1
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Wang TW, Nakanishi M. Immune surveillance of senescence: potential application to age-related diseases. Trends Cell Biol 2024:S0962-8924(24)00121-1. [PMID: 39025762 DOI: 10.1016/j.tcb.2024.06.007] [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: 03/27/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024]
Abstract
Several lines of evidence suggest that the age-dependent accumulation of senescent cells leads to chronic tissue microinflammation, which in turn contributes to age-related pathologies. In general, senescent cells can be eliminated by the host's innate and adaptive immune surveillance system, including macrophages, NK cells, and T cells. Impaired immune surveillance leads to the accumulation of senescent cells and accelerates the aging process. Recently, senescent cells, like cancer cells, have been shown to express certain types of immune checkpoint proteins as well as non-classical immune-tolerant MHC variants, leading to immune escape from surveillance systems. Thus, immune checkpoint blockade (ICB) may be a promising strategy to enhance immune surveillance of senescence, leading to the amelioration of some age-related diseases and tissue dysfunction.
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Affiliation(s)
- Teh-Wei Wang
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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2
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Muthamil S, Kim HY, Jang HJ, Lyu JH, Shin UC, Go Y, Park SH, Lee HG, Park JH. Biomarkers of Cellular Senescence and Aging: Current State-of-the-Art, Challenges and Future Perspectives. Adv Biol (Weinh) 2024:e2400079. [PMID: 38935557 DOI: 10.1002/adbi.202400079] [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: 02/13/2024] [Revised: 05/29/2024] [Indexed: 06/29/2024]
Abstract
Population aging has increased the global prevalence of aging-related diseases, including cancer, sarcopenia, neurological disease, arthritis, and heart disease. Understanding aging, a fundamental biological process, has led to breakthroughs in several fields. Cellular senescence, evinced by flattened cell bodies, vacuole formation, and cytoplasmic granules, ubiquitously plays crucial roles in tissue remodeling, embryogenesis, and wound repair as well as in cancer therapy and aging. The lack of universal biomarkers for detecting and quantifying senescent cells, in vitro and in vivo, constitutes a major limitation. The applications and limitations of major senescence biomarkers, including senescence-associated β-galactosidase staining, telomere shortening, cell-cycle arrest, DNA methylation, and senescence-associated secreted phenotypes are discussed. Furthermore, explore senotherapeutic approaches for aging-associated diseases and cancer. In addition to the conventional biomarkers, this review highlighted the in vitro, in vivo, and disease models used for aging studies. Further, technologies from the current decade including multi-omics and computational methods used in the fields of senescence and aging are also discussed in this review. Understanding aging-associated biological processes by using cellular senescence biomarkers can enable therapeutic innovation and interventions to improve the quality of life of older adults.
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Affiliation(s)
- Subramanian Muthamil
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Jeollanam-do, Naju, 58245, Republic of Korea
| | - Hyun-Yong Kim
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Jeollanam-do, Naju, 58245, Republic of Korea
| | - Hyun-Jun Jang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Jeollanam-do, Naju, 58245, Republic of Korea
| | - Ji-Hyo Lyu
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Jeollanam-do, Naju, 58245, Republic of Korea
| | - Ung Cheol Shin
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Jeollanam-do, Naju, 58245, Republic of Korea
| | - Younghoon Go
- Korean Medicine (KM)-application Center, Korea Institute of Oriental Medicine, Daegu, 41062, Republic of Korea
| | - Seong-Hoon Park
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Hee Gu Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jun Hong Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Jeollanam-do, Naju, 58245, Republic of Korea
- Korean Convergence Medicine Major, University of Science & Technology (UST), KIOM Campus, Daejeon, 34054, Republic of Korea
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3
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Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver CM, Aguayo-Mazzucato C, Baker DJ, Bernlohr DA, Jurk D, Mangarova DB, Quardokus EM, Enninga EAL, Schmidt EL, Chen F, Duncan FE, Cambuli F, Kaur G, Kuchel GA, Lee G, Daldrup-Link HE, Martini H, Phatnani H, Al-Naggar IM, Rahman I, Nie J, Passos JF, Silverstein JC, Campisi J, Wang J, Iwasaki K, Barbosa K, Metis K, Nernekli K, Niedernhofer LJ, Ding L, Wang L, Adams LC, Ruiyang L, Doolittle ML, Teneche MG, Schafer MJ, Xu M, Hajipour M, Boroumand M, Basisty N, Sloan N, Slavov N, Kuksenko O, Robson P, Gomez PT, Vasilikos P, Adams PD, Carapeto P, Zhu Q, Ramasamy R, Perez-Lorenzo R, Fan R, Dong R, Montgomery RR, Shaikh S, Vickovic S, Yin S, Kang S, Suvakov S, Khosla S, Garovic VD, Menon V, Xu Y, Song Y, Suh Y, Dou Z, Neretti N. SenNet recommendations for detecting senescent cells in different tissues. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00738-8. [PMID: 38831121 DOI: 10.1038/s41580-024-00738-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Once considered a tissue culture-specific phenomenon, cellular senescence has now been linked to various biological processes with both beneficial and detrimental roles in humans, rodents and other species. Much of our understanding of senescent cell biology still originates from tissue culture studies, where each cell in the culture is driven to an irreversible cell cycle arrest. By contrast, in tissues, these cells are relatively rare and difficult to characterize, and it is now established that fully differentiated, postmitotic cells can also acquire a senescence phenotype. The SenNet Biomarkers Working Group was formed to provide recommendations for the use of cellular senescence markers to identify and characterize senescent cells in tissues. Here, we provide recommendations for detecting senescent cells in different tissues based on a comprehensive analysis of existing literature reporting senescence markers in 14 tissues in mice and humans. We discuss some of the recent advances in detecting and characterizing cellular senescence, including molecular senescence signatures and morphological features, and the use of circulating markers. We aim for this work to be a valuable resource for both seasoned investigators in senescence-related studies and newcomers to the field.
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Affiliation(s)
- Vidyani Suryadevara
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University, School of Medicine, Stanford, CA, USA
| | - Adam D Hudgins
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Adarsh Rajesh
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Genome and Epigenetics Program, La Jolla, CA, USA
| | | | - Alla Karpova
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Amit K Dey
- National Institute on Aging, NIH, Baltimore, MD, USA
| | - Ann Hertzel
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Anthony Agudelo
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
- Center on the Biology of Aging, Brown University, Providence, RI, USA
| | - Azucena Rocha
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
- Center on the Biology of Aging, Brown University, Providence, RI, USA
| | - Bikem Soygur
- The Buck Institute for Research on Aging, Novato, CA, USA
| | | | - Chase M Carver
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
| | - Cristina Aguayo-Mazzucato
- Islet Cell Biology and Regenerative Medicine, Joslin Diabetes Center, Harvard Medical School, Boston, USA
| | - Darren J Baker
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Diana Jurk
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Dilyana B Mangarova
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University, School of Medicine, Stanford, CA, USA
| | - Ellen M Quardokus
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | | | - Elizabeth L Schmidt
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Feng Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca E Duncan
- The Buck Institute for Research on Aging, Novato, CA, USA
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Gagandeep Kaur
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - George A Kuchel
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Gung Lee
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
| | - Heike E Daldrup-Link
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University, School of Medicine, Stanford, CA, USA
| | - Helene Martini
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Iman M Al-Naggar
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Jia Nie
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - João F Passos
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
| | - Jonathan C Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Judith Campisi
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Julia Wang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kanako Iwasaki
- Islet Cell Biology and Regenerative Medicine, Joslin Diabetes Center, Harvard Medical School, Boston, USA
| | - Karina Barbosa
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Genome and Epigenetics Program, La Jolla, CA, USA
| | - Kay Metis
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kerem Nernekli
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University, School of Medicine, Stanford, CA, USA
| | - Laura J Niedernhofer
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Li Ding
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lichao Wang
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Lisa C Adams
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University, School of Medicine, Stanford, CA, USA
| | - Liu Ruiyang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Madison L Doolittle
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, USA
| | - Marcos G Teneche
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Genome and Epigenetics Program, La Jolla, CA, USA
| | - Marissa J Schafer
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Ming Xu
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Mohammadjavad Hajipour
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University, School of Medicine, Stanford, CA, USA
| | | | | | - Nicholas Sloan
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Nikolai Slavov
- Center on the Biology of Aging, Brown University, Providence, RI, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Biology, Northeastern University, Boston, MA, USA
- Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA, USA
| | - Olena Kuksenko
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Paul T Gomez
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
| | - Periklis Vasilikos
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Genome and Epigenetics Program, La Jolla, CA, USA
| | - Priscila Carapeto
- Islet Cell Biology and Regenerative Medicine, Joslin Diabetes Center, Harvard Medical School, Boston, USA
| | - Quan Zhu
- Center for Epigenomics, University of California, San Diego, CA, USA
| | | | | | - Rong Fan
- Yale-Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Runze Dong
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Ruth R Montgomery
- Yale-Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Sadiya Shaikh
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Sanja Vickovic
- New York Genome Center, New York, NY, USA
- Herbert Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala University, Uppsala, Sweden
| | - Shanshan Yin
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Genome and Epigenetics Program, La Jolla, CA, USA
| | - Shoukai Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sonja Suvakov
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Sundeep Khosla
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Robert and Arlene Kogod Center on Aging, Rochester, MN, USA
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, USA
| | - Vesna D Garovic
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yanxin Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yizhe Song
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Zhixun Dou
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
- Center on the Biology of Aging, Brown University, Providence, RI, USA.
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4
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Wang X, Fukumoto T, Noma KI. Therapeutic strategies targeting cellular senescence for cancer and other diseases. J Biochem 2024; 175:525-537. [PMID: 38366629 PMCID: PMC11058315 DOI: 10.1093/jb/mvae015] [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: 11/17/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Cellular senescence occurs in response to endogenous or exogenous stresses and is characterized by stable cell cycle arrest, alterations in nuclear morphology and secretion of proinflammatory factors, referred to as the senescence-associated secretory phenotype (SASP). An increase of senescent cells is associated with the development of several types of cancer and aging-related diseases. Therefore, senolytic agents that selectively remove senescent cells may offer opportunities for developing new therapeutic strategies against such cancers and aging-related diseases. This review outlines senescence inducers and the general characteristics of senescent cells. We also discuss the involvement of senescent cells in certain cancers and diseases. Finally, we describe a series of senolytic agents and their utilization in therapeutic strategies.
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Affiliation(s)
- Xuebing Wang
- Institute for Genetic Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-Ku, Sapporo 060-0815, Japan
| | - Takeshi Fukumoto
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Ken-ichi Noma
- Institute for Genetic Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-Ku, Sapporo 060-0815, Japan
- Institute of Molecular Biology, University of Oregon, 1370 Franklin Blvd, Eugene, OR 97403, USA
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5
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Lopes-Paciencia S, Bourdeau V, Rowell MC, Amirimehr D, Guillon J, Kalegari P, Barua A, Quoc-Huy Trinh V, Azzi F, Turcotte S, Serohijos A, Ferbeyre G. A senescence restriction point acting on chromatin integrates oncogenic signals. Cell Rep 2024; 43:114044. [PMID: 38568812 DOI: 10.1016/j.celrep.2024.114044] [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: 12/14/2022] [Revised: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
We identify a senescence restriction point (SeRP) as a critical event for cells to commit to senescence. The SeRP integrates the intensity and duration of oncogenic stress, keeps a memory of previous stresses, and combines oncogenic signals acting on different pathways by modulating chromatin accessibility. Chromatin regions opened upon commitment to senescence are enriched in nucleolar-associated domains, which are gene-poor regions enriched in repeated sequences. Once committed to senescence, cells no longer depend on the initial stress signal and exhibit a characteristic transcriptome regulated by a transcription factor network that includes ETV4, RUNX1, OCT1, and MAFB. Consistent with a tumor suppressor role for this network, the levels of ETV4 and RUNX1 are very high in benign lesions of the pancreas but decrease dramatically in pancreatic ductal adenocarcinomas. The discovery of senescence commitment and its chromatin-linked regulation suggests potential strategies for reinstating tumor suppression in human cancers.
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Affiliation(s)
- Stéphane Lopes-Paciencia
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Véronique Bourdeau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Marie-Camille Rowell
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Davoud Amirimehr
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jordan Guillon
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Paloma Kalegari
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Arnab Barua
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Vincent Quoc-Huy Trinh
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada; Département de pathologie, Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Feryel Azzi
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Simon Turcotte
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; Département de chirurgie, Service de chirurgie hépatopancréatobiliaire, Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Adrian Serohijos
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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6
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Toh H, Sasaki H. Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes. Life Sci Alliance 2024; 7:e202302403. [PMID: 38233073 PMCID: PMC10794778 DOI: 10.26508/lsa.202302403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
DNA methylation is an essential epigenetic mechanism that regulates cellular reprogramming and development. Studies using whole-genome bisulfite sequencing have revealed distinct DNA methylome landscapes in human and mouse cells and tissues. However, the factors responsible for the differences in megabase-scale methylome patterns between cell types remain poorly understood. By analyzing publicly available 258 human and 301 mouse whole-genome bisulfite sequencing datasets, we reveal that genomic regions rich in guanine and cytosine, when located near the nuclear center, are highly susceptible to both global DNA demethylation and methylation events during embryonic and germline reprogramming. Furthermore, we found that regions that generate partially methylated domains during global DNA methylation are more likely to resist global DNA demethylation, contain high levels of adenine and thymine, and are adjacent to the nuclear lamina. The spatial properties of genomic regions, influenced by their guanine-cytosine content, are likely to affect the accessibility of molecules involved in DNA (de)methylation. These properties shape megabase-scale DNA methylation patterns and change as cells differentiate, leading to the emergence of different megabase-scale methylome patterns across cell types.
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Affiliation(s)
- Hidehiro Toh
- https://ror.org/02xg1m795 Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
- https://ror.org/00p4k0j84 Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Sasaki
- https://ror.org/00p4k0j84 Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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7
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Palikyras S, Sofiadis K, Stavropoulou A, Danieli‐Mackay A, Varamogianni‐Mamatsi V, Hörl D, Nasiscionyte S, Zhu Y, Papadionysiou I, Papadakis A, Josipovic N, Zirkel A, O'Connell A, Loughran G, Keane J, Michel A, Wagner W, Beyer A, Harz H, Leonhardt H, Lukinavicius G, Nikolaou C, Papantonis A. Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor. Aging Cell 2024; 23:e14083. [PMID: 38196311 PMCID: PMC11019153 DOI: 10.1111/acel.14083] [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: 10/06/2023] [Revised: 12/07/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Cellular senescence is acknowledged as a key contributor to organismal ageing and late-life disease. Though popular, the study of senescence in vitro can be complicated by the prolonged and asynchronous timing of cells committing to it and by its paracrine effects. To address these issues, we repurposed a small molecule inhibitor, inflachromene (ICM), to induce senescence to human primary cells. Within 6 days of treatment with ICM, senescence hallmarks, including the nuclear eviction of HMGB1 and -B2, are uniformly induced across IMR90 cell populations. By generating and comparing various high throughput datasets from ICM-induced and replicative senescence, we uncovered a high similarity of the two states. Notably though, ICM suppresses the pro-inflammatory secretome associated with senescence, thus alleviating most paracrine effects. In summary, ICM rapidly and synchronously induces a senescent-like phenotype thereby allowing the study of its core regulatory program without confounding heterogeneity.
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Affiliation(s)
- Spiros Palikyras
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Konstantinos Sofiadis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Present address:
Oncode InstituteHubrecht Institute‐KNAW and University Medical Center UtrechtUtrechtThe Netherlands
| | - Athanasia Stavropoulou
- Institute for BioinnovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Adi Danieli‐Mackay
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Clinical Research Unit 5002University Medical Center GöttingenGöttingenGermany
| | | | - David Hörl
- Faculty of BiologyLudwig Maximilians University MunichMunichGermany
| | | | - Yajie Zhu
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | | | - Antonis Papadakis
- Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Natasa Josipovic
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Present address:
Single Cell DiscoveriesUtrechtThe Netherlands
| | - Anne Zirkel
- Center for Molecular Medicine CologneUniversity and University Hospital of CologneCologneGermany
| | | | | | | | | | - Wolfgang Wagner
- Helmholtz‐Institute for Biomedical EngineeringRWTH Aachen University Medical SchoolAachenGermany
- Institute for Stem Cell BiologyRWTH Aachen University Medical SchoolAachenGermany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Hartmann Harz
- Faculty of BiologyLudwig Maximilians University MunichMunichGermany
| | | | - Grazvydas Lukinavicius
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Christoforos Nikolaou
- Institute for BioinnovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Argyris Papantonis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Clinical Research Unit 5002University Medical Center GöttingenGöttingenGermany
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8
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Ruzanov P, Evdokimova V, Pachva MC, Minkovich A, Zhang Z, Langman S, Gassmann H, Thiel U, Orlic-Milacic M, Zaidi SH, Peltekova V, Heisler LE, Sharma M, Cox ME, McKee TD, Zaidi M, Lapouble E, McPherson JD, Delattre O, Radvanyi L, Burdach SE, Stein LD, Sorensen PH. Oncogenic ETS fusions promote DNA damage and proinflammatory responses via pericentromeric RNAs in extracellular vesicles. J Clin Invest 2024; 134:e169470. [PMID: 38530366 PMCID: PMC11060741 DOI: 10.1172/jci169470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Aberrant expression of the E26 transformation-specific (ETS) transcription factors characterizes numerous human malignancies. Many of these proteins, including EWS:FLI1 and EWS:ERG fusions in Ewing sarcoma (EwS) and TMPRSS2:ERG in prostate cancer (PCa), drive oncogenic programs via binding to GGAA repeats. We report here that both EWS:FLI1 and ERG bind and transcriptionally activate GGAA-rich pericentromeric heterochromatin. The respective pathogen-like HSAT2 and HSAT3 RNAs, together with LINE, SINE, ERV, and other repeat transcripts, are expressed in EwS and PCa tumors, secreted in extracellular vesicles (EVs), and are highly elevated in plasma of patients with EwS with metastatic disease. High human satellite 2 and 3 (HSAT2,3) levels in EWS:FLI1- or ERG-expressing cells and tumors were associated with induction of G2/M checkpoint, mitotic spindle, and DNA damage programs. These programs were also activated in EwS EV-treated fibroblasts, coincident with accumulation of HSAT2,3 RNAs, proinflammatory responses, mitotic defects, and senescence. Mechanistically, HSAT2,3-enriched cancer EVs induced cGAS-TBK1 innate immune signaling and formation of cytosolic granules positive for double-strand RNAs, RNA-DNA, and cGAS. Hence, aberrantly expressed ETS proteins derepress pericentromeric heterochromatin, yielding pathogenic RNAs that transmit genotoxic stress and inflammation to local and distant sites. Monitoring HSAT2,3 plasma levels and preventing their dissemination may thus improve therapeutic strategies and blood-based diagnostics.
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Affiliation(s)
- Peter Ruzanov
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Manideep C. Pachva
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alon Minkovich
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Zhenbo Zhang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sofya Langman
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hendrik Gassmann
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Uwe Thiel
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | | | - Syed H. Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vanya Peltekova
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Manju Sharma
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Michael E. Cox
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Trevor D. McKee
- STTARR Innovation Centre, Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Pathomics Inc., Toronto, Ontario, Canada
| | - Mark Zaidi
- Pathomics Inc., Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Eve Lapouble
- Unité Génétique Somatique (UGS), Institut Curie, Centre Hospitalier Paris, France
| | - John D. McPherson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Olivier Delattre
- Unité Génétique Somatique (UGS), Institut Curie, Centre Hospitalier Paris, France
- Diversity and Plasticity of Childhood tumors, INSERM U830, Institut Curie Research Center, PSL Research University, Paris, France
| | - Laszlo Radvanyi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Stefan E.G. Burdach
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- CCC München Comprehensive Cancer Center, DKTK German Cancer Consortium, Munich, Germany
- Institute of Pathology, Translation Pediatric Cancer Research Action, School of Medicine, Technical University of Munich, Munich, Germany
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Poul H. Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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9
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Bisht S, Mao Y, Easwaran H. Epigenetic dynamics of aging and cancer development: current concepts from studies mapping aging and cancer epigenomes. Curr Opin Oncol 2024; 36:82-92. [PMID: 38441107 PMCID: PMC10939788 DOI: 10.1097/cco.0000000000001020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
PURPOSE OF REVIEW This review emphasizes the role of epigenetic processes as incidental changes occurring during aging, which, in turn, promote the development of cancer. RECENT FINDINGS Aging is a complex biological process associated with the progressive deterioration of normal physiological functions, making age a significant risk factor for various disorders, including cancer. The increasing longevity of the population has made cancer a global burden, as the risk of developing most cancers increases with age due to the cumulative effect of exposure to environmental carcinogens and DNA replication errors. The classical 'somatic mutation theory' of cancer cause is being challenged by the observation that multiple normal cells harbor cancer driver mutations without resulting in cancer. In this review, we discuss the role of age-associated epigenetic alterations, including DNA methylation, which occur across all cell types and tissues with advancing age. There is an increasing body of evidence linking these changes with cancer risk and prognosis. SUMMARY A better understanding about the epigenetic changes acquired during aging is critical for comprehending the mechanisms leading to the age-associated increase in cancer and for developing novel therapeutic strategies for cancer treatment and prevention.
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Affiliation(s)
- Shilpa Bisht
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yiqing Mao
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hariharan Easwaran
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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10
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Luan Y, Zhu X, Jiao Y, Liu H, Huang Z, Pei J, Xu Y, Yang Y, Ren K. Cardiac cell senescence: molecular mechanisms, key proteins and therapeutic targets. Cell Death Discov 2024; 10:78. [PMID: 38355681 PMCID: PMC10866973 DOI: 10.1038/s41420-023-01792-5] [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: 09/04/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 02/16/2024] Open
Abstract
Cardiac aging, particularly cardiac cell senescence, is a natural process that occurs as we age. Heart function gradually declines in old age, leading to continuous heart failure, even in people without a prior history of heart disease. To address this issue and improve cardiac cell function, it is crucial to investigate the molecular mechanisms underlying cardiac senescence. This review summarizes the main mechanisms and key proteins involved in cardiac cell senescence. This review further discusses the molecular modulators of cellular senescence in aging hearts. Furthermore, the discussion will encompass comprehensive descriptions of the key drugs, modes of action and potential targets for intervention in cardiac senescence. By offering a fresh perspective and comprehensive insights into the molecular mechanisms of cardiac senescence, this review seeks to provide a fresh perspective and important theoretical foundations for the development of drugs targeting this condition.
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Affiliation(s)
- Yi Luan
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Xiaofan Zhu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Yuxue Jiao
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
| | - Hui Liu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Zhen Huang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Jinyan Pei
- Quality Management Department, Henan No.3 Provincial People's Hospital, Zhengzhou, 450052, P. R. China
| | - Yawei Xu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
| | - Yang Yang
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
| | - Kaidi Ren
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, P. R. China.
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11
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Kołacz K, Robaszkiewicz A. PARP1 at the crossroad of cellular senescence and nucleolar processes. Ageing Res Rev 2024; 94:102206. [PMID: 38278370 DOI: 10.1016/j.arr.2024.102206] [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: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Senescent cells that occur in response to telomere shortening, oncogenes, extracellular and intracellular stress factors are characterized by permanent cell cycle arrest, the morphological and structural changes of the cell that include the senescence-associated secretory phenotype (SASP) and nucleoli rearrangement. The associated DNA lesions induce DNA damage response (DDR), which activates the DNA repair protein - poly-ADP-ribose polymerase 1 (PARP1). This protein consumes NAD+ to synthesize ADP-ribose polymer (PAR) on its own protein chain and on other interacting proteins. The involvement of PARP1 in nucleoli processes, such as rRNA transcription and ribosome biogenesis, the maintenance of heterochromatin and nucleoli structure, as well as controlling the crucial DDR protein release from the nucleoli to nucleus, links PARP1 with cellular senescence and nucleoli functioning. In this review we describe and discuss the impact of PARP1-mediated ADP-ribosylation on early cell commitment to senescence with the possible role of senescence-induced PARP1 transcriptional repression and protein degradation on nucleoli structure and function. The cause-effect interplay between PARP1 activation/decline and nucleoli functioning during senescence needs to be studied in detail.
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Affiliation(s)
- Kinga Kołacz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha 12 /16, 90-237 Lodz, Poland.
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research (IFBR), 600 5th Street South, St. Petersburgh, FL 33701, USA.
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12
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Mitin N, Entwistle A, Knecht A, Strum SL, Ross A, Nyrop K, Muss HB, Tsygankov D, Raffaele JM. Profiling an integrated network of cellular senescence and immune resilience measures in natural aging: a prospective multi-cohort study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.25.23294589. [PMID: 37693401 PMCID: PMC10491274 DOI: 10.1101/2023.08.25.23294589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Biological aging begins decades before the onset of age-related clinical conditions and is mediated by both cellular senescence and declining adaptive immune function. These processes are functionally related with the rate of senescent cell accumulation dependent upon a balance between induction and immune clearance. We previously showed that biomarkers in these domains can identify patients at-risk of surgery-related adverse events. Here, we describe evidence of clinical relevance in early aging and metabolic phenotypes in a general adult population. Methods We enrolled a total of 482 participants (ages 25-90) into two prospective, cross-sectional healthy aging cohorts. Expression of biomarkers of adaptive immune function and cellular senescence (SapereX) was measured in CD3+ T cells isolated from peripheral blood. Findings We established a network of biomarkers of adaptive immune function that correlate with cellular senescence and associate with early aging phenotypes. SapereX immune components associated with a decrease in CD4+ T cells, an increase in cytotoxic CD8+ T cells, and a loss of CD8+ naïve T cells (Pearson correlation 0.3-0.6). These components also associated with a metric of immune resilience, an ability to withstand antigen challenge and inflammation. In contrast, SapereX components were only weakly associated with GlycanAge (Pearson correlation 0.03-0.15) and commonly used DNA methylation clocks (Pearson correlation 0-0.25). Finally, SapereX biomarkers, in particular p16, were associated with chronic inflammation and metabolic dysregulation. Interpretation Measurement of SapereX biomarkers may capture essential elements of the relationship between cellular senescence and dysregulated adaptive immune function and may provide a benchmark for clinically relevant health decisions.
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13
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Lee YC, Nam Y, Kim M, Kim SI, Lee JW, Eun YG, Kim D. Prognostic significance of senescence-related tumor microenvironment genes in head and neck squamous cell carcinoma. Aging (Albany NY) 2023; 16:985-1001. [PMID: 38154113 PMCID: PMC10866405 DOI: 10.18632/aging.205346] [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: 08/24/2023] [Accepted: 11/06/2023] [Indexed: 12/30/2023]
Abstract
The impact of the senescence related microenvironment on cancer prognosis and therapeutic response remains poorly understood. In this study, we investigated the prognostic significance of senescence related tumor microenvironment genes (PSTGs) and their potential implications for immunotherapy response. Using the Cancer Genome Atlas- head and neck squamous cell carcinoma (HNSC) data, we identified two subtypes based on the expression of PSTGs, acquired from tumor-associated senescence genes, tumor microenvironment (TME)-related genes, and immune-related genes, using consensus clustering. Using the LASSO, we constructed a risk model consisting of senescence related TME core genes (STCGs). The two subtypes exhibited significant differences in prognosis, genetic alterations, methylation patterns, and enriched pathways, and immune infiltration. Our risk model stratified patients into high-risk and low-risk groups and validated in independent cohorts. The high-risk group showed poorer prognosis and immune inactivation, suggesting reduced responsiveness to immunotherapy. Additionally, we observed a significant enrichment of STCGs in stromal cells using single-cell RNA transcriptome data. Our findings highlight the importance of the senescence related TME in HNSC prognosis and response to immunotherapy. This study contributes to a deeper understanding of the complex interplay between senescence and the TME, with potential implications for precision medicine and personalized treatment approaches in HNSC.
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Affiliation(s)
- Young Chan Lee
- Department of Otolaryngology-Head and Neck Surgery, Kyung Hee University School of Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea
- Department of Medicine (AgeTech-Service Convergence Major) College of Medicine, Kyung Hee University, Seoul, Republic of Korea
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yonghyun Nam
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Minjeong Kim
- Department of Medicine (AgeTech-Service Convergence Major) College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Su Il Kim
- Department of Otolaryngology-Head and Neck Surgery, Kyung Hee University School of Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea
| | - Jung-Woo Lee
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Kyung Hee University, Seoul, Republic of Korea
| | - Young-Gyu Eun
- Department of Otolaryngology-Head and Neck Surgery, Kyung Hee University School of Medicine, Kyung Hee University Medical Center, Seoul, Republic of Korea
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
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14
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Switzer CH. Non-canonical nitric oxide signalling and DNA methylation: Inflammation induced epigenetic alterations and potential drug targets. Br J Pharmacol 2023. [PMID: 38116806 DOI: 10.1111/bph.16302] [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: 05/31/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 12/21/2023] Open
Abstract
DNA methylation controls DNA accessibility to transcription factors and other regulatory proteins, thereby affecting gene expression and hence cellular identity and function. As epigenetic modifications control the transcriptome, epigenetic dysfunction is strongly associated with pathological conditions and ageing. The development of pharmacological agents that modulate the activity of major epigenetic proteins are in pre-clinical development and clinical use. However, recent publications have identified novel redox-based signalling pathways, and therefore novel drug targets, that may exert epigenetic effects. This review will discuss the recent developments in nitric oxide (NO) signalling on DNA methylation as well as potential epigenetic drug targets that have emerged from the intersection of inflammation/redox biology and epigenetic regulation.
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Affiliation(s)
- Christopher H Switzer
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
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15
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Abstract
Keratinocyte senescence contributes to skin ageing and epidermal dysfunction. According to the existing knowledge, the transcription factor ΔNp63α plays pivotal roles in differentiation and proliferation of keratinocytes. It is traditionally accepted that ΔNp63α exerts its functions via binding to promoter regions to activate or repress gene transcription. However, accumulating evidence demonstrates that ΔNp63α can bind to elements away from promoter regions of its target genes, mediating epigenetic regulation. On the other hand, several epigenetic alterations, including DNA methylation, histone modification and variation, chromatin remodelling, as well as enhancer-promoter looping, are found to be related to cell senescence. To systematically elucidate how ΔNp63α affects keratinocyte senescence via epigenetic regulation, we comprehensively compiled the literatures on the roles of ΔNp63α in keratinocyte senescence, epigenetics in cellular senescence, and the relation between ΔNp63α-mediated epigenetic regulation and keratinocyte senescence. Based on the published data, we conclude that ΔNp63α mediates epigenetic regulation via multiple mechanisms: recruiting epigenetic enzymes to modify DNA or histones, coordinating chromatin remodelling complexes (CRCs) or regulating their expression, and mediating enhancer-promoter looping. Consequently, the expression of genes related to cell cycle is modulated, and proliferation of keratinocytes and renewal of stem cells are maintained, by ΔNp63α. During skin inflammaging, the decline of ΔNp63α may lead to epigenetic dysregulation, resultantly deteriorating keratinocyte senescence.
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Affiliation(s)
- Linghan Kuang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - Chenghua Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Biological Resources and Ecological Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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16
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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Miller KN, Li B, Pierce-Hoffman HR, Lei X, Havas AP, Patel S, Macip CC, Victorelli SG, Woo SH, Lagnado AB, Liu T, Dasgupta N, Lyu J, Altman Y, Porritt RA, Garcia G, Mogler C, Dou Z, Chen C, Passos JF, Adams PD. A mitochondria-regulated p53-CCF circuit integrates genome integrity with inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567963. [PMID: 38045344 PMCID: PMC10690201 DOI: 10.1101/2023.11.20.567963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genomic instability and inflammation are distinct hallmarks of aging, but the connection between them is poorly understood. Understanding their interrelationship will help unravel new mechanisms and therapeutic targets of aging and age-associated diseases. Here we report a novel mechanism directly linking genomic instability and inflammation in senescent cells, through a mitochondria-regulated molecular circuit that connects the p53 tumor suppressor and cytoplasmic chromatin fragments (CCF), a driver of inflammation through the cGAS-STING pathway. Activation or inactivation of p53 by genetic and pharmacologic approaches showed that p53 suppresses CCF accumulation and the downstream inflammatory senescence-associated secretory phenotype (SASP), independent of its effects on cell cycle arrest. p53 activation suppressed CCF formation by promoting DNA repair, reflected in maintenance of genomic integrity, particularly in subtelomeric regions, as shown by single cell genome resequencing. Activation of p53 by pharmacological inhibition of MDM2 in old mice decreased features of SASP in liver, indicating a senomorphic role in vivo . Remarkably, mitochondria in senescent cells suppressed p53 activity by promoting CCF formation and thereby restricting ATM-dependent nuclear DNA damage signaling. These data provide evidence for a mitochondria-regulated p53-CCF circuit in senescent cells that controls DNA repair, genome integrity and inflammatory SASP, and is a potential target for senomorphic healthy aging interventions.
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Blokhina Y, Buchwalter A. Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562830. [PMID: 37904963 PMCID: PMC10614900 DOI: 10.1101/2023.10.18.562830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ribosomal DNA (rDNA) genes encode the structural RNAs of the ribosome and are present in hundreds of copies in mammalian genomes. Age-linked DNA hypermethylation throughout the rDNA constitutes a robust "methylation clock" that accurately reports age, yet the consequences of hypermethylation on rDNA function are unknown. We confirmed that pervasive hypermethylation of rDNA occurs during mammalian aging and senescence while rDNA copy number remains stable. We found that DNA methylation is exclusively found on the promoters and gene bodies of inactive rDNA. To model the effects of age-linked methylation on rDNA function, we directed de novo DNA methylation to the rDNA promoter or gene body with a nuclease-dead Cas9 (dCas9) - DNA methyltransferase fusion enzyme in human cells. Hypermethylation at each target site had no detectable effect on rRNA transcription, nucleolar morphology, or cellular growth rate. Instead, human UBF and Pol I remain bound to rDNA promoters in the presence of increased DNA methylation. These data suggest that promoter methylation is not sufficient to impair transcription of the human rDNA and imply that the human rDNA transcription machinery may be resilient to age-linked rDNA hypermethylation.
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Affiliation(s)
- Yana Blokhina
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco
- present address: NewLimit, South San Francisco, CA
| | - Abigail Buchwalter
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco
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19
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Li D, Li Y, Ding H, Wang Y, Xie Y, Zhang X. Cellular Senescence in Cardiovascular Diseases: From Pathogenesis to Therapeutic Challenges. J Cardiovasc Dev Dis 2023; 10:439. [PMID: 37887886 PMCID: PMC10607269 DOI: 10.3390/jcdd10100439] [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: 09/16/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Cellular senescence (CS), classically considered a stable cell cycle withdrawal, is hallmarked by a progressive decrease in cell growth, differentiation, and biological activities. Senescent cells (SNCs) display a complicated senescence-associated secretory phenotype (SASP), encompassing a variety of pro-inflammatory factors that exert influence on the biology of both the cell and surrounding tissue. Among global mortality causes, cardiovascular diseases (CVDs) stand out, significantly impacting the living quality and functional abilities of patients. Recent data suggest the accumulation of SNCs in aged or diseased cardiovascular systems, suggesting their potential role in impairing cardiovascular function. CS operates as a double-edged sword: while it can stimulate the restoration of organs under physiological conditions, it can also participate in organ and tissue dysfunction and pave the way for multiple chronic diseases under pathological states. This review explores the mechanisms that underlie CS and delves into the distinctive features that characterize SNCs. Furthermore, we describe the involvement of SNCs in the progression of CVDs. Finally, the study provides a summary of emerging interventions that either promote or suppress senescence and discusses their therapeutic potential in CVDs.
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Affiliation(s)
- Dan Li
- Department of Cardiovascular Medicine, Lanzhou University Second Hospital, Lanzhou 730030, China; (D.L.); (H.D.); (Y.W.); (Y.X.)
| | - Yongnan Li
- Department of Cardiac Surgery, Lanzhou University Second Hospital, Lanzhou 730030, China;
| | - Hong Ding
- Department of Cardiovascular Medicine, Lanzhou University Second Hospital, Lanzhou 730030, China; (D.L.); (H.D.); (Y.W.); (Y.X.)
| | - Yuqin Wang
- Department of Cardiovascular Medicine, Lanzhou University Second Hospital, Lanzhou 730030, China; (D.L.); (H.D.); (Y.W.); (Y.X.)
| | - Yafei Xie
- Department of Cardiovascular Medicine, Lanzhou University Second Hospital, Lanzhou 730030, China; (D.L.); (H.D.); (Y.W.); (Y.X.)
| | - Xiaowei Zhang
- Department of Cardiovascular Medicine, Lanzhou University Second Hospital, Lanzhou 730030, China; (D.L.); (H.D.); (Y.W.); (Y.X.)
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20
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Hughes BK, Wallis R, Bishop CL. Yearning for machine learning: applications for the classification and characterisation of senescence. Cell Tissue Res 2023; 394:1-16. [PMID: 37016180 PMCID: PMC10558380 DOI: 10.1007/s00441-023-03768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/05/2023] [Indexed: 04/06/2023]
Abstract
Senescence is a widely appreciated tumour suppressive mechanism, which acts as a barrier to cancer development by arresting cell cycle progression in response to harmful stimuli. However, senescent cell accumulation becomes deleterious in aging and contributes to a wide range of age-related pathologies. Furthermore, senescence has beneficial roles and is associated with a growing list of normal physiological processes including wound healing and embryonic development. Therefore, the biological role of senescent cells has become increasingly nuanced and complex. The emergence of sophisticated, next-generation profiling technologies, such as single-cell RNA sequencing, has accelerated our understanding of the heterogeneity of senescence, with distinct final cell states emerging within models as well as between cell types and tissues. In order to explore data sets of increasing size and complexity, the senescence field has begun to employ machine learning (ML) methodologies to probe these intricacies. Most notably, ML has been used to aid the classification of cells as senescent, as well as to characterise the final senescence phenotypes. Here, we provide a background to the principles of ML tasks, as well as some of the most commonly used methodologies from both traditional and deep ML. We focus on the application of these within the context of senescence research, by addressing the utility of ML for the analysis of data from different laboratory technologies (microscopy, transcriptomics, proteomics, methylomics), as well as the potential within senolytic drug discovery. Together, we aim to highlight both the progress and potential for the application of ML within senescence research.
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Affiliation(s)
- Bethany K Hughes
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Ryan Wallis
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Cleo L Bishop
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
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21
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Lyons CE, Razzoli M, Bartolomucci A. The impact of life stress on hallmarks of aging and accelerated senescence: Connections in sickness and in health. Neurosci Biobehav Rev 2023; 153:105359. [PMID: 37586578 PMCID: PMC10592082 DOI: 10.1016/j.neubiorev.2023.105359] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/03/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]
Abstract
Chronic stress is a risk factor for numerous aging-related diseases and has been shown to shorten lifespan in humans and other social mammals. Yet how life stress causes such a vast range of diseases is still largely unclear. In recent years, the impact of stress on health and aging has been increasingly associated with the dysregulation of the so-called hallmarks of aging. These are basic biological mechanisms that influence intrinsic cellular functions and whose alteration can lead to accelerated aging. Here, we review correlational and experimental literature (primarily focusing on evidence from humans and murine models) on the contribution of life stress - particularly stress derived from adverse social environments - to trigger hallmarks of aging, including cellular senescence, sterile inflammation, telomere shortening, production of reactive oxygen species, DNA damage, and epigenetic changes. We also evaluate the validity of stress-induced senescence and accelerated aging as an etiopathological proposition. Finally, we highlight current gaps of knowledge and future directions for the field, and discuss perspectives for translational geroscience.
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Affiliation(s)
- Carey E Lyons
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA; Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Maria Razzoli
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Alessandro Bartolomucci
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine and Surgery, University of Parma, Parma, Italy.
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22
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Ninomiya K, Yamazaki T, Hirose T. Satellite RNAs: emerging players in subnuclear architecture and gene regulation. EMBO J 2023; 42:e114331. [PMID: 37526230 PMCID: PMC10505914 DOI: 10.15252/embj.2023114331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/13/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
Satellite DNA is characterized by long, tandemly repeated sequences mainly found in centromeres and pericentromeric chromosomal regions. The recent advent of telomere-to-telomere sequencing data revealed the complete sequences of satellite regions, including centromeric α-satellites and pericentromeric HSat1-3, which together comprise ~ 5.7% of the human genome. Despite possessing constitutive heterochromatin features, these regions are transcribed to produce long noncoding RNAs with highly repetitive sequences that associate with specific sets of proteins to play various regulatory roles. In certain stress or pathological conditions, satellite RNAs are induced to assemble mesoscopic membraneless organelles. Specifically, under heat stress, nuclear stress bodies (nSBs) are scaffolded by HSat3 lncRNAs, which sequester hundreds of RNA-binding proteins. Upon removal of the stressor, nSBs recruit additional regulatory proteins, including protein kinases and RNA methylases, which modify the previously sequestered nSB components. The sequential recruitment of substrates and enzymes enables nSBs to efficiently regulate the splicing of hundreds of pre-mRNAs under limited temperature conditions. This review discusses the structural features and regulatory roles of satellite RNAs in intracellular architecture and gene regulation.
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Affiliation(s)
- Kensuke Ninomiya
- Graduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
| | | | - Tetsuro Hirose
- Graduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI)Osaka UniversitySuitaJapan
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23
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Miyata K, Zhou X, Nishio M, Hanyu A, Chiba M, Kawasaki H, Osako T, Takeuchi K, Ohno S, Ueno T, Maruyama R, Takahashi A. Chromatin conformational changes at human satellite II contribute to the senescence phenotype in the tumor microenvironment. Proc Natl Acad Sci U S A 2023; 120:e2305046120. [PMID: 37523559 PMCID: PMC10410700 DOI: 10.1073/pnas.2305046120] [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: 04/01/2023] [Accepted: 06/23/2023] [Indexed: 08/02/2023] Open
Abstract
Cellular senescence and senescence-associated secretory phenotype (SASP) in stromal cells within the tumor microenvironment promote cancer progression. Although cellular senescence has been shown to induce changes in the higher-order chromatin structure and abnormal transcription of repetitive elements in the genome, the functional significance of these changes is unclear. In this study, we examined the human satellite II (hSATII) loci in the pericentromere to understand these changes and their functional significance. Our results indicated that the hSATII loci decompact during senescence induction, resulting in new DNA-DNA interactions in distinct genomic regions, which we refer to as DRISR (Distinctive Regions Interacted with Satellite II in Replicative senescent Fibroblasts). Interestingly, decompaction occurs before the expression of hSATII RNA. The DRISR with altered chromatin accessibility was enriched for motifs associated with cellular senescence and inflammatory SASP genes. Moreover, DNA-fluorescence in situ hybridization analysis of the breast cancer tissues revealed hSATII decompaction in cancer and stromal cells. Furthermore, we reanalyzed the single-cell assay for transposase-accessible chromatin with sequencing data and found increased SASP-related gene expression in fibroblasts exhibiting hSATII decompaction in breast cancer tissues. These findings suggest that changes in the higher-order chromatin structure of the pericentromeric repetitive sequences during cellular senescence might directly contribute to the cellular senescence phenotype and cancer progression via inflammatory gene expression.
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Affiliation(s)
- Kenichi Miyata
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Cancer Cell Communication Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Xiangyu Zhou
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Mika Nishio
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Aki Hanyu
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Masatomo Chiba
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Hiroko Kawasaki
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Tomo Osako
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Kengo Takeuchi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Shinji Ohno
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Takayuki Ueno
- Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
| | - Akiko Takahashi
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Cancer Cell Communication Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Advanced Research and Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development, Tokyo100-0004, Japan
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24
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Wang L, Donahue G, Zhang C, Havas A, Lei X, Xu C, Wang W, Vahedi G, Adams PD, Berger SL. Dynamic enhancer interactome promotes senescence and aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541769. [PMID: 37292952 PMCID: PMC10245931 DOI: 10.1101/2023.05.22.541769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Gene expression programs are regulated by enhancers which act in a context-specific manner, and can reside at great distances from their target genes. Extensive three-dimensional (3D) genome reorganization occurs in senescence, but how enhancer interactomes are reconfigured during this process is just beginning to be understood. Here we generated high-resolution contact maps of active enhancers and their target genes, assessed chromatin accessibility, and established one-dimensional maps of various histone modifications and transcription factors to comprehensively understand the regulation of enhancer configuration during senescence. Hyper-connected enhancer communities/cliques formed around genes that are highly expressed and within essential gene pathways in each cell state. In addition, motif analysis indicates the involvement of specific transcription factors in hyper-connected regulatory elements in each condition; importantly, MafK, a bZIP family transcription factor, was upregulated in senescence, and reduced expression of MafK ameliorated the senescence phenotypes. Because the accumulation of senescent cells is a key feature of aging, we further investigated enhancer connectomes in the liver of young and aged mice. Hyper-connected enhancer communities were identified during aging, which regulate essential genes that maintain cell differentiation and homeostasis. These findings reveal that hyper-connected enhancer communities correlate with high gene expression in senescence and aging and provide potential hotspots for therapeutic intervention in aging and age-associated diseases.
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25
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Ramadhiani R, Ikeda K, Miyagawa K, Ryanto GRT, Tamada N, Suzuki Y, Kirita Y, Matoba S, Hirata KI, Emoto N. Endothelial cell senescence exacerbates pulmonary hypertension by inducing juxtacrine Notch signaling in smooth muscle cells. iScience 2023; 26:106662. [PMID: 37192975 PMCID: PMC10182325 DOI: 10.1016/j.isci.2023.106662] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 03/17/2023] [Accepted: 04/06/2023] [Indexed: 05/18/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a fatal disease characterized by a progressive increase in pulmonary artery pressure caused by pathological pulmonary artery remodeling. Here, we demonstrate that endothelial cell (EC) senescence plays a negative role in pulmonary hypertension via juxtacrine interaction with smooth muscle cells (SMCs). By using EC-specific progeroid mice, we discovered that EC progeria deteriorated vascular remodeling in the lungs, and exacerbated pulmonary hypertension in mice. Mechanistically, senescent ECs overexpressed Notch ligands, which resulted in increased Notch signaling and activated proliferation and migration capacities in neighboring SMCs. Pharmacological inhibition of Notch signaling reduced the effects of senescent ECs on SMCs functions in vitro, and improved the worsened pulmonary hypertension in EC-specific progeroid mice in vivo. Our findings show that EC senescence is a critical disease-modifying factor in PAH and that EC-mediated Notch signaling is a pharmacotherapeutic target for the treatment of PAH, particularly in the elderly.
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Affiliation(s)
- Risa Ramadhiani
- Laboratory of Clinical Pharmaceutical Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada, Kobe 658-8558, Japan
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki, Chuo, Kobe 6500017, Japan
| | - Koji Ikeda
- Laboratory of Clinical Pharmaceutical Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada, Kobe 658-8558, Japan
- Department of Epidemiology for Longevity and Regional Health, Kyoto Prefectural University of Medicine, 465 Kajii, Kawaramachi-Hirokoji, Kamigyou, Kyoto 6028566, Japan
- Department of Cardiology and Nephrology, Kyoto Prefectural University of Medicine, 465 Kajii, Kawaramachi-Hirokoji, Kamigyou, Kyoto 6028566, Japan
- Corresponding author
| | - Kazuya Miyagawa
- Laboratory of Clinical Pharmaceutical Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada, Kobe 658-8558, Japan
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki, Chuo, Kobe 6500017, Japan
| | - Gusty Rizky Tough Ryanto
- Laboratory of Clinical Pharmaceutical Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada, Kobe 658-8558, Japan
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki, Chuo, Kobe 6500017, Japan
| | - Naoki Tamada
- Laboratory of Clinical Pharmaceutical Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada, Kobe 658-8558, Japan
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki, Chuo, Kobe 6500017, Japan
| | - Yoko Suzuki
- Laboratory of Clinical Pharmaceutical Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada, Kobe 658-8558, Japan
| | - Yuhei Kirita
- Department of Cardiology and Nephrology, Kyoto Prefectural University of Medicine, 465 Kajii, Kawaramachi-Hirokoji, Kamigyou, Kyoto 6028566, Japan
| | - Satoaki Matoba
- Department of Cardiology and Nephrology, Kyoto Prefectural University of Medicine, 465 Kajii, Kawaramachi-Hirokoji, Kamigyou, Kyoto 6028566, Japan
| | - Ken-ichi Hirata
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki, Chuo, Kobe 6500017, Japan
| | - Noriaki Emoto
- Laboratory of Clinical Pharmaceutical Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakitamachi, Higashinada, Kobe 658-8558, Japan
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki, Chuo, Kobe 6500017, Japan
- Corresponding author
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26
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Liu J, Zheng R, Zhang Y, Jia S, He Y, Liu J. The Cross Talk between Cellular Senescence and Melanoma: From Molecular Pathogenesis to Target Therapies. Cancers (Basel) 2023; 15:cancers15092640. [PMID: 37174106 PMCID: PMC10177054 DOI: 10.3390/cancers15092640] [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: 03/26/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Melanoma is a malignant skin tumor that originates from melanocytes. The pathogenesis of melanoma involves a complex interaction that occurs between environmental factors, ultraviolet (UV)-light damage, and genetic alterations. UV light is the primary driver of the skin aging process and development of melanoma, which can induce reactive oxygen species (ROS) production and the presence of DNA damage in the cells, and results in cell senescence. As cellular senescence plays an important role in the relationship that exists between the skin aging process and the development of melanoma, the present study provides insight into the literature concerning the topic at present and discusses the relationship between skin aging and melanoma, including the mechanisms of cellular senescence that drive melanoma progression, the microenvironment in relation to skin aging and melanoma factors, and the therapeutics concerning melanoma. This review focuses on defining the role of cellular senescence in the process of melanoma carcinogenesis and discusses the targeting of senescent cells through therapeutic approaches, highlighting the areas that require more extensive research in the field.
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Affiliation(s)
- Jiahua Liu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Runzi Zheng
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Yanghuan Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Shuting Jia
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Yonghan He
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Jing Liu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming 650500, China
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27
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Kehrberg RJ, Bhyravbhatla N, Batra SK, Kumar S. Epigenetic regulation of cancer-associated fibroblast heterogeneity. Biochim Biophys Acta Rev Cancer 2023; 1878:188901. [PMID: 37120098 PMCID: PMC10375465 DOI: 10.1016/j.bbcan.2023.188901] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/13/2023] [Accepted: 04/22/2023] [Indexed: 05/01/2023]
Abstract
Cancer-associated fibroblasts (CAFs), a significant component of the tumor microenvironment (TME), contribute to cancer progression through the secretion of extracellular matrix (ECM), growth factors, and metabolites. It is now well recognized that CAFs are a heterogenous population with ablation experiments leading to reduced tumor growth and single-cell RNA sequencing demonstrating CAF subgroups. CAFs lack genetic mutations yet substantially differ from their normal stromal precursors. Here, we review epigenetic changes in CAF maturation, focusing on DNA methylation and histone modifications. DNA methylation changes in CAFs have been demonstrated globally, while roles of methylation at specific genes affect tumor growth. Further, loss of CAF histone methylation and gain of histone acetylation has been shown to promote CAF activation and tumor promotion. Many CAF activating factors, such as transforming growth factor β (TGFβ), lead to these epigenetic changes. MicroRNAs (miRNAs) serve as targets and orchestrators of epigenetic modifications that influence gene expression. Bromodomain and extra-terminal domain (BET), an epigenetic reader, recognizes histone acetylation and activates the transcription of genes leading to the pro-tumor phenotype of CAFs.
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Affiliation(s)
- Rachel J Kehrberg
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Namita Bhyravbhatla
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Sushil Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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28
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la Torre A, Lo Vecchio F, Greco A. Epigenetic Mechanisms of Aging and Aging-Associated Diseases. Cells 2023; 12:cells12081163. [PMID: 37190071 DOI: 10.3390/cells12081163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
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Affiliation(s)
- Annamaria la Torre
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Filomena Lo Vecchio
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Antonio Greco
- Complex Unit of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
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29
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Sen P, Donahue G, Li C, Egervari G, Yang N, Lan Y, Robertson N, Shah PP, Kerkhoven E, Schultz DC, Adams PD, Berger SL. Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. NATURE AGING 2023; 3:402-417. [PMID: 37117791 PMCID: PMC10165726 DOI: 10.1038/s43587-023-00384-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2023] [Indexed: 04/30/2023]
Abstract
Mammalian aging is characterized by the progressive loss of tissue function and increased risk for disease. Accumulation of senescent cells in aging tissues partly contributes to this decline, and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. The fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal aberrant transcription initiation inside genes during senescence and aging that co-occurs with changes in the chromatin landscape. Interventions that alter these spurious transcripts have profound consequences on cellular health, primarily affecting intracellular signal transduction pathways. We propose that age-related spurious transcription promotes a noisy transcriptome and degradation of coherent transcriptional networks.
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Affiliation(s)
- Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Greg Donahue
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine Li
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabor Egervari
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neil Robertson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Parisha P Shah
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik Kerkhoven
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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30
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Desaulniers D, Cummings-Lorbetskie C, Leingartner K, Meier MJ, Pickles JC, Yauk CL. DNA methylation changes from primary cultures through senescence-bypass in Syrian hamster fetal cells initially exposed to benzo[a]pyrene. Toxicology 2023; 487:153451. [PMID: 36754249 DOI: 10.1016/j.tox.2023.153451] [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: 12/06/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Current chemical testing strategies are limited in their ability to detect non-genotoxic carcinogens (NGTxC). Epigenetic anomalies develop during carcinogenesis regardless of whether the molecular initiating event is associated with genotoxic (GTxC) or NGTxC events; therefore, epigenetic markers may be harnessed to develop new approach methodologies that improve the detection of both types of carcinogens. This study used Syrian hamster fetal cells to establish the chronology of carcinogen-induced DNA methylation changes from primary cells until senescence-bypass as an essential carcinogenic step. Cells exposed to solvent control for 7 days were compared to naïve primary cultures, to cells exposed for 7 days to benzo[a]pyrene, and to cells at the subsequent transformation stages: normal colonies, morphologically transformed colonies, senescence, senescence-bypass, and sustained proliferation in vitro. DNA methylation changes identified by reduced representation bisulphite sequencing were minimal at day-7. Profound DNA methylation changes arose during cellular senescence and some of these early differentially methylated regions (DMRs) were preserved through the final sustained proliferation stage. A set of these DMRs (e.g., Pou4f1, Aifm3, B3galnt2, Bhlhe22, Gja8, Klf17, and L1l) were validated by pyrosequencing and their reproducibility was confirmed across multiple clones obtained from a different laboratory. These DNA methylation changes could serve as biomarkers to enhance objectivity and mechanistic understanding of cell transformation and could be used to predict senescence-bypass and chemical carcinogenicity.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | | | - Karen Leingartner
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | | | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
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31
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Zhao Y, Li H, Guo Q, Hui H. Multiple characteristic alterations and available therapeutic strategies of cellular senescence. J Zhejiang Univ Sci B 2023; 24:101-114. [PMID: 36751697 PMCID: PMC9936135 DOI: 10.1631/jzus.b2200178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Given its state of stable proliferative inhibition, cellular senescence is primarily depicted as a critical mechanism by which organisms delay the progression of carcinogenesis. Cells undergoing senescence are often associated with the alteration of a series of specific features and functions, such as metabolic shifts, stemness induction, and microenvironment remodeling. However, recent research has revealed more complexity associated with senescence, including adverse effects on both physiological and pathological processes. How organisms evade these harmful consequences and survive has become an urgent research issue. Several therapeutic strategies targeting senescence, including senolytics, senomorphics, immunotherapy, and function restoration, have achieved initial success in certain scenarios. In this review, we describe in detail the characteristic changes associated with cellular senescence and summarize currently available countermeasures.
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Affiliation(s)
- Yunzi Zhao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, 210009 China
| | - Hui Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, 210009 China
| | - Qinglong Guo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, 210009 China
| | - Hui Hui
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 210009, China.
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32
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Dasgupta N, Adams PD. Is aging a "Retro"spective event? Cell 2023; 186:233-235. [PMID: 36669469 DOI: 10.1016/j.cell.2022.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 01/20/2023]
Abstract
Reactivation of endogenous retroviruses (ERVs), the relics of ancient infections, has been implicated in a number of disease contexts. In this issue of Cell, Liu et al. show how reactivation of ERVs in old age can induce senescence. This awakening of ERVs is associated with their epigenetic derepression and contributes to age-associated chronic inflammation.
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Affiliation(s)
- Nirmalya Dasgupta
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Peter D Adams
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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Stewart-Morgan KR, Requena CE, Flury V, Du Q, Heckhausen Z, Hajkova P, Groth A. Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS. Nat Cell Biol 2023; 25:183-193. [PMID: 36635504 PMCID: PMC9859752 DOI: 10.1038/s41556-022-01048-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 11/10/2022] [Indexed: 01/14/2023]
Abstract
DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized; however, the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we develop isolation of DNA by 5-ethynyl-deoxyuridine labelling for mass spectrometry (iDEMS), a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. iDEMS reveals an unexpectedly hemi-methylated landscape on nascent DNA. Combining iDEMS with metabolic labelling reveals that methylation maintenance is outpaced by cell division in mouse embryonic stem cells. Our approach shows that hydroxymethylation is perpetually asymmetric between sister strands in favour of the parental, template strand. iDEMS can be coupled with immunoprecipitation of chromatin proteins, revealing features of DNA methylation-histone modification crosstalk and suggesting a model for interplay between methylation and nucleosome assembly. iDEMS therefore elucidates long-standing questions about DNA modification propagation and provides an important orthogonal technology to understanding this process in dynamic cellular contexts.
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Affiliation(s)
- Kathleen R Stewart-Morgan
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cristina E Requena
- MRC London Institute of Medical Sciences (LMS), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Valentin Flury
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Qian Du
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Zoe Heckhausen
- MRC London Institute of Medical Sciences (LMS), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Petra Hajkova
- MRC London Institute of Medical Sciences (LMS), London, UK. .,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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METTL14 Regulates Intestine Cellular Senescence through m 6A Modification of Lamin B Receptor. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9096436. [PMID: 36578521 PMCID: PMC9792243 DOI: 10.1155/2022/9096436] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/01/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
N-6-Methyladenosine (m6A) modification is involved in multiple biological processes including aging. However, the regulation of m6A methyltransferase-like 14 (METTL14) in aging remains unclear. Here, we revealed that the level of m6A modification and the expression of METTL14 were particularly decreased in the intestine of aged mice as compared to young mice. Similar results were confirmed in Drosophila melanogaster. Knockdown of Mettl14 in Drosophila resulted in a short lifespan, associated disrupted intestinal integrity, and reduced climbing ability. In human CCD-18Co cells, knockdown of METTL14 accelerated cellular senescence, and the overexpression of METTL14 rescued senescent phenotypes. We also identified the lamin B receptor (LBR) as a target gene for METTL14-mediated m6A modification. Knockdown of METTL14 decreased m6A level of LBR, resulted in LBR mRNA instability, and thus induced cellular senescence. Our findings suggest that METTL14 plays an essential role in the m6A modification-dependent aging process via the regulation of LBR and provides a potential target for cellular senescence.
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Cell division drives DNA methylation loss in late-replicating domains in primary human cells. Nat Commun 2022; 13:6659. [PMID: 36347867 PMCID: PMC9643452 DOI: 10.1038/s41467-022-34268-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
DNA methylation undergoes dramatic age-related changes, first described more than four decades ago. Loss of DNA methylation within partially methylated domains (PMDs), late-replicating regions of the genome attached to the nuclear lamina, advances with age in normal tissues, and is further exacerbated in cancer. We present here experimental evidence that this DNA hypomethylation is directly driven by proliferation-associated DNA replication. Within PMDs, loss of DNA methylation at low-density CpGs in A:T-rich immediate context (PMD solo-WCGWs) tracks cumulative population doublings in primary cell culture. Cell cycle deceleration results in a proportional decrease in the rate of DNA hypomethylation. Blocking DNA replication via Mitomycin C treatment halts methylation loss. Loss of methylation continues unabated after TERT immortalization until finally reaching a severely hypomethylated equilibrium. Ambient oxygen culture conditions increases the rate of methylation loss compared to low-oxygen conditions, suggesting that some methylation loss may occur during unscheduled, oxidative damage repair-associated DNA synthesis. Finally, we present and validate a model to estimate the relative cumulative replicative histories of human cells, which we call "RepliTali" (Replication Times Accumulated in Lifetime).
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36
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Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X, Ren B. Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain. Cell Res 2022; 32:1008-1021. [PMID: 36207411 PMCID: PMC9652396 DOI: 10.1038/s41422-022-00719-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/21/2022] [Indexed: 01/31/2023] Open
Abstract
Loss of heterochromatin has been implicated as a cause of pre-mature aging and age-associated decline in organ functions in mammals; however, the specific cell types and gene loci affected by this type of epigenetic change have remained unclear. To address this knowledge gap, we probed chromatin accessibility at single-cell resolution in the brains, hearts, skeletal muscles, and bone marrows from young, middle-aged, and old mice, and assessed age-associated changes at 353,126 candidate cis-regulatory elements (cCREs) across 32 major cell types. Unexpectedly, we detected increased chromatin accessibility within specific heterochromatin domains in old mouse excitatory neurons. The gain of chromatin accessibility at these genomic loci was accompanied by the cell-type-specific loss of heterochromatin and activation of LINE1 elements. Immunostaining further confirmed the loss of the heterochromatin mark H3K9me3 in the excitatory neurons but not in inhibitory neurons or glial cells. Our results reveal the cell-type-specific changes in chromatin landscapes in old mice and shed light on the scope of heterochromatin loss in mammalian aging.
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Affiliation(s)
- Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- School of Life Sciences, Westlake University, Hangzhou, China.
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Chenxu Zhu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Steven Francis Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Liqi Tong
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA.
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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37
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Han X, Liu T, Zhai J, Liu C, Wang W, Nie C, Wang Q, Zhu X, Zhou H, Tian W. Association between EPHA5 methylation status in peripheral blood leukocytes and the risk and prognosis of gastric cancer. PeerJ 2022; 10:e13774. [PMID: 36164608 PMCID: PMC9508887 DOI: 10.7717/peerj.13774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/01/2022] [Indexed: 01/19/2023] Open
Abstract
Purpose Altered DNA methylation, genetic alterations, and environmental factors are involved in tumorigenesis. As a tumor suppressor gene, abnormal EPHA5 methylation was found in gastric cancer (GC) tissues and was linked to the initiation, progression and prognosis of GC. In this study, the EPHA5 methylation level in peripheral blood leukocytes (PBLs) was detected to explore its relationship with GC risk and prognosis. Methods A total of 366 GC cases and 374 controls were selected as the subjects of this study to collect their environmental factors, and the EPHA5 methylation status was detected through the methylation-sensitive high-resolution melting method. Logistic regression analysis was utilized to evaluate the associations among EPHA5 methylation, environmental factors and GC risk. Meanwhile, the propensity score (PS) was used to adjust the imbalance of some independent variables. Results After PS adjustment, EPHA5 Pm (positive methylation) was more likely to increase the GC risk than EPHA5 Nm (negative methylation) (ORb = 1.827, 95% CI [1.202-2.777], P = 0.005). EPHA5 Pm had a more significant association with GC risk in the elderly (ORa = 2.785, 95% CI [1.563-4.961], P = 0.001) and H. pylori-negative groups (ORa = 2.758, 95% CI [1.369-5.555], P = 0.005). Moreover, the combined effects of EPHA5 Pm and H. pylori infection (ORc a = 3.543, 95% CI [2.233-5.621], P < 0.001), consumption of alcohol (ORc a = 2.893, 95% CI [1.844-4.539], P < 0.001), and salty food intake (ORc a = 4.018, 95% CI [2.538-6.362], P < 0.001) on increasing the GC risk were observed. In addition, no convincing association was found between EPHA5 Pm and the GC prognosis. Conclusions EPHA5 methylation in PBLs and its combined effects with environmental risk factors are related to the GC risk.
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38
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Cassidy LD, Narita M. Autophagy at the intersection of aging, senescence, and cancer. Mol Oncol 2022; 16:3259-3275. [PMID: 35689420 PMCID: PMC9490138 DOI: 10.1002/1878-0261.13269] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/24/2022] [Accepted: 06/09/2022] [Indexed: 01/18/2023] Open
Abstract
Autophagy is an evolutionarily conserved cellular process in which macromolecules undergo lysosomal degradation. It fulfills essential roles in quality controlling cellular constituents and in energy homeostasis. Basal autophagy is also widely accepted to provide a protective role in aging and aging-related disorders, and its decline with age might precipitate the onset of a variety of diseases. In this review, we discuss the role of basal autophagy in maintaining homeostasis, in part through the maintenance of stem cell populations and the prevention of cellular senescence. We also consider how stress-induced senescence, for example, during oncogene activation and in premalignant disease, might rely on autophagy, and the possibility that the age-associated decline in autophagy might promote tumour development through a variety of mechanisms. Ultimately, evidence suggests that autophagy is required for malignant cancer progression in a number of settings. Thus, autophagy appears to be tumour-suppressive during the early stages of tumorigenesis and tumour-promoting at later stages.
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Affiliation(s)
- Liam D. Cassidy
- Cancer Research UK Cambridge InstituteUniversity of CambridgeUK
| | - Masashi Narita
- Cancer Research UK Cambridge InstituteUniversity of CambridgeUK
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
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Chen Y, Liang L, Wu C, Cao Z, Xia L, Meng J, Wang Z. Epigenetic Control of Vascular Smooth Muscle Cell Function in Atherosclerosis: A Role for DNA Methylation. DNA Cell Biol 2022; 41:824-837. [PMID: 35900288 DOI: 10.1089/dna.2022.0278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Atherosclerosis is a complex vascular inflammatory disease in which multiple cell types are involved, including vascular smooth muscle cells (VSMCs). In response to vascular injury and inflammatory stimuli, VSMCs undergo a "phenotypic switching" characterized by extracellular matrix secretion, loss of contractility, and abnormal proliferation and migration, which play a key role in the progression of atherosclerosis. DNA methylation modification is an important epigenetic mechanism that plays an important role in atherosclerosis. Studies investigating abnormal DNA methylation in patients with atherosclerosis have determined a specific DNA methylation profile, and proposed multiple pathways and genes involved in the etiopathogenesis of atherosclerosis. Recent studies have also revealed that DNA methylation modification controls VSMC function by regulating gene expression involved in atherosclerosis. In this review, we summarize the recent advances regarding the epigenetic control of VSMC function by DNA methylation in atherosclerosis and provide insights into the development of VSMC-centered therapeutic strategies.
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Affiliation(s)
- Yanjun Chen
- Key Laboratory for Arteriosclerology of Hunan Province, Institute of Cardiovascular Disease, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, China
| | - Lingli Liang
- Key Laboratory for Arteriosclerology of Hunan Province, Institute of Cardiovascular Disease, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, China
| | - Chunyan Wu
- The Third Affiliated Hospital of University of South China, Hengyang, China
| | - Zitong Cao
- Key Laboratory for Arteriosclerology of Hunan Province, Institute of Cardiovascular Disease, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, China
| | - Linzhen Xia
- Key Laboratory for Arteriosclerology of Hunan Province, Institute of Cardiovascular Disease, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, China
| | - Jun Meng
- Functional Department, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Zuo Wang
- Key Laboratory for Arteriosclerology of Hunan Province, Institute of Cardiovascular Disease, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, China
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Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells. Cancers (Basel) 2022; 14:cancers14143402. [PMID: 35884461 PMCID: PMC9319119 DOI: 10.3390/cancers14143402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary We exposed LUHMES cells, differentiated into mature neurons, to bortezomib (BTZ) in two treatment cycles and analyzed the methylomes of these cells after each cycle, controlling the analysis for the methylation changes potentially induced by the long-term culture. Our results show that BTZ induces methylation changes that may affect cell morphogenesis, neurogenesis, and neurotransmission. These changes are specifically enriched within transcription factor binding sites of EBF, PAX, DLX, LHX, and HNF family members, which have been shown to regulate neurogenesis and neuronal differentiation. We further show that the observed methylation changes are not present in the SH-SY5Y cells that we used to study mechanisms of development of BTZ resistance. Altogether, our results show that BTZ treatment induces very specific changes in the methylomes of neuronal cells. Abstract Bortezomib (BTZ) is proteasome inhibitor, effectively used in the treatment of multiple myeloma, but frequently discontinued due to peripheral neuropathy, which develops in patients after consecutive treatment cycles. The molecular mechanisms affected by BTZ in neuronal cells, which result in neuropathy, remain unknown. However, BTZ is unlikely to lead to permanent morphological nerve damage, because neuropathy reverses after discontinuation of treatment, and nerve cells have very limited renewal capacity. We have previously shown that BTZ induces methylation changes in SH-SY5Y cells, which take part in the development of treatment resistance. Here, we hypothesized that BTZ affects the methylomes of mature neurons, and these changes are associated with BTZ neurotoxicity. Thus, we studied methylomes of neuronal cells, differentiated from the LUHMES cell line, after cycles of treatment with BTZ. Our results show that BTZ induces specific methylation changes in mature neurons, which are not present in SH-SY5Y cells after BTZ treatment. These changes appear to affect genes involved in morphogenesis, neurogenesis, and neurotransmission. Furthermore, identified methylation changes are significantly enriched within binding sites of transcription factors previously linked to neuron physiology, including EBF, PAX, DLX, LHX, and HNF family members. Altogether, our results indicate that methylation changes are likely to be involved in BTZ neurotoxicity.
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Revisiting Epithelial Carcinogenesis. Int J Mol Sci 2022; 23:ijms23137437. [PMID: 35806442 PMCID: PMC9267463 DOI: 10.3390/ijms23137437] [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: 05/10/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
The origin of cancer remains one of the most important enigmas in modern biology. This paper presents a hypothesis for the origin of carcinomas in which cellular aging and inflammation enable the recovery of cellular plasticity, which may ultimately result in cancer. The hypothesis describes carcinogenesis as the result of the dedifferentiation undergone by epithelial cells in hyperplasia due to replicative senescence towards a mesenchymal cell state with potentially cancerous behavior. In support of this hypothesis, the molecular, cellular, and histopathological evidence was critically reviewed and reinterpreted when necessary to postulate a plausible generic series of mechanisms for the origin and progression of carcinomas. In addition, the implications of this theoretical framework for the current strategies of cancer treatment are discussed considering recent evidence of the molecular events underlying the epigenetic switches involved in the resistance of breast carcinomas. The hypothesis also proposes an epigenetic landscape for their progression and a potential mechanism for restraining the degree of dedifferentiation and malignant behavior. In addition, the manuscript revisits the gradual degeneration of the nonalcoholic fatty liver disease to propose an integrative generalized mechanistic explanation for the involution and carcinogenesis of tissues associated with aging. The presented hypothesis might serve to understand and structure new findings into a more encompassing view of the genesis of degenerative diseases and may inspire novel approaches for their study and therapy.
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Tan SYX, Zhang J, Tee WW. Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer. Front Cell Dev Biol 2022; 10:931493. [PMID: 35757000 PMCID: PMC9213816 DOI: 10.3389/fcell.2022.931493] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Epigenetics comprise a diverse array of reversible and dynamic modifications to the cell’s genome without implicating any DNA sequence alterations. Both the external environment surrounding the organism, as well as the internal microenvironment of cells and tissues, contribute to these epigenetic processes that play critical roles in cell fate specification and organismal development. On the other hand, dysregulation of epigenetic activities can initiate and sustain carcinogenesis, which is often augmented by inflammation. Chronic inflammation, one of the major hallmarks of cancer, stems from proinflammatory cytokines that are secreted by tumor and tumor-associated cells in the tumor microenvironment. At the same time, inflammatory signaling can establish positive and negative feedback circuits with chromatin to modulate changes in the global epigenetic landscape. In this review, we provide an in-depth discussion of the interconnected crosstalk between epigenetics and inflammation, specifically how epigenetic mechanisms at different hierarchical levels of the genome control inflammatory gene transcription, which in turn enact changes within the cell’s epigenomic profile, especially in the context of inflammation-induced cancer.
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Affiliation(s)
- Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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43
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Lyu Y, Ge Y. Toward Elucidating Epigenetic and Metabolic Regulation of Stem Cell Lineage Plasticity in Skin Aging. Front Cell Dev Biol 2022; 10:903904. [PMID: 35663405 PMCID: PMC9160930 DOI: 10.3389/fcell.2022.903904] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Skin is the largest organ in human body, harboring a plethora of cell types and serving as the organismal barrier. Skin aging such as wrinkling and hair graying is graphically pronounced, and the molecular mechanisms behind these phenotypic manifestations are beginning to unfold. As in many other organs and tissues, epigenetic and metabolic deregulations have emerged as key aging drivers. Particularly in the context of the skin epithelium, the epigenome and metabolome coordinately shape lineage plasticity and orchestrate stem cell function during aging. Our review discusses recent studies that proposed molecular mechanisms that drive the degeneration of hair follicles, a major appendage of the skin. By focusing on skin while comparing it to model organisms and adult stem cells of other tissues, we summarize literature on genotoxic stress, nutritional sensing, metabolic rewiring, mitochondrial activity, and epigenetic regulations of stem cell plasticity. Finally, we speculate about the rejuvenation potential of rate-limiting upstream signals during aging and the dominant role of the tissue microenvironment in dictating aged epithelial stem cell function.
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Affiliation(s)
| | - Yejing Ge
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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44
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Colonna Romano N, Fanti L. Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. Cells 2022; 11:cells11061048. [PMID: 35326499 PMCID: PMC8947103 DOI: 10.3390/cells11061048] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.
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45
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Hu L, Li H, Zi M, Li W, Liu J, Yang Y, Zhou D, Kong QP, Zhang Y, He Y. Why Senescent Cells Are Resistant to Apoptosis: An Insight for Senolytic Development. Front Cell Dev Biol 2022; 10:822816. [PMID: 35252191 PMCID: PMC8890612 DOI: 10.3389/fcell.2022.822816] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/26/2022] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a process that leads to a state of irreversible cell growth arrest induced by a variety of intrinsic and extrinsic stresses. Senescent cells (SnCs) accumulate with age and have been implicated in various age-related diseases in part via expressing the senescence-associated secretory phenotype. Elimination of SnCs has the potential to delay aging, treat age-related diseases and extend healthspan. However, once cells becoming senescent, they are more resistant to apoptotic stimuli. Senolytics can selectively eliminate SnCs by targeting the SnC anti-apoptotic pathways (SCAPs). They have been developed as a novel pharmacological strategy to treat various age-related diseases. However, the heterogeneity of the SnCs indicates that SnCs depend on different proteins or pathways for their survival. Thus, a better understanding of the underlying mechanisms for apoptotic resistance of SnCs will provide new molecular targets for the development of cell-specific or broad-spectrum therapeutics to clear SnCs. In this review, we discussed the latest research progresses and challenge in senolytic development, described the significance of regulation of senescence and apoptosis in aging, and systematically summarized the SCAPs involved in the apoptotic resistance in SnCs.
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Affiliation(s)
- Li Hu
- Department of Geriatrics, The Second Affiliated Hospital of Hainan Medical University, Haikou, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,College of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, China
| | - Huiqin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Meiting Zi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wen Li
- Department of Endocrinology, The Third People's Hospital of Yunnan Province, Kunming, China
| | - Jing Liu
- Lab of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, China
| | - Yang Yang
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yunxia Zhang
- Department of Geriatrics, The Second Affiliated Hospital of Hainan Medical University, Haikou, China.,College of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, China
| | - Yonghan He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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46
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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.
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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
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47
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Fakhri S, Zachariah Moradi S, DeLiberto LK, Bishayee A. Cellular senescence signaling in cancer: A novel therapeutic target to combat human malignancies. Biochem Pharmacol 2022; 199:114989. [DOI: 10.1016/j.bcp.2022.114989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 12/26/2022]
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48
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Miyata K, Takahashi A. Pericentromeric repetitive ncRNA regulates chromatin interaction and inflammatory gene expression. Nucleus 2022; 13:74-78. [PMID: 35167425 PMCID: PMC8855862 DOI: 10.1080/19491034.2022.2034269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellular senescence provokes a dramatic alteration of chromatin organization and gene expression profile of proinflammatory factors, thereby contributing to various age-related pathologies via the senescence-associated secretory phenotype (SASP). Chromatin organization and global gene expression are maintained through the CCCTC-binding factor (CTCF). However, the molecular mechanism underlying CTCF regulation and its association with SASP gene expression remains to be fully elucidated. A recent study by our team showed that noncoding RNA (ncRNA) derived from normally silenced pericentromeric repetitive sequences directly impair the DNA binding of CTCF. This CTCF disturbance increases the accessibility of chromatin at the loci of SASP genes and caused the transcription of inflammatory factors. This mechanism may promote malignant transformation.
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Affiliation(s)
- Kenichi Miyata
- Project for Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Cancer Cell Communication Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Akiko Takahashi
- Project for Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Cancer Cell Communication Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan.,Advanced Research & Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development (Amed), Tokyo, Japan
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49
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Crouch J, Shvedova M, Thanapaul RJRS, Botchkarev V, Roh D. Epigenetic Regulation of Cellular Senescence. Cells 2022; 11:672. [PMID: 35203320 PMCID: PMC8870565 DOI: 10.3390/cells11040672] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Senescence is a complex cellular stress response that abolishes proliferative capacity and generates a unique secretory pattern that is implicated in organismal aging and age-related disease. How a cell transitions to a senescent state is multifactorial and often requires transcriptional regulation of multiple genes. Epigenetic alterations to DNA and chromatin are powerful regulators of genome architecture and gene expression, and they play a crucial role in mediating the induction and maintenance of senescence. This review will highlight the changes in chromatin, DNA methylation, and histone alterations that establish and maintain cellular senescence, alongside the specific epigenetic regulation of the senescence-associated secretory phenotype (SASP).
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Affiliation(s)
- Jack Crouch
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Maria Shvedova
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Rex Jeya Rajkumar Samdavid Thanapaul
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Vladimir Botchkarev
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Daniel Roh
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
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50
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Interconnections between Inflammageing and Immunosenescence during Ageing. Cells 2022; 11:cells11030359. [PMID: 35159168 PMCID: PMC8834134 DOI: 10.3390/cells11030359] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 02/04/2023] Open
Abstract
Acute inflammation is a physiological response to injury or infection, with a cascade of steps that ultimately lead to the recruitment of immune cells to clear invading pathogens and heal wounds. However, chronic inflammation arising from the continued presence of the initial trigger, or the dysfunction of signalling and/or effector pathways, is harmful to health. While successful ageing in older adults, including centenarians, is associated with low levels of inflammation, elevated inflammation increases the risk of poor health and death. Hence inflammation has been described as one of seven pillars of ageing. Age-associated sterile, chronic, and low-grade inflammation is commonly termed inflammageing-it is not simply a consequence of increasing chronological age, but is also a marker of biological ageing, multimorbidity, and mortality risk. While inflammageing was initially thought to be caused by "continuous antigenic load and stress", reports from the last two decades describe a much more complex phenomenon also involving cellular senescence and the ageing of the immune system. In this review, we explore some of the main sources and consequences of inflammageing in the context of immunosenescence and highlight potential interventions. In particular, we assess the contribution of cellular senescence to age-associated inflammation, identify patterns of pro- and anti-inflammatory markers characteristic of inflammageing, describe alterations in the ageing immune system that lead to elevated inflammation, and finally assess the ways that diet, exercise, and pharmacological interventions can reduce inflammageing and thus, improve later life health.
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