; 12:809179. [PMID: 35174086 PMCID: PMC8843014 DOI: 10.3389/fonc.2022.809179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers due to low therapeutic response rates and poor prognoses. Majority of patients present with symptoms post metastatic spread, which contributes to its overall lethality as the 4th leading cause of cancer-related deaths. Therapeutic approaches thus far target only one or two of the cancer specific hallmarks, such as high proliferation rate, apoptotic evasion, or immune evasion. Recent genomic discoveries reveal that genetic heterogeneity, early micrometastases, and an immunosuppressive tumor microenvironment contribute to the inefficacy of current standard treatments and specific molecular-targeted therapies. To effectively combat cancers like PDAC, we need an innovative approach that can simultaneously impact the multiple hallmarks driving cancer progression. Here, we present the mechanical properties generated by the cell’s cortical cytoskeleton, with a spotlight on PDAC, as an ideal therapeutic target that can concurrently attack multiple systems driving cancer. We start with an introduction to cancer cell mechanics and PDAC followed by a compilation of studies connecting the cortical cytoskeleton and mechanical properties to proliferation, metastasis, immune cell interactions, cancer cell stemness, and/or metabolism. We further elaborate on the implications of these findings in disease progression, therapeutic resistance, and clinical relapse. Manipulation of the cancer cell’s mechanical system has already been shown to prevent metastasis in preclinical models, but it has greater potential for target exploration since it is a foundational property of the cell that regulates various oncogenic behaviors.
Collapse
Affiliation(s)
- Shantel Angstadt
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Qingfeng Zhu
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Elizabeth M. Jaffee
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Douglas N. Robinson
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Douglas N. Robinson, ; Robert A. Anders,
| | - Robert A. Anders
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Douglas N. Robinson, ; Robert A. Anders,
| |
Collapse
|
24
|
Woodward K, Shirokikh NE. Translational control in cell ageing: an update. Biochem Soc Trans 2021; 49:2853-2869. [PMID: 34913471 PMCID: PMC8786278 DOI: 10.1042/bst20210844] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/28/2022]
Abstract
Cellular ageing is one of the main drivers of organismal ageing and holds keys towards improving the longevity and quality of the extended life. Elucidating mechanisms underlying the emergence of the aged cells as well as their altered responses to the environment will help understanding the evolutionarily defined longevity preferences across species with different strategies of survival. Much is understood about the role of alterations in the DNA, including many epigenetic modifications such as methylation, in relation to the aged cell phenotype. While transcriptomes of the aged cells are beginning to be better-characterised, their translational responses remain under active investigation. Many of the translationally controlled homeostatic pathways are centred around mitigation of DNA damage, cell stress response and regulation of the proliferative potential of the cells, and thus are critical for the aged cell function. Translation profiling-type studies have boosted the opportunities in discovering the function of protein biosynthesis control and are starting to be applied to the aged cells. Here, we provide a summary of the current knowledge about translational mechanisms considered to be commonly altered in the aged cells, including the integrated stress response-, mechanistic target of Rapamycin- and elongation factor 2 kinase-mediated pathways. We enlist and discuss findings of the recent works that use broad profiling-type approaches to investigate the age-related translational pathways. We outline the limitations of the methods and the remaining unknowns in the established ageing-associated translation mechanisms, and flag translational mechanisms with high prospective importance in ageing, for future studies.
Collapse
Affiliation(s)
- Katrina Woodward
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra, ACT 2601, Australia
| | - Nikolay E. Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra, ACT 2601, Australia
| |
Collapse
|
25
|
Ohori M, Nakayama Y, Ogasawara-Shimizu M, Toyoshiba H, Nakanishi A, Aparicio S, Araki S. Gene regulatory network analysis defines transcriptome landscape with alternative splicing of human umbilical vein endothelial cells during replicative senescence. BMC Genomics 2021; 22:869. [PMID: 34856941 PMCID: PMC8641155 DOI: 10.1186/s12864-021-08185-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 11/18/2021] [Indexed: 01/10/2023] Open
Abstract
Background Endothelial cell senescence is the state of permanent cell cycle arrest and plays a critical role in the pathogenesis of age-related diseases. However, a comprehensive understanding of the gene regulatory network, including genome-wide alternative splicing machinery, involved in endothelial cell senescence is lacking. Results We thoroughly described the transcriptome landscape of replicative senescent human umbilical vein endothelial cells. Genes with high connectivity showing a monotonic expression increase or decrease with the culture period were defined as hub genes in the co-expression network. Computational network analysis of these genes led to the identification of canonical and non-canonical senescence pathways, such as E2F and SIRT2 signaling, which were down-regulated in lipid metabolism, and chromosome organization processes pathways. Additionally, we showed that endothelial cell senescence involves alternative splicing. Importantly, the first and last exon types of splicing, as observed in FLT1 and ACACA, were preferentially altered among the alternatively spliced genes during endothelial senescence. We further identified novel microexons in PRUNE2 and PSAP, each containing 9 nt, which were altered within the specific domain during endothelial senescence. Conclusions These findings unveil the comprehensive transcriptome pathway and novel signaling regulated by RNA processing, including gene expression and splicing, in replicative endothelial senescence. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08185-x.
Collapse
Affiliation(s)
- Momoko Ohori
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
| | - Yusuke Nakayama
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.,Present address: Discovery Technology Research Laboratories, Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd, 17-2 Wadai, 300-4247, Tsukuba, Ibaraki, Japan
| | - Mari Ogasawara-Shimizu
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Hiroyoshi Toyoshiba
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.,Present address: Life Science AI, FRONTEO Healthcare Inc., 2-12-23 Konan, Minato-ku, 108-0075, Tokyo, Japan
| | - Atsushi Nakanishi
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Samuel Aparicio
- Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, V5Z 1L3, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, V6T 2B5, Vancouver, BC, Canada
| | - Shinsuke Araki
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
| |
Collapse
|
26
|
Thorin-Trescases N, Labbé P, Mury P, Lambert M, Thorin E. Angptl2 is a Marker of Cellular Senescence: The Physiological and Pathophysiological Impact of Angptl2-Related Senescence. Int J Mol Sci 2021; 22:12232. [PMID: 34830112 PMCID: PMC8624568 DOI: 10.3390/ijms222212232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023] Open
Abstract
Cellular senescence is a cell fate primarily induced by DNA damage, characterized by irreversible growth arrest in an attempt to stop the damage. Senescence is a cellular response to a stressor and is observed with aging, but also during wound healing and in embryogenic developmental processes. Senescent cells are metabolically active and secrete a multitude of molecules gathered in the senescence-associated secretory phenotype (SASP). The SASP includes inflammatory cytokines, chemokines, growth factors and metalloproteinases, with autocrine and paracrine activities. Among hundreds of molecules, angiopoietin-like 2 (angptl2) is an interesting, although understudied, SASP member identified in various types of senescent cells. Angptl2 is a circulatory protein, and plasma angptl2 levels increase with age and with various chronic inflammatory diseases such as cancer, atherosclerosis, diabetes, heart failure and a multitude of age-related diseases. In this review, we will examine in which context angptl2 was identified as a SASP factor, describe the experimental evidence showing that angptl2 is a marker of senescence in vitro and in vivo, and discuss the impact of angptl2-related senescence in both physiological and pathological conditions. Future work is needed to demonstrate whether the senescence marker angptl2 is a potential clinical biomarker of age-related diseases.
Collapse
Affiliation(s)
- Nathalie Thorin-Trescases
- Montreal Heart Institute, University of Montreal, Montreal, QC H1T 1C8, Canada; (P.L.); (P.M.); (M.L.); (E.T.)
| | - Pauline Labbé
- Montreal Heart Institute, University of Montreal, Montreal, QC H1T 1C8, Canada; (P.L.); (P.M.); (M.L.); (E.T.)
- Department of Pharmacology and Physiology, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Pauline Mury
- Montreal Heart Institute, University of Montreal, Montreal, QC H1T 1C8, Canada; (P.L.); (P.M.); (M.L.); (E.T.)
- Department of Pharmacology and Physiology, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Mélanie Lambert
- Montreal Heart Institute, University of Montreal, Montreal, QC H1T 1C8, Canada; (P.L.); (P.M.); (M.L.); (E.T.)
- Department of Pharmacology and Physiology, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Eric Thorin
- Montreal Heart Institute, University of Montreal, Montreal, QC H1T 1C8, Canada; (P.L.); (P.M.); (M.L.); (E.T.)
- Department of Surgery, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| |
Collapse
|
27
|
McCauley BS, Sun L, Yu R, Lee M, Liu H, Leeman DS, Huang Y, Webb AE, Dang W. Altered Chromatin States Drive Cryptic Transcription in Aging Mammalian Stem Cells. ACTA ACUST UNITED AC 2021; 1:684-697. [PMID: 34746802 DOI: 10.1038/s43587-021-00091-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A repressive chromatin state featuring trimethylated lysine 36 on histone H3 (H3K36me3) and DNA methylation suppresses cryptic transcription in embryonic stem cells. Cryptic transcription is elevated with age in yeast and nematodes, and reducing it extends yeast lifespan, though whether this occurs in mammals is unknown. We show that cryptic transcription is elevated in aged mammalian stem cells, including murine hematopoietic stem cells (mHSCs) and neural stem cells (NSCs) and human mesenchymal stem cells (hMSCs). Precise mapping allowed quantification of age-associated cryptic transcription in hMSCs aged in vitro. Regions with significant age-associated cryptic transcription have a unique chromatin signature: decreased H3K36me3 and increased H3K4me1, H3K4me3, and H3K27ac with age. Genomic regions undergoing such changes resemble known promoter sequences and are bound by TBP even in young cells. Hence, the more permissive chromatin state at intragenic cryptic promoters likely underlies increased cryptic transcription in aged mammalian stem cells.
Collapse
Affiliation(s)
- Brenna S McCauley
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luyang Sun
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruofan Yu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Minjung Lee
- Center for Epigenetics & Disease Prevention, Institute of Bioscience and Technology, Texas A&M University, Houston, TX 77030, USA.,Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Haiying Liu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dena S Leeman
- Department of Genetics, Stanford University, Stanford, CA, 94305 USA.,Department of Discovery Immunology, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Bioscience and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Ashley E Webb
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
28
|
Sahu B, Pihlajamaa P, Zhang K, Palin K, Ahonen S, Cervera A, Ristimäki A, Aaltonen LA, Hautaniemi S, Taipale J. Human cell transformation by combined lineage conversion and oncogene expression. Oncogene 2021; 40:5533-5547. [PMID: 34302118 PMCID: PMC8429043 DOI: 10.1038/s41388-021-01940-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/17/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
Cancer is the most complex genetic disease known, with mutations implicated in more than 250 genes. However, it is still elusive which specific mutations found in human patients lead to tumorigenesis. Here we show that a combination of oncogenes that is characteristic of liver cancer (CTNNB1, TERT, MYC) induces senescence in human fibroblasts and primary hepatocytes. However, reprogramming fibroblasts to a liver progenitor fate, induced hepatocytes (iHeps), makes them sensitive to transformation by the same oncogenes. The transformed iHeps are highly proliferative, tumorigenic in nude mice, and bear gene expression signatures of liver cancer. These results show that tumorigenesis is triggered by a combination of three elements: the set of driver mutations, the cellular lineage, and the state of differentiation of the cells along the lineage. Our results provide direct support for the role of cell identity as a key determinant in transformation and establish a paradigm for studying the dynamic role of oncogenic drivers in human tumorigenesis.
Collapse
Affiliation(s)
- Biswajyoti Sahu
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Päivi Pihlajamaa
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kaiyang Zhang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Saija Ahonen
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alejandra Cervera
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB and HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Lauri A Aaltonen
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
29
|
de Paiva CS, Trujillo-Vargas CM, Schaefer L, Yu Z, Britton RA, Pflugfelder SC. Differentially Expressed Gene Pathways in the Conjunctiva of Sjögren Syndrome Keratoconjunctivitis Sicca. Front Immunol 2021; 12:702755. [PMID: 34349764 PMCID: PMC8326832 DOI: 10.3389/fimmu.2021.702755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/01/2021] [Indexed: 12/24/2022] Open
Abstract
Sjögren syndrome (SS) is an autoimmune condition that targets the salivary and lacrimal glands, with cardinal clinical signs of dry eye (keratoconjunctivitis sicca, KCS) and dry mouth. The conjunctiva of SS patients is often infiltrated by immune cells that participate in the induction and maintenance of local inflammation. The purpose of this study was to investigate immune-related molecular pathways activated in the conjunctiva of SS patients. Female SS patients (n=7) and controls (n=19) completed a series of oral, ocular surface exams. Symptom severity scores were evaluated using validated questionnaires (OSDI and SANDE). All patients fulfilled the ACR/EULAR criteria for SS and the criteria for KCS. Fluorescein and lissamine green dye staining evaluated tear-break-up time (TBUT), corneal and conjunctival disease, respectively. Impression cytology of the temporal bulbar conjunctiva was performed to collect cells lysed and subjected to gene expression analysis using the NanoString Immunology Panel. 53/594 differentially expressed genes (DEGs) were observed between SS and healthy controls; 49 DEGs were upregulated, and 4 were downregulated (TRAF5, TGFBI, KLRAP1, and CMKLRI). The top 10 DEGs in descending order were BST2, IFITM1, LAMP3, CXCL1, IL19, CFB, LY96, MX1, IL4R, CDKN1A. Twenty pathways had a global significance score greater or equal to 2. Spearman correlations showed that 29/49 upregulated DEGs correlated with either TBUT (inverse) or OSDI or conjunctival staining score (positive correlations). Venn diagrams identified that 26/29 DEGs correlated with TBUT, 5/26 DEGs correlated with OSDI, and 16/26 correlated with conjunctival staining scores. Five upregulated DEGs (CFB, CFI, IL1R1, IL2RG, IL4R) were uniquely negatively correlated with TBUT. These data indicate that the conjunctiva of SS patients exhibits a phenotype of immune activation, although some genes could be inhibitory. Some of the DEGs and pathways overlap with previous DEGs in salivary gland biopsies, but new DEGs were identified, and some of these correlated with symptoms and signs of dry eye. Our results indicate that gene analysis of conjunctiva imprints is a powerful tool to understand the pathogenesis of SS and develop new therapeutic targets.
Collapse
Affiliation(s)
- Cintia S. de Paiva
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Claudia M. Trujillo-Vargas
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
- Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Grupo de Inmunodeficiencias Primarias, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Laura Schaefer
- Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Zhiyuan Yu
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Robert A. Britton
- Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | | |
Collapse
|
30
|
Chemoinformatic Screening for the Selection of Potential Senolytic Compounds from Natural Products. Biomolecules 2021; 11:biom11030467. [PMID: 33809876 PMCID: PMC8004226 DOI: 10.3390/biom11030467] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022] Open
Abstract
Cellular senescence is a cellular condition that involves significant changes in gene expression and the arrest of cell proliferation. Recently, it has been suggested in experimental models that the elimination of senescent cells with pharmacological methods delays, prevents, and improves multiple adverse outcomes related to age. In this sense, the so-called senoylitic compounds are a class of drugs that selectively eliminates senescent cells (SCs) and that could be used in order to delay such adverse outcomes. Interestingly, the first senolytic drug (navitoclax) was discovered by using chemoinformatic and network analyses. Thus, in the present study, we searched for novel senolytic compounds through the use of chemoinformatic tools (fingerprinting and network pharmacology) over different chemical databases (InflamNat and BIOFACQUIM) coming from natural products (NPs) that have proven to be quite remarkable for drug development. As a result of screening, we obtained three molecules (hinokitiol, preussomerin C, and tanshinone I) that could be considered senolytic compound candidates since they share similarities in structure with senolytic leads (tunicamycin, ginsenoside Rb1, ABT 737, rapamycin, navitoclax, timosaponin A-III, digoxin, roxithromycin, and azithromycin) and targets involved in senescence pathways with potential use in the treatment of age-related diseases.
Collapse
|
31
|
Zhang C, Zhang X, Huang L, Guan Y, Huang X, Tian X, Zhang L, Tao W. ATF3 drives senescence by reconstructing accessible chromatin profiles. Aging Cell 2021; 20:e13315. [PMID: 33539668 PMCID: PMC7963335 DOI: 10.1111/acel.13315] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/11/2022] Open
Abstract
Chromatin organization and transcriptional profiles undergo tremendous reordering during senescence. However, uncovering the regulatory mechanisms between chromatin reconstruction and gene expression in senescence has been elusive. Here, we depicted the landscapes of both chromatin accessibility and gene expression to reveal gene regulatory networks in human umbilical vein endothelial cell (HUVEC) senescence and found that chromatin accessibilities are redistributed during senescence. Particularly, the intergenic chromatin was massively shifted with the increased accessibility regions (IARs) or decreased accessibility regions (DARs), which were mainly enhancer elements. We defined AP‐1 transcription factor family as being responsible for driving chromatin accessibility reconstruction in IARs, where low DNA methylation improved binding affinity of AP‐1 and further increased the chromatin accessibility. Among AP‐1 transcription factors, we confirmed ATF3 was critical to reconstruct chromatin accessibility to promote cellular senescence. Our results described a dynamic landscape of chromatin accessibility whose remodeling contributes to the senescence program, we identified that AP‐1 was capable of reorganizing the chromatin accessibility profile to regulate senescence.
Collapse
Affiliation(s)
- Chao Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
- PKU‐Tsinghua‐NIBS Graduate Program School of Life Sciences Peking University Beijing China
| | - Xuebin Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Li Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Yiting Guan
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Xiaoke Huang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Xiao‐Li Tian
- Department of Human Population Genetics Human Aging Research Institute (HARI) and School of Life Sciences Nanchang University Nanchang China
| | - Lijun Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| | - Wei Tao
- The MOE Key Laboratory of Cell Proliferation and Differentiation School of Life Sciences Peking University Beijing China
| |
Collapse
|
32
|
Tamura I, Maekawa R, Jozaki K, Ohkawa Y, Takagi H, Doi-Tanaka Y, Shirafuta Y, Mihara Y, Taketani T, Sato S, Tamura H, Sugino N. Transcription factor C/EBPβ induces genome-wide H3K27ac and upregulates gene expression during decidualization of human endometrial stromal cells. Mol Cell Endocrinol 2021; 520:111085. [PMID: 33232782 DOI: 10.1016/j.mce.2020.111085] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022]
Abstract
We previously reported that H3K27 acetylation (H3K27ac) increases throughout the genome during decidualization of human endometrial stromal cells (ESCs). However, its mechanisms have not been clarified. We also reported that C/EBPβ acts as a pioneer factor initiating chromatin remodeling by increasing H3K27ac of IGFBP-1 and PRL promoters. Therefore, C/EBPβ may be involved in the genome-wide increase of H3K27ac during decidualization. In this study, we investigated whether C/EBPβ causes genome-wide H3K27ac modifications and regulates gene expressions during decidualization. cAMP was used to induce decidualization. Three types of cells (control cells, cAMP-treated cells, and cAMP-treated + C/EBPβ-knockdowned cells by siRNA) were generated. Of 4190 genes that were upregulated by cAMP, C/EBPβ knockdown inhibited these upregulation in 2239 genes (53.4%), indicating that they are under the regulation of C/EBPβ. cAMP increased H3K27ac in 1272 of the 2239 genes. C/EBPβ knockdown abolished the increase of H3K27ac in almost all genes (1263 genes, 99.3%), suggesting that C/EBPβ can upregulate gene expression by increasing H3K27ac. To investigate how C/EBPβ regulates H3K27ac throughout the genome, we tested the hypothesis that C/EBPβ binds to its binding regions and recruits cofactors with histone acetyltransferase activities. To do this, we collated our ChIP-sequence data with public ChIP-sequence database of transcription factors, and found that p300 is the most likely cofactor that binds to the H3K27ac-increased-regions with C/EBPβ. ChIP-qPCR of several genes confirmed that C/EBPβ binds to the target regions, recruits p300, and increases H3K27ac. Our genome-wide analysis revealed that C/EBPβ induces H3K27ac throughout the genome and upregulates gene expressions during decidualization by recruiting p300 to the promoters.
Collapse
Affiliation(s)
- Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan.
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Kosuke Jozaki
- Department of Immunology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Japan
| | - Haruka Takagi
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yumiko Doi-Tanaka
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yuichiro Shirafuta
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Yumiko Mihara
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Toshiaki Taketani
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Japan
| |
Collapse
|
33
|
KarakÜlah G, Yandim C. Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence. ACTA ACUST UNITED AC 2021; 44:356-370. [PMID: 33402863 PMCID: PMC7759191 DOI: 10.3906/biy-2005-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022]
Abstract
Replicative cellular senescence is the main cause of aging. It is important to note that early senescence is linked to tissue regeneration, whereas late senescence is known to trigger a chronically inflammatory phenotype. Despite the presence of various genome-wide studies, there is a lack of information on distinguishing early and late senescent phenotypes at the transcriptome level. Particularly, the changes in the noncoding RNA portion of the aging cell have not been fully elucidated. By utilising RNA sequencing data of fibroblasts, hereby, we are not only reporting changes in gene expression profiles and relevant biological processes in the early and late senescent phenotypes but also presenting significant differences in the expressions of many unravelled long noncoding RNAs (lncRNAs) and transcripts arisen from repetitive DNA. Our results indicate that, in addition to previously reported L1 elements, various LTR and DNA transposons, as well as members of the classical satellites including HSAT5 and α-satellites (ALR/Alpha), are expressed at higher levels in late senescence. Moreover, we revealed finer links between the expression levels of repeats with the genes located near them and known to be involved in cell cycle and senescence. Noncoding elements reported here provide a new perspective to be explored in further experimental studies.
Collapse
Affiliation(s)
- Gökhan KarakÜlah
- İzmir Biomedicine and Genome Center, İzmir Turkey.,İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir Turkey
| | - Cihangir Yandim
- İzmir Biomedicine and Genome Center, İzmir Turkey.,Department of Genetics and Bioengineering, Faculty of Engineering, İzmir University of Economics, İzmir Turkey
| |
Collapse
|
34
|
Naydenov NG, Koblinski JE, Ivanov AI. Anillin is an emerging regulator of tumorigenesis, acting as a cortical cytoskeletal scaffold and a nuclear modulator of cancer cell differentiation. Cell Mol Life Sci 2021; 78:621-633. [PMID: 32880660 PMCID: PMC11072349 DOI: 10.1007/s00018-020-03605-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022]
Abstract
Remodeling of the intracellular cytoskeleton plays a key role in accelerating tumor growth and metastasis. Targeting different cytoskeletal elements is important for existing and future anticancer therapies. Anillin is a unique scaffolding protein that interacts with major cytoskeletal structures, e.g., actin filaments, microtubules and septin polymers. A well-studied function of this scaffolding protein is the regulation of cytokinesis at the completion of cell division. Emerging evidence suggest that anillin has other important activities in non-dividing cells, including control of intercellular adhesions and cell motility. Anillin is markedly overexpressed in different solid cancers and its high expression is commonly associated with poor prognosis of patient survival. This review article summarizes rapidly accumulating evidence that implicates anillin in the regulation of tumor growth and metastasis. We focus on molecular and cellular mechanisms of anillin-dependent tumorigenesis that include both canonical control of cytokinesis and novel poorly understood functions as a nuclear regulator of the transcriptional reprogramming and phenotypic plasticity of cancer cells.
Collapse
Affiliation(s)
- Nayden G Naydenov
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic Foundation, 9500 Euclid Avenue, NC22, Cleveland, OH, 44195, USA
| | - Jennifer E Koblinski
- Department of Pathology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Andrei I Ivanov
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic Foundation, 9500 Euclid Avenue, NC22, Cleveland, OH, 44195, USA.
| |
Collapse
|
35
|
Fujimaki K, Yao G. Cell dormancy plasticity: quiescence deepens into senescence through a dimmer switch. Physiol Genomics 2020; 52:558-562. [PMID: 32986540 DOI: 10.1152/physiolgenomics.00068.2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Both being dormant cellular states, quiescence and senescence are traditionally considered distinct. Quiescence is reversible to proliferation upon growth signals, whereas senescence is irreversible in physiological conditions. Recent findings, however, suggest that quiescence deepening with a decreased proliferative tendency, but not capability, is a common transition path toward senescence in many cell and tissue types. This transition is associated with the continuously increased activation threshold of an RB-E2F-CDK gene network switch.
Collapse
Affiliation(s)
- Kotaro Fujimaki
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona
| | - Guang Yao
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona.,Arizona Cancer Center, University of Arizona, Tucson, Arizona
| |
Collapse
|
36
|
Guvatova Z, Dalina A, Marusich E, Pudova E, Snezhkina A, Krasnov G, Kudryavtseva A, Leonov S, Moskalev A. Protective effects of carotenoid fucoxanthin in fibroblasts cellular senescence. Mech Ageing Dev 2020; 189:111260. [DOI: 10.1016/j.mad.2020.111260] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/27/2022]
|
37
|
Sha J, Arbesman J, Harter ML. Premature senescence in human melanocytes after exposure to solar UVR: An exosome and UV-miRNA connection. Pigment Cell Melanoma Res 2020; 33:671-684. [PMID: 32386350 DOI: 10.1111/pcmr.12888] [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] [Received: 12/18/2019] [Revised: 04/27/2020] [Accepted: 05/02/2020] [Indexed: 01/10/2023]
Abstract
Ultraviolet radiation (UVR) can play two roles: induce cellular senescence and convert skin melanocytes into melanoma. To assess whether this conversion might rely on melanocytes having to first acquire a senescent phenotype, we studied the effects of physiological doses of UVR (UVA + UVB) on quiescent melanocytes in vitro. Repeated doses of UVR induced these melanocytes into a senescent-like state. Additionally, these cells secrete exosomes with specific miRNAs that differ in quantity from those of the un-irradiated melanocytes. Many of the exosomal miRNAs that were differentially enriched regulated genes comprising a "senescence core signature" and encoding factors of the senescence-messaging secretome (SASP), while a subset of the differentially reduced miRNAs targeted DNA repair genes that have been experimentally shown to be repressed in senescent melanocytes. Thus, the selection of specific miRNAs by exosomes and their release from melanocytes after exposure to UVR have activities in inducing these cells into premature senescence.
Collapse
Affiliation(s)
- Jingfeng Sha
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Joshua Arbesman
- Dermatology and Plastic Surgery Institute and Cancer Biology, Cleveland Clinic, Cleveland, OH, USA
| | - Marian L Harter
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
38
|
Stojanović SD, Fuchs M, Kunz M, Xiao K, Just A, Pich A, Bauersachs J, Fiedler J, Sedding D, Thum T. Inflammatory Drivers of Cardiovascular Disease: Molecular Characterization of Senescent Coronary Vascular Smooth Muscle Cells. Front Physiol 2020; 11:520. [PMID: 32523550 PMCID: PMC7261939 DOI: 10.3389/fphys.2020.00520] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 12/18/2022] Open
Abstract
The senescence of vascular smooth muscle cells (VSMCs) has been implicated as a causal pro-inflammatory mechanism for cardiovascular disease development and progression of atherosclerosis, the instigator of ischemic heart disease. Contemporary limitations related to studying this cellular population and senescence-related therapeutics are caused by a lack of specific markers enabling their detection. Therefore, we aimed to profile a phenotypical and molecular signature of senescent VSMCs to allow reliable identification. To achieve this goal, we have compared non-senescent and senescent VSMCs from two in vitro models of senescence, replicative senescence (RS) and DNA-damage induced senescence (DS), by analyzing the expressions of established senescence markers: cell cycle inhibitors- p16 INK4a, p14 ARF, p21 and p53; pro-inflammatory factors-Interleukin 1β (IL-1β), IL-6 and high mobility group box-1 (HMGB-1); contractile proteins-smooth muscle heavy chain- (MYH11), smoothelin and transgelin (TAGLN), as well as structural features (nuclear morphology and LMNB1 (Lamin B1) expression). The different senescence-inducing modalities resulted in a lack of the proliferative activity. Nucleomegaly was seen in senescent VSMC as compared to freshly isolated VSMC Phenotypically, senescent VSMC appeared with a significantly larger cell size and polygonal, non-spindle-shaped cell morphology. In line with the supposed switch to a pro-inflammatory phenotype known as the senescence associated secretory phenotype (SASP), we found that both RS and DS upregulated IL-1β and released HMGB-1 from the nucleus, while RS also showed IL-6 upregulation. In regard to cell cycle-regulating molecules, we detected modestly increased p16 levels in both RS and DS, but largely inconsistent p21, p14ARF, and p53 expressions in senescent VSMCs. Since these classical markers of senescence showed insufficient deregulation to warrant senescent VSMC detection, we have conducted a non-biased proteomics and in silico analysis of RS VSMC demonstrating altered RNA biology as the central molecular feature of senescence in this cell type. Therefore, key proteins involved with RNA functionality, HMGB-1 release, LMNB-1 downregulation, in junction with nuclear enlargement, can be used as markers of VSMC senescence, enabling the detection of these pathogenic pro-inflammatory cells in future therapeutic studies in ischemic heart disease and atherosclerosis.
Collapse
Affiliation(s)
- Stevan D Stojanović
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hanover, Germany.,Department of Cardiology and Angiology, Hannover Medical School, Hanover, Germany
| | - Maximilian Fuchs
- Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.,Functional Genomics and Systems Biology Group, Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Meik Kunz
- Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Ke Xiao
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hanover, Germany
| | - Annette Just
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hanover, Germany
| | - Andreas Pich
- Institute of Toxicology and Core Unit Proteomics, Hannover Medical School, Hanover, Germany
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, Hanover, Germany.,REBIRTH Center of Translational Regenerative Medicine, Hannover Medical School, Hanover, Germany
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hanover, Germany
| | - Daniel Sedding
- Department of Internal Medicine III, Cardiology, Angiology and Intensive Care Medicine Martin-Luther-University Halle (Saale), Halle (Saale), Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hanover, Germany.,REBIRTH Center of Translational Regenerative Medicine, Hannover Medical School, Hanover, Germany
| |
Collapse
|
39
|
Cheng Q, Ouyang X, Zhang R, Zhu L, Song X. Senescence-associated genes and non-coding RNAs function in pancreatic cancer progression. RNA Biol 2020; 17:1693-1706. [PMID: 31997706 DOI: 10.1080/15476286.2020.1719752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Pancreatic cancer is a major cause of mortality with a poor diagnosis and prognosis that most often occurs in elderly patients. Few studies, however, focus on the interplay of age and pancreatic cancer at the transcriptional level. Here we evaluated the possible roles of age-dependent, differentially expressed genes (DEGs) in pancreatic cancer. These DEGs were used to construct a correlation network and clustered in six gene modules, among which two modules were highly correlated with patients' survival time. Integrating different datasets, including ATAC-Seq and ChIP-Seq, we performed multi-parallel analyses and identified eight age-dependent protein coding genes and two non-coding RNAs as potential candidates. These candidates, together with KLF5, a potent functional transcription factor in pancreatic cancer, are likely to be key elements linking cellular senescence and pancreatic cancer, providing insights on the balance between them, as well as on diagnosis and subsequent prognosis of pancreatic cancer.
Collapse
Affiliation(s)
- Qingyu Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China
| | - Xuan Ouyang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China
| | - Ran Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China
| | - Lianbang Zhu
- The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China
| | - Xiaoyuan Song
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China , Hefei, Anhui, China
| |
Collapse
|
40
|
A proteomic atlas of senescence-associated secretomes for aging biomarker development. PLoS Biol 2020; 18:e3000599. [PMID: 31945054 PMCID: PMC6964821 DOI: 10.1371/journal.pbio.3000599] [Citation(s) in RCA: 605] [Impact Index Per Article: 151.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/13/2019] [Indexed: 12/02/2022] Open
Abstract
The senescence-associated secretory phenotype (SASP) has recently emerged as a driver of and promising therapeutic target for multiple age-related conditions, ranging from neurodegeneration to cancer. The complexity of the SASP, typically assessed by a few dozen secreted proteins, has been greatly underestimated, and a small set of factors cannot explain the diverse phenotypes it produces in vivo. Here, we present the “SASP Atlas,” a comprehensive proteomic database of soluble proteins and exosomal cargo SASP factors originating from multiple senescence inducers and cell types. Each profile consists of hundreds of largely distinct proteins but also includes a subset of proteins elevated in all SASPs. Our analyses identify several candidate biomarkers of cellular senescence that overlap with aging markers in human plasma, including Growth/differentiation factor 15 (GDF15), stanniocalcin 1 (STC1), and serine protease inhibitors (SERPINs), which significantly correlated with age in plasma from a human cohort, the Baltimore Longitudinal Study of Aging (BLSA). Our findings will facilitate the identification of proteins characteristic of senescence-associated phenotypes and catalog potential senescence biomarkers to assess the burden, originating stimulus, and tissue of origin of senescent cells in vivo. The first comprehensive proteomic characterization of senescence-associated secretory phenotypes (SASPs) to our knowledge reveals substantial heterogeneity based on senescence inducer and cell type. The SASP Atlas represents a valuable resource for the identification of further candidate biomarkers of ageing.
Collapse
|
41
|
Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch. Proc Natl Acad Sci U S A 2019; 116:22624-22634. [PMID: 31636214 DOI: 10.1073/pnas.1915905116] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The reactivation of quiescent cells to proliferate is fundamental to tissue repair and homeostasis in the body. Often referred to as the G0 state, quiescence is, however, not a uniform state but with graded depth. Shallow quiescent cells exhibit a higher tendency to revert to proliferation than deep quiescent cells, while deep quiescent cells are still fully reversible under physiological conditions, distinct from senescent cells. Cellular mechanisms underlying the control of quiescence depth and the connection between quiescence and senescence are poorly characterized, representing a missing link in our understanding of tissue homeostasis and regeneration. Here we measured transcriptome changes as rat embryonic fibroblasts moved from shallow to deep quiescence over time in the absence of growth signals. We found that lysosomal gene expression was significantly up-regulated in deep quiescence, and partially compensated for gradually reduced autophagy flux. Reducing lysosomal function drove cells progressively deeper into quiescence and eventually into a senescence-like irreversibly arrested state; increasing lysosomal function, by lowering oxidative stress, progressively pushed cells into shallower quiescence. That is, lysosomal function modulates graded quiescence depth between proliferation and senescence as a dimmer switch. Finally, we found that a gene-expression signature developed by comparing deep and shallow quiescence in fibroblasts can correctly classify a wide array of senescent and aging cell types in vitro and in vivo, suggesting that while quiescence is generally considered to protect cells from irreversible arrest of senescence, quiescence deepening likely represents a common transition path from cell proliferation to senescence, related to aging.
Collapse
|
42
|
Zhang L, Liu M, Li Q, Shen B, Hu C, Fu R, Liu M, Deng J, Cao Q, Wang Y, Wang Y. Identification of differential gene expression in endothelial cells from young and aged mice using RNA-Seq technique. Am J Transl Res 2019; 11:6553-6560. [PMID: 31737206 PMCID: PMC6834518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
Aging is a complex phenomenon. Endothelial cell senescence is regarded as a vital characteristic of cardiovascular diseases. This study aims to identify differentially expressed genes in vascular endothelial cells (ECs) of different age groups by RNA sequencing (RNA-Seq) technique, and to explore which molecular pathways differentially expressed genes (DEGs) may enrich in. In this study, we used RNA-Seq to analyze DEGs in primary endothelial cells of young and old mice, and further analyzed them by gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Our results showed that in total identified 229 of the DEGs, 104 were upregulated and 125 were downregulated in endothelial cells of aged mice compared with young mice. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the involvement of these DEGs in the regulation of morphogenesis of a branching structure, angiogenesis, upregulation of cell proliferation, and extracellular matrix (ECM)-receptor interaction. These results provided a novel insight to understand the molecular mechanisms underlying aortic endothelial cell senescence, and some of the novel candidate genes identified in this study may be valuable in elucidating the molecular mechanisms underlying endothelial cell senescence.
Collapse
Affiliation(s)
- Liang Zhang
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Manli Liu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Qing Li
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
- The Central Laboratory of Medical Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of ChinaHefei 230001, Anhui, PR China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical UniversityHefei 230032, Anhui, PR China
| | - Chaojie Hu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
- The Central Laboratory of Medical Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of ChinaHefei 230001, Anhui, PR China
| | - Rui Fu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Mengdie Liu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Jie Deng
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Qi Cao
- The Centre for Transplantation and Renal Research, Westmead Institute for Medical Research, University of SydneySydney, NSW, Australia
| | - Yiping Wang
- The Centre for Transplantation and Renal Research, Westmead Institute for Medical Research, University of SydneySydney, NSW, Australia
| | - Yuanmin Wang
- Centre for Kidney Research, Children’s Hospital at WestmeadSydney, NSW, Australia
| |
Collapse
|
43
|
Cho SY, Kim AY, Kim J, Choi DH, Son ED, Shin DW. Oxytocin alleviates cellular senescence through oxytocin receptor-mediated extracellular signal-regulated kinase/Nrf2 signalling. Br J Dermatol 2019; 181:1216-1225. [PMID: 30801661 DOI: 10.1111/bjd.17824] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Oxytocin (OT) is a neuropeptide hormone that has many beneficial biological effects, including protection against age-related disorders. However, less is known about its role in intrinsic skin ageing, which is accelerated by an increase in senescent cell fraction in skin tissue. OBJECTIVES To investigate the novel function and the underlying mechanism of OT in preventing cellular senescence in normal human dermal fibroblasts (NHDFs) isolated from the skin of female donors of different ages. METHODS NHDFs from young and old donors were exposed to conditioned medium from senescent or control NHDFs in the presence or absence of 10 nmol L-1 OT for 3 days, and were continuously subcultured for 12 days. Subsequently, various age-associated signs of senescence including decreased proliferation rate, elevated p16 and p21 levels, and positivity for senescence-associated β-galactosidase expression were examined. RESULTS We found that OT suppressed senescence-associated secretory phenotype-induced senescence in NHDFs, and its effect depended on the age of the donor's NHDFs. The inhibitory effects of OT required signalling by OT receptor-mediated extracellular signal-regulated kinase/Nrf2 (nuclear factor erythroid 2-related factor 2). The age-dependent antisenescence effects of OT are closely related to hypermethylation of the OT receptor gene (OXTR). CONCLUSIONS Our findings bring to light the role of OT in the prevention of skin ageing, which might allow development of new clinical strategies. What's already known about this topic? Senescent keratinocytes and fibroblasts accumulate with age in the skin and contribute to the loss of skin function and integrity during ageing. Senescent cells secrete senescence-associated secretory phenotype (SASP), which includes the release of proinflammatory cytokines such as interleukin (IL)-6 and IL-1, chemokines, extracellular matrix-remodelling proteases and growth factors. The neuropeptide oxytocin (OT) and its receptor (OXTR) have protective effects against various age-related disorders. What does this study add? OT suppressed SASP-induced cellular senescence in normal human dermal fibroblasts (NHDFs), depending on the age of the NHDFs' donor. The inhibitory effects of OT on cellular senescence required OXTR-mediated phosphorylation of extracellular signal-regulated kinase, which enhanced nuclear localization of Nrf2, a vital factor in the antioxidant defence system. The age-specific antisenescent effects of OT were closely related to hypermethylation of OXTR. What is the translational message? Our results suggest that OT and OXTR agonists could be clinically promising agents for the improvement of age-associated skin ageing, especially in women.
Collapse
Affiliation(s)
- S-Y Cho
- R&D Unit, Amorepacific Corporation, Yongin-si, Gyeonggi-do, 17074, Republic of Korea
| | - A Y Kim
- R&D Unit, Amorepacific Corporation, Yongin-si, Gyeonggi-do, 17074, Republic of Korea
| | - J Kim
- R&D Unit, Amorepacific Corporation, Yongin-si, Gyeonggi-do, 17074, Republic of Korea
| | - D-H Choi
- Bio Center, Gyeonggido Business & Science Accelerator, Suwon, 16229, Republic of Korea
| | - E D Son
- R&D Unit, Amorepacific Corporation, Yongin-si, Gyeonggi-do, 17074, Republic of Korea
| | - D W Shin
- College of Biomedical & Health Science, Konkuk University, Chungju, 27478, Republic of Korea
| |
Collapse
|
44
|
Wezyk M, Szybinska A, Wojsiat J, Szczerba M, Day K, Ronnholm H, Kele M, Berdynski M, Peplonska B, Fichna JP, Ilkowski J, Styczynska M, Barczak A, Zboch M, Filipek-Gliszczynska A, Bojakowski K, Skrzypczak M, Ginalski K, Kabza M, Makalowska I, Barcikowska-Kotowicz M, Wojda U, Falk A, Zekanowski C. Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer's Disease. J Alzheimers Dis 2019; 62:175-202. [PMID: 29439343 DOI: 10.3233/jad-170830] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The BRCA1 protein, one of the major players responsible for DNA damage response has recently been linked to Alzheimer's disease (AD). Using primary fibroblasts and neurons reprogrammed from induced pluripotent stem cells (iPSC) derived from familial AD (FAD) patients, we studied the role of the BRCA1 protein underlying molecular neurodegeneration. By whole-transcriptome approach, we have found wide range of disturbances in cell cycle and DNA damage response in FAD fibroblasts. This was manifested by significantly increased content of BRCA1 phosphorylated on Ser1524 and abnormal ubiquitination and subcellular distribution of presenilin 1 (PS1). Accordingly, the iPSC-derived FAD neurons showed increased content of BRCA1(Ser1524) colocalized with degraded PS1, accompanied by an enhanced immunostaining pattern of amyloid-β. Finally, overactivation of BRCA1 was followed by an increased content of Cdc25C phosphorylated on Ser216, likely triggering cell cycle re-entry in FAD neurons. This study suggests that overactivated BRCA1 could both influence PS1 turnover leading to amyloid-β pathology and promote cell cycle re-entry-driven cell death of postmitotic neurons in AD.
Collapse
Affiliation(s)
- Michalina Wezyk
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Szybinska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Wojsiat
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcelina Szczerba
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Kelly Day
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Harriet Ronnholm
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Malin Kele
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Mariusz Berdynski
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland.,Department of Pharmacology and Clinical Neuroscience, Umea Universitet, Umea, Sweden
| | - Beata Peplonska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Piotr Fichna
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Jan Ilkowski
- Department of Emergency Medicine, Faculty of Health Sciences, Poznan University of Medical Sciences, Poznan, Poland
| | - Maria Styczynska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Anna Barczak
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Marzena Zboch
- Center of Alzheimer's Disease of Wroclaw Medical University, Scinawa, Poland
| | - Anna Filipek-Gliszczynska
- Clinical Department of Neurology, Extrapyramidal Disorders and Alzheimer's Outpatient Clinic, Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Krzysztof Bojakowski
- Clinical Department of General and Vascular Surgery, Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michal Kabza
- Department of Integrated Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | - Izabela Makalowska
- Department of Integrated Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | - Maria Barcikowska-Kotowicz
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cezary Zekanowski
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
45
|
Despres J, Ramdani Y, di Giovanni M, Bénard M, Zahid A, Montero-Hadjadje M, Yvergnaux F, Saguet T, Driouich A, Follet-Gueye ML. Replicative senescence of human dermal fibroblasts affects structural and functional aspects of the Golgi apparatus. Exp Dermatol 2019; 28:922-932. [DOI: 10.1111/exd.13886] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/14/2018] [Accepted: 01/02/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Julie Despres
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale; Normandie Université; UNIROUEN, Fédération de recherche Normandie-Végétal - FED 4277, GDR CNRS 3711, COSM'ACTIFS; Mont-Saint-Aignan France
- Bioeurope; Groupe SOLABIA; Route d'OulinsAnet France
| | - Yasmina Ramdani
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale; Normandie Université; UNIROUEN, Fédération de recherche Normandie-Végétal - FED 4277, GDR CNRS 3711, COSM'ACTIFS; Mont-Saint-Aignan France
| | - Marine di Giovanni
- Cell Imaging Platform (PRIMACEN-IRIB); Normandie Université; UNIROUEN; Mont-Saint-Aignan France
| | - Magalie Bénard
- Cell Imaging Platform (PRIMACEN-IRIB); Normandie Université; UNIROUEN; Mont-Saint-Aignan France
| | - Abderrakib Zahid
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale; Normandie Université; UNIROUEN, Fédération de recherche Normandie-Végétal - FED 4277, GDR CNRS 3711, COSM'ACTIFS; Mont-Saint-Aignan France
| | - Maité Montero-Hadjadje
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine; Institut de Recherche et d'Innovation Biomédicale de Normandie; Normandie Univ; UNIROUEN; INSERM U1239; Rouen France
| | | | | | - Azeddine Driouich
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale; Normandie Université; UNIROUEN, Fédération de recherche Normandie-Végétal - FED 4277, GDR CNRS 3711, COSM'ACTIFS; Mont-Saint-Aignan France
- Cell Imaging Platform (PRIMACEN-IRIB); Normandie Université; UNIROUEN; Mont-Saint-Aignan France
| | - Marie-Laure Follet-Gueye
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale; Normandie Université; UNIROUEN, Fédération de recherche Normandie-Végétal - FED 4277, GDR CNRS 3711, COSM'ACTIFS; Mont-Saint-Aignan France
- Cell Imaging Platform (PRIMACEN-IRIB); Normandie Université; UNIROUEN; Mont-Saint-Aignan France
| |
Collapse
|
46
|
Eberhardt K, Matthäus C, Marthandan S, Diekmann S, Popp J. Raman and infrared spectroscopy reveal that proliferating and quiescent human fibroblast cells age by biochemically similar but not identical processes. PLoS One 2018; 13:e0207380. [PMID: 30507927 PMCID: PMC6277109 DOI: 10.1371/journal.pone.0207380] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022] Open
Abstract
Dermal fibroblast cells can adopt different cell states such as proliferation, quiescence, apoptosis or senescence, in order to ensure tissue homeostasis. Proliferating (dividing) cells pass through the phases of the cell cycle, while quiescent and senescent cells exist in a non-proliferating cell cycle-arrested state. However, the reversible quiescence state is in contrast to the irreversible senescence state. Long-term quiescent cells transit into senescence indicating that cells age also when not passing through the cell cycle. Here, by label-free in vitro vibrational spectroscopy, we studied the biomolecular composition of quiescent dermal fibroblast cells and compared them with those of proliferating and senescent cells. Spectra were examined by multivariate statistical analysis using a PLS-LDA classification model, revealing differences in the biomolecular composition between the cell states mainly associated with protein alterations (variations in the side chain residues of amino acids and protein secondary structure), but also within nucleic acids and lipids. We observed spectral changes in quiescent compared to proliferating cells, which increased with quiescence cultivation time. Raman and infrared spectroscopy, which yield complementary biochemical information, clearly distinguished contact-inhibited from serum-starved quiescent cells. Furthermore, the spectra displayed spectral differences between quiescent cells and proliferating cells, which had recovered from quiescence. This became more distinct with increasing quiescence cultivation time. When comparing proliferating, (in particular long-term) quiescent and senescent cells, we found that Raman as well as infrared spectroscopy can separate these three cellular states from each other due to differences in their biomolecular composition. Our spectroscopic analysis shows that proliferating and quiescent fibroblast cells age by similar but biochemically not identical processes. Despite their aging induced changes, over long time periods quiescent cells can return into the cell cycle. Finally however, the cell cycle arrest becomes irreversible indicating senescence.
Collapse
Affiliation(s)
- Katharina Eberhardt
- Spectroscopy and Imaging, Leibniz Institute of Photonic Technology, Jena, Germany
| | - Christian Matthäus
- Spectroscopy and Imaging, Leibniz Institute of Photonic Technology, Jena, Germany
- Institute for Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
| | - Shiva Marthandan
- Department of Molecular Biology, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Stephan Diekmann
- Department of Molecular Biology, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Jürgen Popp
- Spectroscopy and Imaging, Leibniz Institute of Photonic Technology, Jena, Germany
- Institute for Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
- * E-mail:
| |
Collapse
|
47
|
Hernandez-Segura A, Brandenburg S, Demaria M. Induction and Validation of Cellular Senescence in Primary Human Cells. J Vis Exp 2018. [PMID: 29985363 DOI: 10.3791/57782] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cellular senescence is a state of permanent cell cycle arrest activated in response to different damaging stimuli. Activation of cellular senescence is a hallmark of various pathophysiological conditions including tumor suppression, tissue remodeling and aging. The inducers of cellular senescence in vivo are still poorly characterized. However, a number of stimuli can be used to promote cellular senescence ex vivo. Among them, most common senescence-inducers are replicative exhaustion, ionizing and non-ionizing radiation, genotoxic drugs, oxidative stress, and demethylating and acetylating agents. Here, we will provide detailed instructions on how to use these stimuli to induce fibroblasts into senescence. This protocol can easily be adapted for different types of primary cells and cell lines, including cancer cells. We also describe different methods for the validation of senescence induction. In particular, we focus on measuring the activity of the lysosomal enzyme Senescence-Associated β-galactosidase (SA-β-gal), the rate of DNA synthesis using 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay, the levels of expression of the cell cycle inhibitors p16 and p21, and the expression and secretion of members of the Senescence-Associated Secretory Phenotype (SASP). Finally, we provide example results and discuss further applications of these protocols.
Collapse
Affiliation(s)
- Alejandra Hernandez-Segura
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen
| | - Simone Brandenburg
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen
| | - Marco Demaria
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen;
| |
Collapse
|
48
|
Hernandez-Segura A, Nehme J, Demaria M. Hallmarks of Cellular Senescence. Trends Cell Biol 2018; 28:436-453. [PMID: 29477613 DOI: 10.1016/j.tcb.2018.02.001] [Citation(s) in RCA: 1299] [Impact Index Per Article: 216.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 01/10/2023]
Abstract
Cellular senescence is a permanent state of cell cycle arrest that promotes tissue remodeling during development and after injury, but can also contribute to the decline of the regenerative potential and function of tissues, to inflammation, and to tumorigenesis in aged organisms. Therefore, the identification, characterization, and pharmacological elimination of senescent cells have gained attention in the field of aging research. However, the nonspecificity of current senescence markers and the existence of different senescence programs strongly limit these tasks. Here, we describe the molecular regulators of senescence phenotypes and how they are used for identifying senescent cells in vitro and in vivo. We also highlight the importance that these levels of regulations have in the development of therapeutic targets.
Collapse
Affiliation(s)
- Alejandra Hernandez-Segura
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jamil Nehme
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marco Demaria
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
49
|
Transcriptional repression of DNA repair genes is a hallmark and a cause of cellular senescence. Cell Death Dis 2018; 9:259. [PMID: 29449545 PMCID: PMC5833687 DOI: 10.1038/s41419-018-0300-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/19/2022]
Abstract
Cellular senescence response is (i) activated by numerous stresses, (ii) is characterized by a stable proliferation arrest, and (iii) by a set of specific features. Timely regulated senescence is thought to be beneficial, whereas chronic senescence such as during normal or premature aging is deleterious as it favors most, if not all, age-related diseases. In this study, using in-house or publicly available microarray analyses of transcriptomes of senescent cells, as well as analyses of the level of expression of several DNA repair genes by RT-qPCR and immunoblot, we show that repression of DNA repair gene expression is associated with cellular senescence. This repression is mediated by the RB/E2F pathway and it may play a causal role in senescence induction, as single DNA repair gene repression by siRNA induced features of premature senescence. Importantly, activating RB independently of direct DNA damage also results in repression of DNA repair genes and in the subsequent induction of DNA damage and senescence. The dogma is that DNA damage observed during cellular senescence is directly provoked by DNA lesions following genotoxic attack (UV, IR, and ROS) or by induction of replicative stress upon oncogenic activation. Our in vitro results support a largely unsuspected contribution of the loss of DNA repair gene expression in the induction and the accumulation of the DNA damage observed in most, if not all, kinds of cellular senescence, and thus in the induction of cellular senescence. Further demonstration using in vivo models will help to generalize our findings.
Collapse
|
50
|
Saitou M, Lizardo DY, Taskent RO, Millner A, Gokcumen O, Atilla-Gokcumen GE. An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence. Mol Omics 2018; 14:237-246. [DOI: 10.1039/c8mo00099a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CD36 was identified as a core replicative senescence gene and a potential mediator of this process through membrane remodeling.
Collapse
Affiliation(s)
- Marie Saitou
- Department of Biological Sciences
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | - Darleny Y. Lizardo
- Department of Chemistry
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | - Recep Ozgur Taskent
- Department of Biological Sciences
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | - Alec Millner
- Department of Chemistry
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | - Omer Gokcumen
- Department of Biological Sciences
- University at Buffalo
- The State University of New York
- Buffalo
- USA
| | | |
Collapse
|