1
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Manzo SG, Mazouzi A, Leemans C, van Schaik T, Neyazi N, van Ruiten MS, Rowland BD, Brummelkamp TR, van Steensel B. Chromatin protein complexes involved in gene repression in lamina-associated domains. EMBO J 2024:10.1038/s44318-024-00214-1. [PMID: 39322756 DOI: 10.1038/s44318-024-00214-1] [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: 03/26/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/27/2024] Open
Abstract
Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina (NL) and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here, we performed FACS-based whole-genome genetic screens in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few NL proteins, but revealed roles for dozens of known chromatin regulators. Among these are the negative elongation factor (NELF) complex and interacting factors involved in RNA polymerase pausing, suggesting that regulation of transcription elongation is a mechanism to repress transcription in LADs. Furthermore, the chromatin remodeler complex BAF and the activation complex Mediator can work both as activators and repressors in LADs, depending on the local context and possibly by rewiring heterochromatin. Our data indicate that the fundamental regulators of transcription and chromatin remodeling, rather than interaction with NL proteins, play a major role in transcription regulation within LADs.
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Affiliation(s)
- Stefano G Manzo
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Abdelghani Mazouzi
- Oncode Institute, Amsterdam, the Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christ Leemans
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Tom van Schaik
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Nadia Neyazi
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Marjon S van Ruiten
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Amsterdam, the Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Oncode Institute, Amsterdam, the Netherlands.
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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2
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Scanlan RL, Pease L, O'Keefe H, Martinez-Guimera A, Rasmussen L, Wordsworth J, Shanley D. Systematic transcriptomic analysis and temporal modelling of human fibroblast senescence. FRONTIERS IN AGING 2024; 5:1448543. [PMID: 39267611 PMCID: PMC11390594 DOI: 10.3389/fragi.2024.1448543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/19/2024] [Indexed: 09/15/2024]
Abstract
Cellular senescence is a diverse phenotype characterised by permanent cell cycle arrest and an associated secretory phenotype (SASP) which includes inflammatory cytokines. Typically, senescent cells are removed by the immune system, but this process becomes dysregulated with age causing senescent cells to accumulate and induce chronic inflammatory signalling. Identifying senescent cells is challenging due to senescence phenotype heterogeneity, and senotherapy often requires a combinatorial approach. Here we systematically collected 119 transcriptomic datasets related to human fibroblasts, forming an online database describing the relevant variables for each study allowing users to filter for variables and genes of interest. Our own analysis of the database identified 28 genes significantly up- or downregulated across four senescence types (DNA damage induced senescence (DDIS), oncogene induced senescence (OIS), replicative senescence, and bystander induced senescence) compared to proliferating controls. We also found gene expression patterns of conventional senescence markers were highly specific and reliable for different senescence inducers, cell lines, and timepoints. Our comprehensive data supported several observations made in existing studies using single datasets, including stronger p53 signalling in DDIS compared to OIS. However, contrary to some early observations, both p16 and p21 mRNA levels rise quickly, depending on senescence type, and persist for at least 8-11 days. Additionally, little evidence was found to support an initial TGFβ-centric SASP. To support our transcriptomic analysis, we computationally modelled temporal protein changes of select core senescence proteins during DDIS and OIS, as well as perform knockdown interventions. We conclude that while universal biomarkers of senescence are difficult to identify, conventional senescence markers follow predictable profiles and construction of a framework for studying senescence could lead to more reproducible data and understanding of senescence heterogeneity.
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Affiliation(s)
- R-L Scanlan
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - L Pease
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - H O'Keefe
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - A Martinez-Guimera
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - L Rasmussen
- Center for Healthy Aging, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - J Wordsworth
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
| | - D Shanley
- Campus for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
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3
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Marin H, Simental E, Allen C, Martin E, Panning B, Al-Sady B, Buchwalter A. The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602542. [PMID: 39026839 PMCID: PMC11257442 DOI: 10.1101/2024.07.08.602542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Heterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the effect of spatial position on heterochromatin function has not been defined. Here, we remove three nuclear lamins and lamin B receptor (LBR) in mouse embryonic stem cells (mESCs) and show that heterochromatin detaches from the nuclear periphery. Mutant mESCs sustain naïve pluripotency and maintain H3K9me2 across the genome but cannot repress H3K9me2-marked genes or transposons. Further, mutant cells fail to differentiate into epiblast-like cells (EpiLCs), a transition that requires the expansion of H3K9me2 across the genome. Mutant EpiLCs can silence naïve pluripotency genes and activate epiblast-stage genes. However, H3K9me2 cannot repress markers of alternative fates, including primitive endoderm. We conclude that the nuclear periphery controls the spatial position, dynamic remodeling, and repressive capacity of H3K9me2-marked heterochromatin to shape cell fate decisions.
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Affiliation(s)
- Harold Marin
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Eric Simental
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Department of Biochemistry, University of California, San Francisco, CA, USA
| | - Charlie Allen
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Eric Martin
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Barbara Panning
- Department of Biochemistry, University of California, San Francisco, CA, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Physiology, University of California, San Francisco, CA, USA
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4
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Tao W, Yu Z, Han JDJ. Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators. Cell Metab 2024; 36:1126-1143.e5. [PMID: 38604170 DOI: 10.1016/j.cmet.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/15/2023] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Cellular senescence underlies many aging-related pathologies, but its heterogeneity poses challenges for studying and targeting senescent cells. We present here a machine learning program senescent cell identification (SenCID), which accurately identifies senescent cells in both bulk and single-cell transcriptome. Trained on 602 samples from 52 senescence transcriptome datasets spanning 30 cell types, SenCID identifies six major senescence identities (SIDs). Different SIDs exhibit different senescence baselines, stemness, gene functions, and responses to senolytics. SenCID enables the reconstruction of senescent trajectories under normal aging, chronic diseases, and COVID-19. Additionally, when applied to single-cell Perturb-seq data, SenCID helps reveal a hierarchy of senescence modulators. Overall, SenCID is an essential tool for precise single-cell analysis of cellular senescence, enabling targeted interventions against senescent cells.
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Affiliation(s)
- Wanyu Tao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Zhengqing Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China; Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China.
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5
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Biggs LC, Miroshnikova YA. Nuclear mechanotransduction on skin stem cell fate regulation. Curr Opin Cell Biol 2024; 87:102328. [PMID: 38340567 DOI: 10.1016/j.ceb.2024.102328] [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: 11/01/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Mammalian skin is a highly dynamic and regenerative organ that has long been recognized as a mechanically active composite of tissues withstanding daily compressive and tensile forces that arise from body movement. Importantly, cell- and tissue-scale mechanical signals are critical regulators of skin morphogenesis and homeostasis. These signals are sensed at the cellular periphery and transduced by mechanosensitive proteins within the plasma membrane to the cytoskeletal networks, and eventually into the nucleus to regulate chromatin organization and gene expression. The role of each of these nodes in producing a coherent mechanoresponse at both cell- and tissue-scales is emerging. Here we focus on the key cytoplasmic and nuclear mechanosensitive structures that are critical for the mammalian skin development and homeostatic maintenance. We propose that the mechanical state of the skin, in particular of its nuclear compartment, is a critical rheostat that fine-tunes developmental and homeostatic processes essential for the proper function of the organ.
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Affiliation(s)
- Leah C Biggs
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.
| | - Yekaterina A Miroshnikova
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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6
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Zhegalova IV, Vasiluev PA, Flyamer IM, Shtompel AS, Glazyrina E, Shilova N, Minzhenkova M, Markova Z, Petrova NV, Dashinimaev EB, Razin SV, Ulianov SV. Trisomies Reorganize Human 3D Genome. Int J Mol Sci 2023; 24:16044. [PMID: 38003233 PMCID: PMC10671006 DOI: 10.3390/ijms242216044] [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: 09/06/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
Trisomy is the presence of one extra copy of an entire chromosome or its part in a cell nucleus. In humans, autosomal trisomies are associated with severe developmental abnormalities leading to embryonic lethality, miscarriage or pronounced deviations of various organs and systems at birth. Trisomies are characterized by alterations in gene expression level, not exclusively on the trisomic chromosome, but throughout the genome. Here, we applied the high-throughput chromosome conformation capture technique (Hi-C) to study chromatin 3D structure in human chorion cells carrying either additional chromosome 13 (Patau syndrome) or chromosome 16 and in cultured fibroblasts with extra chromosome 18 (Edwards syndrome). The presence of extra chromosomes results in systematic changes of contact frequencies between small and large chromosomes. Analyzing the behavior of individual chromosomes, we found that a limited number of chromosomes change their contact patterns stochastically in trisomic cells and that it could be associated with lamina-associated domains (LAD) and gene content. For trisomy 13 and 18, but not for trisomy 16, the proportion of compacted loci on a chromosome is correlated with LAD content. We also found that regions of the genome that become more compact in trisomic cells are enriched in housekeeping genes, indicating a possible decrease in chromatin accessibility and transcription level of these genes. These results provide a framework for understanding the mechanisms of pan-genome transcription dysregulation in trisomies in the context of chromatin spatial organization.
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Affiliation(s)
- Irina V. Zhegalova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
| | | | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Anastasia S. Shtompel
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | | | | | | | - Zhanna Markova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Natalia V. Petrova
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Erdem B. Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Sergey V. Razin
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Sergey V. Ulianov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
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7
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Khan M, Shah S, Lv B, Lv Z, Ji N, Song Z, Wu P, Wang X, Mehmood A. Molecular Mechanisms of Alu and LINE-1 Interspersed Repetitive Sequences Reveal Diseases of Visual System Dysfunction. Ocul Immunol Inflamm 2023; 31:1848-1858. [PMID: 36040959 DOI: 10.1080/09273948.2022.2112238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINE-1s) are the abundant and well-characterized repetitive elements in the human genome. METHODS For this review, all relevant original research studies were assessed by searching electronic databases, including PubMed, Google Scholar, and Web of Science, by using relevant keywords. Accumulating evidence indicates that the disorder of gene expression regulated by these repetitive sequences is one of the causes of the diseases of visual system dysfunction, including retinal degenerations, glaucoma, retinitis punctata albescens, retinitis pigmentosa, geographic atrophy, and age-related macular degeneration, suggesting that SINEs and LINE-1s may have great potential implications in ophthalmology. RESULTS Alu elements belonging to the SINEs are present in more than one million copies, comprising 10% of the human genome. CONCLUSION This study offers recent advances in Alu and LINE-1 mechanisms in the development of eye diseases. The current study could advance our knowledge of the roles of SINEs and LINE-1s in the developing process of eye diseases, suggesting new diagnostic biomarkers, therapeutic strategies, and significant points for future studies.
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Affiliation(s)
- Murad Khan
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Suleman Shah
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Baixue Lv
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, Hubei Province, China
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Ning Ji
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Zhixue Song
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Peiyuan Wu
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Arshad Mehmood
- Department of Neurology, the Second Hospital of Hebei Medical University, City Shijiazhuang, P.R. China
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8
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Shevelyov YY. Interactions of Chromatin with the Nuclear Lamina and Nuclear Pore Complexes. Int J Mol Sci 2023; 24:15771. [PMID: 37958755 PMCID: PMC10649103 DOI: 10.3390/ijms242115771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
Heterochromatin and euchromatin form different spatial compartments in the interphase nucleus, with heterochromatin being localized mainly at the nuclear periphery. The mechanisms responsible for peripheral localization of heterochromatin are still not fully understood. The nuclear lamina and nuclear pore complexes were obvious candidates for the role of heterochromatin binders. This review is focused on recent studies showing that heterochromatin interactions with the nuclear lamina and nuclear pore complexes maintain its peripheral localization. Differences in chromatin interactions with the nuclear envelope in cell populations and in individual cells are also discussed.
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Affiliation(s)
- Yuri Y Shevelyov
- Laboratory of Analysis of Gene Regulation, National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, 123182 Moscow, Russia
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9
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Pal M, Altamirano-Pacheco L, Schauer T, Torres-Padilla ME. Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity. Genes Dev 2023; 37:901-912. [PMID: 37914351 PMCID: PMC10691468 DOI: 10.1101/gad.350799.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023]
Abstract
Fertilization in mammals is accompanied by an intense period of chromatin remodeling and major changes in nuclear organization. How the earliest events in embryogenesis, including zygotic genome activation (ZGA) during maternal-to-zygotic transition, influence such remodeling remains unknown. Here, we have investigated the establishment of nuclear architecture, focusing on the remodeling of lamina-associated domains (LADs) during this transition. We report that LADs reorganize gradually in two-cell embryos and that blocking ZGA leads to major changes in nuclear organization, including altered chromatin and genomic features of LADs and redistribution of H3K4me3 toward the nuclear lamina. Our data indicate that the rearrangement of LADs is an integral component of the maternal-to-zygotic transition and that transcription contributes to shaping nuclear organization at the beginning of mammalian development.
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Affiliation(s)
- Mrinmoy Pal
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Luis Altamirano-Pacheco
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Tamas Schauer
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany;
- Faculty of Biology, Ludwig-Maximilians Universität, D-81377 München, Germany
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10
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SoRelle ED, Reinoso-Vizcaino NM, Dai J, Barry AP, Chan C, Luftig MA. Epstein-Barr virus evades restrictive host chromatin closure by subverting B cell activation and germinal center regulatory loci. Cell Rep 2023; 42:112958. [PMID: 37561629 PMCID: PMC10559315 DOI: 10.1016/j.celrep.2023.112958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Chromatin accessibility fundamentally governs gene expression and biological response programs that can be manipulated by pathogens. Here we capture dynamic chromatin landscapes of individual B cells during Epstein-Barr virus (EBV) infection. EBV+ cells that exhibit arrest via antiviral sensing and proliferation-linked DNA damage experience global accessibility reduction. Proliferative EBV+ cells develop expression-linked architectures and motif accessibility profiles resembling in vivo germinal center (GC) phenotypes. Remarkably, EBV elicits dark zone (DZ), light zone (LZ), and post-GC B cell chromatin features despite BCL6 downregulation. Integration of single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), single-cell RNA sequencing (scRNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) data enables genome-wide cis-regulatory predictions implicating EBV nuclear antigens (EBNAs) in phenotype-specific control of GC B cell activation, survival, and immune evasion. Knockouts validate bioinformatically identified regulators (MEF2C and NFE2L2) of EBV-induced GC phenotypes and EBNA-associated loci that regulate gene expression (CD274/PD-L1). These data and methods can inform high-resolution investigations of EBV-host interactions, B cell fates, and virus-mediated lymphomagenesis.
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Affiliation(s)
- Elliott D SoRelle
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Nicolás M Reinoso-Vizcaino
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joanne Dai
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ashley P Barry
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA.
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11
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Shaban HA, Gasser SM. Dynamic 3D genome reorganization during senescence: defining cell states through chromatin. Cell Death Differ 2023:10.1038/s41418-023-01197-y. [PMID: 37596440 DOI: 10.1038/s41418-023-01197-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023] Open
Abstract
Cellular senescence, a cell state characterized by growth arrest and insensitivity to growth stimulatory hormones, is accompanied by a massive change in chromatin organization. Senescence can be induced by a range of physiological signals and pathological stresses and was originally thought to be an irreversible state, implicated in normal development, wound healing, tumor suppression and aging. Recently cellular senescence was shown to be reversible in some cases, with exit being triggered by the modulation of the cell's transcriptional program by the four Yamanaka factors, the suppression of p53 or H3K9me3, PDK1, and/or depletion of AP-1. Coincident with senescence reversal are changes in chromatin organization, most notably the loss of senescence-associated heterochromatin foci (SAHF) found in oncogene-induced senescence. In addition to fixed-cell imaging, chromatin conformation capture and multi-omics have been used to examine chromatin reorganization at different spatial resolutions during senescence. They identify determinants of SAHF formation and other key features that differentiate distinct types of senescence. Not surprisingly, multiple factors, including the time of induction, the type of stress experienced, and the type of cell involved, influence the global reorganization of chromatin in senescence. Here we discuss how changes in the three-dimensional organization of the genome contribute to the regulation of transcription at different stages of senescence. In particular, the distinct contributions of heterochromatin- and lamina-mediated interactions, changes in gene expression, and other cellular control mechanisms are discussed. We propose that high-resolution temporal and spatial analyses of the chromatin landscape during senescence will identify early markers of the different senescence states to help guide clinical diagnosis.
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Affiliation(s)
- Haitham A Shaban
- Precision Oncology Center, Department of Oncology, Lausanne University Hospital, 1005, Lausanne, Switzerland.
- Agora Cancer Research Center Lausanne, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.
- Spectroscopy Department, Institute of Physics Research National Research Centre, Cairo, 33 El-Behouth St., Dokki, Giza, 12311, Egypt.
| | - Susan M Gasser
- Fondation ISREC, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
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12
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Yang JH, Petty CA, Dixon-McDougall T, Lopez MV, Tyshkovskiy A, Maybury-Lewis S, Tian X, Ibrahim N, Chen Z, Griffin PT, Arnold M, Li J, Martinez OA, Behn A, Rogers-Hammond R, Angeli S, Gladyshev VN, Sinclair DA. Chemically induced reprogramming to reverse cellular aging. Aging (Albany NY) 2023; 15:5966-5989. [PMID: 37437248 PMCID: PMC10373966 DOI: 10.18632/aging.204896] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
A hallmark of eukaryotic aging is a loss of epigenetic information, a process that can be reversed. We have previously shown that the ectopic induction of the Yamanaka factors OCT4, SOX2, and KLF4 (OSK) in mammals can restore youthful DNA methylation patterns, transcript profiles, and tissue function, without erasing cellular identity, a process that requires active DNA demethylation. To screen for molecules that reverse cellular aging and rejuvenate human cells without altering the genome, we developed high-throughput cell-based assays that distinguish young from old and senescent cells, including transcription-based aging clocks and a real-time nucleocytoplasmic compartmentalization (NCC) assay. We identify six chemical cocktails, which, in less than a week and without compromising cellular identity, restore a youthful genome-wide transcript profile and reverse transcriptomic age. Thus, rejuvenation by age reversal can be achieved, not only by genetic, but also chemical means.
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Affiliation(s)
- Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Christopher A. Petty
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Thomas Dixon-McDougall
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Maria Vina Lopez
- Molecular and Biomedical Sciences, University of Maine, Orono, ME 04467, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Sun Maybury-Lewis
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Xiao Tian
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Nabilah Ibrahim
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Zhili Chen
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Patrick T. Griffin
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Matthew Arnold
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Jien Li
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Oswaldo A. Martinez
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
- Department of Biology and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Alexander Behn
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Ryan Rogers-Hammond
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Suzanne Angeli
- Molecular and Biomedical Sciences, University of Maine, Orono, ME 04467, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David A. Sinclair
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
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13
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Pennarun G, Picotto J, Bertrand P. Close Ties between the Nuclear Envelope and Mammalian Telomeres: Give Me Shelter. Genes (Basel) 2023; 14:genes14040775. [PMID: 37107534 PMCID: PMC10137478 DOI: 10.3390/genes14040775] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
The nuclear envelope (NE) in eukaryotic cells is essential to provide a protective compartment for the genome. Beside its role in connecting the nucleus with the cytoplasm, the NE has numerous important functions including chromatin organization, DNA replication and repair. NE alterations have been linked to different human diseases, such as laminopathies, and are a hallmark of cancer cells. Telomeres, the ends of eukaryotic chromosomes, are crucial for preserving genome stability. Their maintenance involves specific telomeric proteins, repair proteins and several additional factors, including NE proteins. Links between telomere maintenance and the NE have been well established in yeast, in which telomere tethering to the NE is critical for their preservation and beyond. For a long time, in mammalian cells, except during meiosis, telomeres were thought to be randomly localized throughout the nucleus, but recent advances have uncovered close ties between mammalian telomeres and the NE that play important roles for maintaining genome integrity. In this review, we will summarize these connections, with a special focus on telomere dynamics and the nuclear lamina, one of the main NE components, and discuss the evolutionary conservation of these mechanisms.
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Affiliation(s)
- Gaëlle Pennarun
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Julien Picotto
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
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14
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Yang BA, da Rocha AM, Newton I, Shcherbina A, Wong SW, Fraczek PM, Larouche JA, Hiraki HL, Baker BM, Shin JW, Takayama S, Thouless MD, Aguilar CA. Manipulation of the nucleoscaffold potentiates cellular reprogramming kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.532246. [PMID: 36993714 PMCID: PMC10055010 DOI: 10.1101/2023.03.12.532246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Somatic cell fate is an outcome set by the activities of specific transcription factors and the chromatin landscape and is maintained by gene silencing of alternate cell fates through physical interactions with the nuclear scaffold. Here, we evaluate the role of the nuclear scaffold as a guardian of cell fate in human fibroblasts by comparing the effects of transient loss (knockdown) and mutation (progeria) of functional Lamin A/C, a core component of the nuclear scaffold. We observed that Lamin A/C deficiency or mutation disrupts nuclear morphology, heterochromatin levels, and increases access to DNA in lamina-associated domains. Changes in Lamin A/C were also found to impact the mechanical properties of the nucleus when measured by a microfluidic cellular squeezing device. We also show that transient loss of Lamin A/C accelerates the kinetics of cellular reprogramming to pluripotency through opening of previously silenced heterochromatin domains while genetic mutation of Lamin A/C into progerin induces a senescent phenotype that inhibits the induction of reprogramming genes. Our results highlight the physical role of the nuclear scaffold in safeguarding cellular fate.
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Affiliation(s)
- Benjamin A. Yang
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Isabel Newton
- Dept. of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna Shcherbina
- Dept. of Biomedical Informatics, Stanford University, Palo Alto, CA 94305, USA
| | - Sing-Wan Wong
- Dept. of Pharmacology and Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Paula M. Fraczek
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jacqueline A. Larouche
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harrison L. Hiraki
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brendon M. Baker
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jae-Won Shin
- Dept. of Pharmacology and Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Shuichi Takayama
- Wallace Coulter Dept. of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332
| | - M. D. Thouless
- Dept. of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Dept. of Materials Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carlos A. Aguilar
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Ayala-Guerrero L, Claudio-Galeana S, Furlan-Magaril M, Castro-Obregón S. Chromatin Structure from Development to Ageing. Subcell Biochem 2023; 102:7-51. [PMID: 36600128 DOI: 10.1007/978-3-031-21410-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Nuclear structure influences genome architecture, which contributes to determine patterns of gene expression. Global changes in chromatin dynamics are essential during development and differentiation, and are one of the hallmarks of ageing. This chapter describes the molecular dynamics of chromatin structure that occur during development and ageing. In the first part, we introduce general information about the nuclear lamina, the chromatin structure, and the 3D organization of the genome. Next, we detail the molecular hallmarks found during development and ageing, including the role of DNA and histone modifications, 3D genome dynamics, and changes in the nuclear lamina. Within the chapter we discuss the implications that genome structure has on the mechanisms that drive development and ageing, and the physiological consequences when these mechanisms fail.
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Affiliation(s)
- Lorelei Ayala-Guerrero
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
| | - Sherlyn Claudio-Galeana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
| | - Susana Castro-Obregón
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
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16
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Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
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Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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17
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Abstract
Cellular senescence is implicated in a wide range of physiological and pathological conditions throughout an organism's entire lifetime. In particular, it has become evident that senescence plays a causative role in aging and age-associated disorders. This is not due simply to the loss of function of senescent cells. Instead, the substantial alterations of the cellular activities of senescent cells, especially the array of secretory factors, impact the surrounding tissues or even entire organisms. Such non-cell-autonomous functionality is largely coordinated by tissue-specific genes, constituting a cell fate-determining state. Senescence can be viewed as a gain-of-function phenotype or a process of cell identity shift. Cellular functionality or lineage-specific gene expression is tightly linked to the cell type-specific epigenetic landscape, reinforcing the heterogeneity of senescence across cell types. Here, we aim to define the senescence cellular functionality and epigenetic features that may contribute to the gain-of-function phenotype.
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Affiliation(s)
- Ioana Olan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom; ,
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom; ,
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18
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Tran JR, Zheng X, Adam SA, Goldman RD, Zheng Y. High quality mapping of chromatin at or near the nuclear lamina from small numbers of cells reveals cell cycle and developmental changes of chromatin at the nuclear periphery. Nucleic Acids Res 2022; 50:e117. [PMID: 36130229 PMCID: PMC9723609 DOI: 10.1093/nar/gkac762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 07/28/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022] Open
Abstract
The chromatin associated with the nuclear lamina (NL) is referred to as lamina-associated domains (LADs). Here, we present an adaptation of the tyramide-signal amplification sequencing (TSA-seq) protocol, which we call chromatin pull down-based TSA-seq (cTSA-seq), that can be used to map chromatin regions at or near the NL from as little as 50 000 cells. The cTSA-seq mapped regions are composed of previously defined LADs and smaller chromatin regions that fall within the Hi-C defined B-compartment containing nuclear peripheral heterochromatin. We used cTSA-seq to map chromatin at or near the assembling NL in cultured cells progressing through early G1. cTSA-seq revealed that the distal ends of chromosomes are near or at the reassembling NL during early G1, a feature similar to those found in senescent cells. We expand the use of cTSA-seq to the mapping of chromatin at or near the NL from fixed-frozen mouse cerebellar tissue sections. This mapping reveals a general conservation of NL-associated chromatin and identifies global and local changes during cerebellar development. The cTSA-seq method reported here is useful for analyzing chromatin at or near the NL from small numbers of cells derived from both in vitro and in vivo sources.
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Affiliation(s)
- Joseph R Tran
- Correspondence may also be addressed to Joseph R. Tran. Tel: +1 410 246 3032; Fax: +1 410 243 6311;
| | - Xiaobin Zheng
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Stephen A Adam
- Department of Cell and Developmental Biology, Northwestern University, Feinberg School of Medicine, Ward Building 11-145, 303 E. Chicago Ave. Chicago, IL 60611, USA
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University, Feinberg School of Medicine, Ward Building 11-145, 303 E. Chicago Ave. Chicago, IL 60611, USA
| | - Yixian Zheng
- To whom correspondence should be addressed. Tel: +1 410 246 3032; Fax: +1 410 243 6311;
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19
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Klaasen SJ, Truong MA, van Jaarsveld RH, Koprivec I, Štimac V, de Vries SG, Risteski P, Kodba S, Vukušić K, de Luca KL, Marques JF, Gerrits EM, Bakker B, Foijer F, Kind J, Tolić IM, Lens SMA, Kops GJPL. Nuclear chromosome locations dictate segregation error frequencies. Nature 2022; 607:604-609. [PMID: 35831506 PMCID: PMC9300461 DOI: 10.1038/s41586-022-04938-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/07/2022] [Indexed: 12/25/2022]
Abstract
Chromosome segregation errors during cell divisions generate aneuploidies and micronuclei, which can undergo extensive chromosomal rearrangements such as chromothripsis1-5. Selective pressures then shape distinct aneuploidy and rearrangement patterns-for example, in cancer6,7-but it is unknown whether initial biases in segregation errors and micronucleation exist for particular chromosomes. Using single-cell DNA sequencing8 after an error-prone mitosis in untransformed, diploid cell lines and organoids, we show that chromosomes have different segregation error frequencies that result in non-random aneuploidy landscapes. Isolation and sequencing of single micronuclei from these cells showed that mis-segregating chromosomes frequently also preferentially become entrapped in micronuclei. A similar bias was found in naturally occurring micronuclei of two cancer cell lines. We find that segregation error frequencies of individual chromosomes correlate with their location in the interphase nucleus, and show that this is highest for peripheral chromosomes behind spindle poles. Randomization of chromosome positions, Cas9-mediated live tracking and forced repositioning of individual chromosomes showed that a greater distance from the nuclear centre directly increases the propensity to mis-segregate. Accordingly, chromothripsis in cancer genomes9 and aneuploidies in early development10 occur more frequently for larger chromosomes, which are preferentially located near the nuclear periphery. Our findings reveal a direct link between nuclear chromosome positions, segregation error frequencies and micronucleus content, with implications for our understanding of tumour genome evolution and the origins of specific aneuploidies during development.
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Affiliation(s)
- Sjoerd J Klaasen
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - My Anh Truong
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | | | - Sippe G de Vries
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | | | | | - Kim L de Luca
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Joana F Marques
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Elianne M Gerrits
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Bjorn Bakker
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Floris Foijer
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Jop Kind
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands.,Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Susanne M A Lens
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands.
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20
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Bellanger A, Madsen-Østerbye J, Galigniana NM, Collas P. Restructuring of Lamina-Associated Domains in Senescence and Cancer. Cells 2022; 11:1846. [PMID: 35681541 PMCID: PMC9180887 DOI: 10.3390/cells11111846] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 01/01/2023] Open
Abstract
Induction of cellular senescence or cancer is associated with a reshaping of the nuclear envelope and a broad reorganization of heterochromatin. At the periphery of mammalian nuclei, heterochromatin is stabilized at the nuclear lamina via lamina-associated domains (LADs). Alterations in the composition of the nuclear lamina during senescence lead to a loss of peripheral heterochromatin, repositioning of LADs, and changes in epigenetic states of LADs. Cancer initiation and progression are also accompanied by a massive reprogramming of the epigenome, particularly in domains coinciding with LADs. Here, we review recent knowledge on alterations in chromatin organization and in the epigenome that affect LADs and related genomic domains in senescence and cancer.
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Affiliation(s)
- Aurélie Bellanger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
| | - Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
| | - Natalia M. Galigniana
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
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21
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Madsen-Østerbye J, Bellanger A, Galigniana NM, Collas P. Biology and Model Predictions of the Dynamics and Heterogeneity of Chromatin-Nuclear Lamina Interactions. Front Cell Dev Biol 2022; 10:913458. [PMID: 35693945 PMCID: PMC9178083 DOI: 10.3389/fcell.2022.913458] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Associations of chromatin with the nuclear lamina, at the nuclear periphery, help shape the genome in 3 dimensions. The genomic landscape of lamina-associated domains (LADs) is well characterized, but much remains unknown on the physical and mechanistic properties of chromatin conformation at the nuclear lamina. Computational models of chromatin folding at, and interactions with, a surface representing the nuclear lamina are emerging in attempts to characterize these properties and predict chromatin behavior at the lamina in health and disease. Here, we highlight the heterogeneous nature of the nuclear lamina and LADs, outline the main 3-dimensional chromatin structural modeling methods, review applications of modeling chromatin-lamina interactions and discuss biological insights inferred from these models in normal and disease states. Lastly, we address perspectives on future developments in modeling chromatin interactions with the nuclear lamina.
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Affiliation(s)
- Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Aurélie Bellanger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Natalia M. Galigniana
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
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22
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Liu Z, Ji Q, Ren J, Yan P, Wu Z, Wang S, Sun L, Wang Z, Li J, Sun G, Liang C, Sun R, Jiang X, Hu J, Ding Y, Wang Q, Bi S, Wei G, Cao G, Zhao G, Wang H, Zhou Q, Belmonte JCI, Qu J, Zhang W, Liu GH. Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging. Dev Cell 2022; 57:1347-1368.e12. [PMID: 35613614 DOI: 10.1016/j.devcel.2022.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/24/2022] [Accepted: 05/02/2022] [Indexed: 01/10/2023]
Abstract
Nuclear deformation, a hallmark frequently observed in senescent cells, is presumed to be associated with the erosion of chromatin organization at the nuclear periphery. However, how such gradual changes in higher-order genome organization impinge on local epigenetic modifications to drive cellular mechanisms of aging has remained enigmatic. Here, through large-scale epigenomic analyses of isogenic young, senescent, and progeroid human mesenchymal progenitor cells (hMPCs), we delineate a hierarchy of integrated structural state changes that manifest as heterochromatin loss in repressive compartments, euchromatin weakening in active compartments, switching in interfacing topological compartments, and increasing epigenetic entropy. We found that the epigenetic de-repression unlocks the expression of pregnancy-specific beta-1 glycoprotein (PSG) genes that exacerbate hMPC aging and serve as potential aging biomarkers. Our analyses provide a rich resource for uncovering the principles of epigenomic landscape organization and its changes in cellular aging and for identifying aging drivers and intervention targets with a genome-topology-based mechanism.
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Affiliation(s)
- Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengze Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Liang Sun
- NHC Beijing Institute of Geriatrics, NHC Key Laboratory of Geriatrics, Institute of Geriatric Medicine of Chinese Academy of Medical Sciences, National Center of Gerontology/ Beijing Hospital, Beijing 100730, China; Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Zehua Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuqian Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Run Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianli Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingjie Ding
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijia Bi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Bio-Medical Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoguang Zhao
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
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23
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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24
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Zakharova VV, Magnitov MD, Del Maestro L, Ulianov SV, Glentis A, Uyanik B, Williart A, Karpukhina A, Demidov O, Joliot V, Vassetzky Y, Mège RM, Piel M, Razin S, Ait-Si-Ali S. SETDB1 fuels the lung cancer phenotype by modulating epigenome, 3D genome organization and chromatin mechanical properties. Nucleic Acids Res 2022; 50:4389-4413. [PMID: 35474385 PMCID: PMC9071401 DOI: 10.1093/nar/gkac234] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/15/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
Imbalance in the finely orchestrated system of chromatin-modifying enzymes is a hallmark of many pathologies such as cancers, since causing the affection of the epigenome and transcriptional reprogramming. Here, we demonstrate that a loss-of-function mutation (LOF) of the major histone lysine methyltransferase SETDB1 possessing oncogenic activity in lung cancer cells leads to broad changes in the overall architecture and mechanical properties of the nucleus through genome-wide redistribution of heterochromatin, which perturbs chromatin spatial compartmentalization. Together with the enforced activation of the epithelial expression program, cytoskeleton remodeling, reduced proliferation rate and restricted cellular migration, this leads to the reversed oncogenic potential of lung adenocarcinoma cells. These results emphasize an essential role of chromatin architecture in the determination of oncogenic programs and illustrate a relationship between gene expression, epigenome, 3D genome and nuclear mechanics.
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Affiliation(s)
- Vlada V Zakharova
- Epigenetics and Cell Fate (EDC) department, UMR7216, CNRS, Université Paris Cité, F-75013 Paris, France
| | - Mikhail D Magnitov
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
| | - Laurence Del Maestro
- Epigenetics and Cell Fate (EDC) department, UMR7216, CNRS, Université Paris Cité, F-75013 Paris, France
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexandros Glentis
- Institute Jacques Monod, CNRS, Université Paris Cité, F-75013 Paris, France
| | - Burhan Uyanik
- INSERM UMR1231, LipSTIC, University of Burgundy Franche-Comté F-21000, Dijon, France
| | - Alice Williart
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR 144, 75248 Paris, France
| | - Anna Karpukhina
- UMR9018, CNRS, Université Paris-Sud Paris-Saclay, Institut Gustave Roussy; 94805 Villejuif, France,Koltzov Institute of Developmental Biology, 119334 Moscow, Russia
| | - Oleg Demidov
- INSERM UMR1231, LipSTIC, University of Burgundy Franche-Comté F-21000, Dijon, France,Institute of Cytology, RAS, 194064 St. Petersburg, Russia,NTU Sirius, 354340 Sochi, Russia
| | - Veronique Joliot
- Epigenetics and Cell Fate (EDC) department, UMR7216, CNRS, Université Paris Cité, F-75013 Paris, France
| | - Yegor S Vassetzky
- UMR9018, CNRS, Université Paris-Sud Paris-Saclay, Institut Gustave Roussy; 94805 Villejuif, France,Koltzov Institute of Developmental Biology, 119334 Moscow, Russia
| | - René-Marc Mège
- Institute Jacques Monod, CNRS, Université Paris Cité, F-75013 Paris, France
| | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR 144, 75248 Paris, France
| | - Sergey V Razin
- Correspondence may also be addressed to Sergey V. Razin. Tel: +7 499 135 3092;
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25
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Liang C, Ke Q, Liu Z, Ren J, Zhang W, Hu J, Wang Z, Chen H, Xia K, Lai X, Wang Q, Yang K, Li W, Wu Z, Wang C, Yan H, Jiang X, Ji Z, Ma M, Long X, Wang S, Wang H, Sun H, Belmonte J, Qu J, Xiang A, Liu GH. BMAL1 moonlighting as a gatekeeper for LINE1 repression and cellular senescence in primates. Nucleic Acids Res 2022; 50:3323-3347. [PMID: 35286396 PMCID: PMC8989534 DOI: 10.1093/nar/gkac146] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/14/2022] [Accepted: 02/19/2022] [Indexed: 11/13/2022] Open
Abstract
Aging in humans is intricately linked with alterations in circadian rhythms concomitant with physiological decline and stem cell exhaustion. However, whether the circadian machinery directly regulates stem cell aging, especially in primates, remains poorly understood. In this study, we found that deficiency of BMAL1, the only non-redundant circadian clock component, results in an accelerated aging phenotype in both human and cynomolgus monkey mesenchymal progenitor cells (MPCs). Unexpectedly, this phenotype was mainly attributed to a transcription-independent role of BMAL1 in stabilizing heterochromatin and thus preventing activation of the LINE1-cGAS-STING pathway. In senescent primate MPCs, we observed decreased capacity of BMAL1 to bind to LINE1 and synergistic activation of LINE1 expression. Likewise, in the skin and muscle tissues from the BMAL1-deficient cynomolgus monkey, we observed destabilized heterochromatin and aberrant LINE1 transcription. Altogether, these findings uncovered a noncanonical role of BMAL1 in stabilizing heterochromatin to inactivate LINE1 that drives aging in primate cells.
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Affiliation(s)
- Chuqian Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiong Ke
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
- Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Ren
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqi Zhang
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianli Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zehua Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Chen
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Kai Xia
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Xingqiang Lai
- Cardiovascular Department, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518033, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
- Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Haoteng Yan
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Miyang Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Long
- Division of Plastic Surgery, Peking Union Medical College Hospital, Beijing 100032, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Chongqing Renji Hospital, University of Chinese Academy of Sciences, Chongqing 400062, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
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26
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Zhao H, Ji Q, Wu Z, Wang S, Ren J, Yan K, Wang Z, Hu J, Chu Q, Hu H, Cai Y, Wang Q, Huang D, Ji Z, Li J, Belmonte JCI, Song M, Zhang W, Qu J, Liu GH. Destabilizing heterochromatin by APOE mediates senescence. NATURE AGING 2022; 2:303-316. [PMID: 35368774 DOI: 10.1038/s43587-022-00186-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 02/01/2022] [Indexed: 04/30/2023]
Abstract
Apolipoprotein E (APOE) is a component of lipoprotein particles that function in the homeostasis of cholesterol and other lipids. Although APOE is genetically associated with human longevity and Alzheimer's disease, its mechanistic role in aging is largely unknown. Here, we used human genetic, stress-induced and physiological cellular aging models to explore APOE-driven processes in stem cell homeostasis and aging. We report that in aged human mesenchymal progenitor cells (MPCs), APOE accumulation is a driver for cellular senescence. By contrast, CRISPR-Cas9-mediated deletion of APOE endows human MPCs with resistance to cellular senescence. Mechanistically, we discovered that APOE functions as a destabilizer for heterochromatin. Specifically, increased APOE leads to the degradation of nuclear lamina proteins and a heterochromatin-associated protein KRAB-associated protein 1 via the autophagy-lysosomal pathway, thereby disrupting heterochromatin and causing senescence. Altogether, our findings uncover a role of APOE as an epigenetic mediator of senescence and provide potential targets to ameliorate aging-related diseases.
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Affiliation(s)
- Hongkai Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Science and Technology of China, Hefei, China
| | - Qianzhao Ji
- University of the Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zeming Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
- Chongqing Renji Hospital, University of the Chinese Academy of Sciences, Chongqing, China
| | - Jie Ren
- University of the Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Zehua Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jianli Hu
- University of the Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Qun Chu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Huifang Hu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Qiaoran Wang
- University of the Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Daoyuan Huang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jingyi Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | | | - Moshi Song
- University of the Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
| | - Weiqi Zhang
- University of the Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Science and Technology of China, Hefei, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
| | - Guang-Hui Liu
- University of the Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, China.
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27
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Lamina-associated domains: Tethers and looseners. Curr Opin Cell Biol 2022; 74:80-87. [DOI: 10.1016/j.ceb.2022.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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28
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Freyter BM, Abd Al-razaq MA, Isermann A, Dietz A, Azimzadeh O, Hekking L, Gomolka M, Rübe CE. Nuclear Fragility in Radiation-Induced Senescence: Blebs and Tubes Visualized by 3D Electron Microscopy. Cells 2022; 11:cells11020273. [PMID: 35053389 PMCID: PMC8774169 DOI: 10.3390/cells11020273] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/19/2021] [Accepted: 01/12/2022] [Indexed: 12/10/2022] Open
Abstract
Irreparable DNA damage following ionizing radiation (IR) triggers prolonged DNA damage response and induces premature senescence. Cellular senescence is a permanent state of cell-cycle arrest characterized by chromatin restructuring, altered nuclear morphology and acquisition of secretory phenotype, which contributes to senescence-related inflammation. However, the mechanistic connections for radiation-induced DNA damage that trigger these senescence-associated hallmarks are poorly understood. In our in vitro model of radiation-induced senescence, mass spectrometry-based proteomics was combined with high-resolution imaging techniques to investigate the interrelations between altered chromatin compaction, nuclear envelope destabilization and nucleo-cytoplasmic chromatin blebbing. Our findings confirm the general pathophysiology of the senescence-response, with disruption of nuclear lamin organization leading to extensive chromatin restructuring and destabilization of the nuclear membrane with release of chromatin fragments into the cytosol, thereby activating cGAS-STING-dependent interferon signaling. By serial block-face scanning electron microscopy (SBF-SEM) whole-cell datasets were acquired to investigate the morphological organization of senescent fibroblasts. High-resolution 3-dimensional (3D) reconstruction of the complex nuclear shape allows us to precisely visualize the segregation of nuclear blebs from the main nucleus and their fusion with lysosomes. By multi-view 3D electron microscopy, we identified nanotubular channels formed in lamin-perturbed nuclei of senescent fibroblasts; the potential role of these nucleo-cytoplasmic nanotubes for expulsion of damaged chromatin has to be examined.
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Affiliation(s)
- Benjamin M. Freyter
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Mutaz A. Abd Al-razaq
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Anna Isermann
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Anne Dietz
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | - Omid Azimzadeh
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | | | - Maria Gomolka
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | - Claudia E. Rübe
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
- Correspondence: ; Tel.: +49-6841-1634614; Fax: +49-6841-1624699
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29
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Meharena HS, Marco A, Dileep V, Lockshin ER, Akatsu GY, Mullahoo J, Watson LA, Ko T, Guerin LN, Abdurob F, Rengarajan S, Papanastasiou M, Jaffe JD, Tsai LH. Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors. Cell Stem Cell 2022; 29:116-130.e7. [PMID: 34995493 PMCID: PMC8805993 DOI: 10.1016/j.stem.2021.12.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/30/2021] [Accepted: 12/09/2021] [Indexed: 01/09/2023]
Abstract
Down syndrome (DS) is a genetic disorder driven by the triplication of chromosome 21 (T21) and characterized by a wide range of neurodevelopmental and physical disabilities. Transcriptomic analysis of tissue samples from individuals with DS has revealed that T21 induces a genome-wide transcriptional disruption. However, the consequences of T21 on the nuclear architecture and its interplay with the transcriptome remain unknown. In this study, we find that unlike human induced pluripotent stem cells (iPSCs), iPSC-derived neural progenitor cells (NPCs) exhibit genome-wide "chromosomal introversion," disruption of lamina-associated domains, and global chromatin accessibility changes in response to T21, consistent with the transcriptional and nuclear architecture changes characteristic of senescent cells. Treatment of T21-harboring NPCs with senolytic drugs alleviates the transcriptional, molecular, and cellular dysfunctions associated with DS. Our findings provide a mechanistic link between T21 and global transcriptional disruption and indicate that senescence-associated phenotypes may play a key role in the neurodevelopmental pathogenesis of DS.
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Affiliation(s)
- Hiruy S. Meharena
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Correspondence: Hiruy Meharena (), Li-Huei Tsai () – Lead Contact
| | - Asaf Marco
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elana R. Lockshin
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grace Y. Akatsu
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James Mullahoo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - L. Ashley Watson
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tak Ko
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lindsey N. Guerin
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fatema Abdurob
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shruthi Rengarajan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | - Jacob D. Jaffe
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Correspondence: Hiruy Meharena (), Li-Huei Tsai () – Lead Contact
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30
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Mojiri A, Walther BK, Jiang C, Matrone G, Holgate R, Xu Q, Morales E, Wang G, Gu J, Wang R, Cooke JP. Telomerase therapy reverses vascular senescence and extends lifespan in progeria mice. Eur Heart J 2021; 42:4352-4369. [PMID: 34389865 PMCID: PMC8603239 DOI: 10.1093/eurheartj/ehab547] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/29/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
AIMS Hutchinson-Gilford progeria syndrome (HGPS) is an accelerated ageing syndrome associated with premature vascular disease and death due to heart attack and stroke. In HGPS a mutation in lamin A (progerin) alters nuclear morphology and gene expression. Current therapy increases the lifespan of these children only modestly. Thus, greater understanding of the underlying mechanisms of HGPS is required to improve therapy. Endothelial cells (ECs) differentiated from induced pluripotent stem cells (iPSCs) derived from these patients exhibit hallmarks of senescence including replication arrest, increased expression of inflammatory markers, DNA damage, and telomere erosion. We hypothesized that correction of shortened telomeres may reverse these measures of vascular ageing. METHODS AND RESULTS We generated ECs from iPSCs belonging to children with HGPS and their unaffected parents. Telomerase mRNA (hTERT) was used to treat HGPS ECs. Endothelial morphology and functions were assessed, as well as proteomic and transcriptional profiles with attention to inflammatory markers, DNA damage, and EC identity genes. In a mouse model of HGPS, we assessed the effects of lentiviral transfection of mTERT on measures of senescence, focusing on the EC phenotype in various organs. hTERT treatment of human HGPS ECs improved replicative capacity; restored endothelial functions such as nitric oxide generation, acetylated low-density lipoprotein uptake and angiogenesis; and reduced the elaboration of inflammatory cytokines. In addition, hTERT treatment improved cellular and nuclear morphology, in association with a normalization of the transcriptional profile, effects that may be mediated in part by a reduction in progerin expression and an increase in sirtuin 1 (SIRT1). Progeria mice treated with mTERT lentivirus manifested similar improvements, with a reduction in inflammatory and DNA damage markers and increased SIRT1 in their vasculature and other organs. Furthermore, mTERT therapy increased the lifespan of HGPS mice. CONCLUSION Vascular rejuvenation using telomerase mRNA is a promising approach for progeria and other age-related diseases.
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Affiliation(s)
- Anahita Mojiri
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Brandon K Walther
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
- Department of Biomedical Engineering, Texas A&M University, 101 Bizzell St., College Station, TX 77840, USA
| | - Chongming Jiang
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gianfranco Matrone
- British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Rhonda Holgate
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Qiu Xu
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Elisa Morales
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Guangyu Wang
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Jianhua Gu
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Rongfu Wang
- Department of Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - John P Cooke
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
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31
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Sikora E, Bielak-Zmijewska A, Mosieniak G. A common signature of cellular senescence; does it exist? Ageing Res Rev 2021; 71:101458. [PMID: 34500043 DOI: 10.1016/j.arr.2021.101458] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023]
Abstract
Cellular senescence is a stress response, which can be evoked in all type of somatic cells by different stimuli. Senescent cells accumulate in the body and participate in aging and aging-related diseases mainly by their secretory activity, commonly known as senescence-associated secretory phenotype-SASP. Senescence is typically described as cell cycle arrest. This definition stems from the original observation concerning limited cell division potential of human fibroblasts in vitro. At present, the process of cell senescence is attributed also to cancer cells and to non-proliferating post-mitotic cells. Many cellular signaling pathways and specific and unspecific markers contribute to the complex, dynamic and heterogeneous phenotype of senescent cells. Considering the diversity of cells that can undergo senescence upon different inducers and variety of mechanisms involved in the execution of this process, we ask if there is a common signature of cell senescence. It seems that cell cycle arrest in G0, G1 or G2 is indispensable for cell senescence; however, to ensure irreversibility of divisions, the exit from the cell cycle to the state, which we call a GS (Gero Stage), is necessary. The DNA damage, changes in nuclear architecture and chromatin rearrangement are involved in signaling pathways leading to altered gene transcription and secretion of SASP components. Thus, nuclear changes and SASP are vital features of cell senescence that, together with temporal arrest in the cell cycle (G1 or/and G2), which may be followed by polyploidisation/depolyploidisation or exit from the cell cycle leading to permanent proliferation arrest (GS), define the signature of cellular senescence.
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32
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Nuclear Dynamics and Chromatin Structure: Implications for Pancreatic Cancer. Cells 2021; 10:cells10102624. [PMID: 34685604 PMCID: PMC8534098 DOI: 10.3390/cells10102624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
Changes in nuclear shape have been extensively associated with the dynamics and functionality of cancer cells. In most normal cells, nuclei have a regular ellipsoid shape and minimal variation in nuclear size; however, an irregular nuclear contour and abnormal nuclear size is often observed in cancer, including pancreatic cancer. Furthermore, alterations in nuclear morphology have become the 'gold standard' for tumor staging and grading. Beyond the utility of altered nuclear morphology as a diagnostic tool in cancer, the implications of altered nuclear structure for the biology and behavior of cancer cells are profound as changes in nuclear morphology could impact cellular responses to physical strain, adaptation during migration, chromatin organization, and gene expression. Here, we aim to highlight and discuss the factors that regulate nuclear dynamics and their implications for pancreatic cancer biology.
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33
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Zhang X, Liu X, Du Z, Wei L, Fang H, Dong Q, Niu J, Li Y, Gao J, Zhang MQ, Xie W, Wang X. The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence. Genome Res 2021; 31:1121-1135. [PMID: 34140314 PMCID: PMC8256869 DOI: 10.1101/gr.275235.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/27/2021] [Indexed: 01/10/2023]
Abstract
Heterochromatin remodeling is critical for various cell processes. In particular, the "loss of heterochromatin" phenotype in cellular senescence is associated with the process of aging and age-related disorders. Although biological processes of senescent cells, including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction, and redistribution of key proteins, have been closely associated with high-order chromatin structure, the relationship between the high-order chromatin reorganization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and deep senescent fibroblasts induced by DNA damage harboring the "loss of heterochromatin" phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, show different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Both types of heterochromatin show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show both similar and distinct multiscale alterations in the 3D map, chromatin accessibility, and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence.
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Affiliation(s)
- Xianglin Zhang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Xuehui Liu
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
- State Key Laboratory of Medical Molecular Biology, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- THU-PKU Center for Life Sciences, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Huan Fang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Qiongye Dong
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Jing Niu
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yanda Li
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Michael Q Zhang
- Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Richardson, Texas 75080-3021, USA
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- THU-PKU Center for Life Sciences, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaowo Wang
- MOE Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Department of Automation, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Beijing 100084, China
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34
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Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct Target Ther 2021; 6:245. [PMID: 34176928 PMCID: PMC8236488 DOI: 10.1038/s41392-021-00646-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art techniques are also discussed.
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35
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Lu JY, Chang L, Li T, Wang T, Yin Y, Zhan G, Han X, Zhang K, Tao Y, Percharde M, Wang L, Peng Q, Yan P, Zhang H, Bi X, Shao W, Hong Y, Wu Z, Ma R, Wang P, Li W, Zhang J, Chang Z, Hou Y, Zhu B, Ramalho-Santos M, Li P, Xie W, Na J, Sun Y, Shen X. Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome. Cell Res 2021; 31:613-630. [PMID: 33514913 PMCID: PMC8169921 DOI: 10.1038/s41422-020-00466-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023] Open
Abstract
Organization of the genome into euchromatin and heterochromatin appears to be evolutionarily conserved and relatively stable during lineage differentiation. In an effort to unravel the basic principle underlying genome folding, here we focus on the genome itself and report a fundamental role for L1 (LINE1 or LINE-1) and B1/Alu retrotransposons, the most abundant subclasses of repetitive sequences, in chromatin compartmentalization. We find that homotypic clustering of L1 and B1/Alu demarcates the genome into grossly exclusive domains, and characterizes and predicts Hi-C compartments. Spatial segregation of L1-rich sequences in the nuclear and nucleolar peripheries and B1/Alu-rich sequences in the nuclear interior is conserved in mouse and human cells and occurs dynamically during the cell cycle. In addition, de novo establishment of L1 and B1 nuclear segregation is coincident with the formation of higher-order chromatin structures during early embryogenesis and appears to be critically regulated by L1 and B1 transcripts. Importantly, depletion of L1 transcripts in embryonic stem cells drastically weakens homotypic repeat contacts and compartmental strength, and disrupts the nuclear segregation of L1- or B1-rich chromosomal sequences at genome-wide and individual sites. Mechanistically, nuclear co-localization and liquid droplet formation of L1 repeat DNA and RNA with heterochromatin protein HP1α suggest a phase-separation mechanism by which L1 promotes heterochromatin compartmentalization. Taken together, we propose a genetically encoded model in which L1 and B1/Alu repeats blueprint chromatin macrostructure. Our model explains the robustness of genome folding into a common conserved core, on which dynamic gene regulation is overlaid across cells.
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Affiliation(s)
- J Yuyang Lu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, China
| | - Tong Li
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ting Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yafei Yin
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ge Zhan
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xue Han
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ke Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yibing Tao
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Michelle Percharde
- MRC London Institute of Medical Sciences (LMS), London, W120NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, W120NN, UK
| | - Liang Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qi Peng
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Pixi Yan
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hui Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xianju Bi
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wen Shao
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yantao Hong
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhongyang Wu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runze Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Peizhe Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wenzhi Li
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jing Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zai Chang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yingping Hou
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, Ontario, M5T 3H7, Canada
| | - Pilong Li
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wei Xie
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jie Na
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871, China.
| | - Xiaohua Shen
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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Saleh T, Alhesa A, Al-Balas M, Abuelaish O, Mansour A, Awad H, El-Sadoni M, Carpenter V, Azab B. Expression of therapy-induced senescence markers in breast cancer samples upon incomplete response to neoadjuvant chemotherapy. Biosci Rep 2021; 41:BSR20210079. [PMID: 33948615 PMCID: PMC8725197 DOI: 10.1042/bsr20210079] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 11/22/2022] Open
Abstract
Senescence is a cell stress response induced by replicative, oxidative, oncogenic, and genotoxic stresses. Tumor cells undergo senescence in response to several cancer therapeutics in vitro (Therapy-Induced Senescence, TIS), including agents utilized as neoadjuvant chemotherapy (NAC) in the treatment of invasive breast cancer. TIS has been proposed to contribute to adverse therapy outcomes including relapse. However, there is limited evidence on the induction of senescence in response to NAC in clinical cancer and its contribution to disease outcomes. In this work, the expression of three senescence-associated markers (p21CIP1, H3K9Me3 (histone H3 lysine 9 trimethylation), and Lamin B1) was investigated in breast cancer samples that developed partial or incomplete pathological response to NAC (n=37). Accordingly, 40.54% of all samples showed marker expression consistent with a senescence-like phenotype, while the remainders were either negative or inconclusive for senescence (2.70 and 56.8%, respectively). Moreover, analysis of core-needle biopsies revealed minimal changes in p21CIP1 and H3K9Me3, but significant changes in Lamin B1 expression levels following NAC, highlighting a more predictive role of Lamin B1 in senescence detection. However, our analysis did not establish an association between TIS and cancer relapse as only three patients (8.1%) with a senescence-like profile developed short-term recurrent disease. Our analysis indicates that identification of TIS in tumor samples requires large-scale transcriptomic and protein marker analyses and extended clinical follow-up. Better understanding of in vivo senescence should elucidate its contribution to therapy outcomes and pave the way for the utilization of senolytic approaches as potential adjuvant cancer therapy.
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Affiliation(s)
- Tareq Saleh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
| | - Ahmad Alhesa
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Mahmoud Al-Balas
- Department of General and Special Surgery, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
| | - Omar Abuelaish
- Department of General Surgery, Royal Medical Services, Amman, Jordan
| | - Ahmad Mansour
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45219, U.S.A
| | - Heyam Awad
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Mohammed El-Sadoni
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Valerie J. Carpenter
- Department of Pharmacology and Toxicology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, U.S.A
| | - Bilal Azab
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
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37
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Mehta IS, Riyahi K, Pereira RT, Meaburn KJ, Figgitt M, Kill IR, Eskiw CH, Bridger JM. Interphase Chromosomes in Replicative Senescence: Chromosome Positioning as a Senescence Biomarker and the Lack of Nuclear Motor-Driven Chromosome Repositioning in Senescent Cells. Front Cell Dev Biol 2021; 9:640200. [PMID: 34113611 PMCID: PMC8185894 DOI: 10.3389/fcell.2021.640200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/25/2021] [Indexed: 01/10/2023] Open
Abstract
This study demonstrates, and confirms, that chromosome territory positioning is altered in primary senescent human dermal fibroblasts (HDFs). The chromosome territory positioning pattern is very similar to that found in HDFs made quiescent either by serum starvation or confluence; but not completely. A few chromosomes are found in different locations. One chromosome in particular stands out, chromosome 10, which is located in an intermediate location in young proliferating HDFs, but is found at the nuclear periphery in quiescent cells and in an opposing location of the nuclear interior in senescent HDFs. We have previously demonstrated that individual chromosome territories can be actively and rapidly relocated, with 15 min, after removal of serum from the culture media. These chromosome relocations require nuclear motor activity through the presence of nuclear myosin 1β (NM1β). We now also demonstrate rapid chromosome movement in HDFs after heat-shock at 42°C. Others have shown that heat shock genes are actively relocated using nuclear motor protein activity via actin or NM1β (Khanna et al., 2014; Pradhan et al., 2020). However, this current study reveals, that in senescent HDFs, chromosomes can no longer be relocated to expected nuclear locations upon these two types of stimuli. This coincides with a entirely different organisation and distribution of NM1β within senescent HDFs.
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Affiliation(s)
- Ishita S Mehta
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom.,Tata Institute of Fundamental Research, Mumbai, India
| | - Kumars Riyahi
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| | - Rita Torres Pereira
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| | - Karen J Meaburn
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| | - Martin Figgitt
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom.,Department of Life Sciences, Birmingham City University, Birmingham, United Kingdom
| | - Ian R Kill
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
| | - Christopher H Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joanna M Bridger
- Centre for Genome Engineering and Maintenance, Division of Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Kingston Lane, Brunel University London, Uxbridge, United Kingdom
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38
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Rocha A, Dalgarno A, Neretti N. The functional impact of nuclear reorganization in cellular senescence. Brief Funct Genomics 2021; 21:24-34. [PMID: 33755107 PMCID: PMC8789270 DOI: 10.1093/bfgp/elab012] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is the irreversible cell cycle arrest in response to DNA damage. Because senescent cells accumulate with age and contribute to chronic inflammation, they are promising therapeutic targets for healthspan extension. The senescent phenotype can vary depending on cell type and on the specific insults that induce senescence. This variability is also reflected in the extensive remodeling of the genome organization within the nucleus of senescent cells. Here, we give an overview of the nuclear changes that occur in different forms of senescence, including changes to chromatin state and composition and to the three-dimensional organization of the genome, as well as alterations to the nuclear envelope and to the accessibility of repetitive genomic regions. Many of these changes are shared across all forms of senescence, implicating nuclear organization as a fundamental driver of the senescent state and of how senescent cells interact with the surrounding tissue.
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Affiliation(s)
- Azucena Rocha
- Molecular Biology, Cell Biology and Biochemistry program at Brown University
| | - Audrey Dalgarno
- Molecular Biology, Cell Biology and Biochemistry program at Brown University
| | - Nicola Neretti
- Associate Professor in the Department of Molecular Biology, Cell Biology and Biochemistry at Brown University
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39
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Karoutas A, Akhtar A. Functional mechanisms and abnormalities of the nuclear lamina. Nat Cell Biol 2021; 23:116-126. [PMID: 33558730 DOI: 10.1038/s41556-020-00630-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Alterations in nuclear shape are present in human diseases and ageing. A compromised nuclear lamina is molecularly interlinked to altered chromatin functions and genomic instability. Whether these alterations are a cause or a consequence of the pathological state are important questions in biology. Here, we summarize the roles of nuclear envelope components in chromatin organization, phase separation and transcriptional and epigenetic regulation. Examining these functions in healthy backgrounds will guide us towards a better understanding of pathological alterations.
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Affiliation(s)
- Adam Karoutas
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Francis Crick Institute, London, UK
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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40
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Miller KN, Dasgupta N, Liu T, Adams PD, Vizioli MG. Cytoplasmic chromatin fragments-from mechanisms to therapeutic potential. eLife 2021; 10:63728. [PMID: 33512316 PMCID: PMC7846272 DOI: 10.7554/elife.63728] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
Senescent cells, damaged cells that permanently exit the cell cycle, play important roles in development, tissue homeostasis, and tumorigenesis. Although many of these roles are beneficial in acute responses to stress and damage, the persistent accumulation of senescent cells is associated with many chronic diseases through their proinflammatory senescence-associated secretory phenotype (SASP). SASP expression is linked to DNA damage; however, the mechanisms that control the SASP are incompletely understood. More recently, it has been shown that senescent cells shed fragments of nuclear chromatin into the cytoplasm, so called cytoplasmic chromatin fragments (CCF). Here, we provide an overview of the current evidence linking DNA damage to the SASP through the formation of CCF. We describe mechanisms of CCF generation and their functional role in senescent cells, with emphasis on therapeutic potential.
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Affiliation(s)
- Karl N Miller
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Nirmalya Dasgupta
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Tianhui Liu
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Peter D Adams
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Maria Grazia Vizioli
- Cancer Research United Kingdom Beatson Institute, Garscube Estate, Glasgow, United Kingdom.,Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, United Kingdom.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, United States.,Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, United States
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41
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Ding T, Zhu L, Fang Y, Liu Y, Tang W, Zou P. Chromophore‐Assisted Proximity Labeling of DNA Reveals Chromosomal Organization in Living Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tao Ding
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Liyuan Zhu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yuxin Fang
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yangluorong Liu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Wei Tang
- Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Peng Zou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- PKU-IDG/McGovern Institute for Brain Research Beijing 100871 China
- Chinese Institute for Brain Research (CIBR) Beijing 102206 China
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42
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Guan Y, Zhang C, Lyu G, Huang X, Zhang X, Zhuang T, Jia L, Zhang L, Zhang C, Li C, Tao W. Senescence-activated enhancer landscape orchestrates the senescence-associated secretory phenotype in murine fibroblasts. Nucleic Acids Res 2020; 48:10909-10923. [PMID: 33045748 PMCID: PMC7641768 DOI: 10.1093/nar/gkaa858] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 09/16/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
The three-dimensional configuration of the chromatin architecture is known to be crucial for alterations in the transcriptional network; however, the underlying mechanisms of epigenetic control of senescence-related gene expression by modulating the chromatin architecture remain unknown. Here, we demonstrate frequent chromosomal compartment switching during mouse embryonic fibroblasts (MEFs) replicative senescence as characterized by senescence-inactivated (SIAEs) and -activated enhancers (SAEs) in topologically associated domains (TADs). Mechanistically, SAEs are closely correlated with senescence-associated secretory phenotype (SASP) genes, which are a key transcriptional feature of an aging microenvironment that contributes to tumor progression, aging acceleration, and immunoinflammatory responses. Moreover, SAEs can positively regulate robust changes in SASP expression. The transcription factor CCAAT/enhancer binding protein α (C/EBPα) is capable of enhancing SAE activity, which accelerates the emergence of SAEs flanking SASPs and the secretion of downstream factors, contributing to the progression of senescence. Our results provide novel insight into the TAD-related control of SASP gene expression by revealing hierarchical roles of the chromatin architecture, transcription factors, and enhancer activity in the regulation of cellular senescence.
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Affiliation(s)
- Yiting Guan
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China.,Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang 524000, China
| | - Chao Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China.,Center for Bioinformatics, School of Life Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Guoliang Lyu
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoke Huang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuebin Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Tenghan Zhuang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Lumeng Jia
- Center for Bioinformatics, School of Life Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Lijun Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chen Zhang
- China Department of Neurobiology, School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Wei Tao
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
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43
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Altemose N, Maslan A, Rios-Martinez C, Lai A, White JA, Streets A. μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells. Cell Syst 2020; 11:354-366.e9. [PMID: 33099405 PMCID: PMC7588622 DOI: 10.1016/j.cels.2020.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 07/01/2020] [Accepted: 08/22/2020] [Indexed: 12/23/2022]
Abstract
DNA adenine methyltransferase identification (DamID) measures a protein's DNA-binding history by methylating adenine bases near each protein-DNA interaction site and then selectively amplifying and sequencing these methylated regions. Additionally, these interactions can be visualized using m6A-Tracer, a fluorescent protein that binds to methyladenines. Here, we combine these imaging and sequencing technologies in an integrated microfluidic platform (μDamID) that enables single-cell isolation, imaging, and sorting, followed by DamID. We use μDamID and an improved m6A-Tracer protein to generate paired imaging and sequencing data from individual human cells. We validate interactions between Lamin-B1 protein and lamina-associated domains (LADs), observe variable 3D chromatin organization and broad gene regulation patterns, and jointly measure single-cell heterogeneity in Dam expression and background methylation. μDamID provides the unique ability to compare paired imaging and sequencing data for each cell and between cells, enabling the joint analysis of the nuclear localization, sequence identity, and variability of protein-DNA interactions. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Annie Maslan
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carolina Rios-Martinez
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andre Lai
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan A White
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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44
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Ding T, Zhu L, Fang Y, Liu Y, Tang W, Zou P. Chromophore‐Assisted Proximity Labeling of DNA Reveals Chromosomal Organization in Living Cells. Angew Chem Int Ed Engl 2020; 59:22933-22937. [DOI: 10.1002/anie.202005486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/11/2020] [Indexed: 01/26/2023]
Affiliation(s)
- Tao Ding
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Liyuan Zhu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yuxin Fang
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yangluorong Liu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Wei Tang
- Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Peng Zou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- PKU-IDG/McGovern Institute for Brain Research Beijing 100871 China
- Chinese Institute for Brain Research (CIBR) Beijing 102206 China
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45
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Cenni V, Capanni C, Mattioli E, Schena E, Squarzoni S, Bacalini MG, Garagnani P, Salvioli S, Franceschi C, Lattanzi G. Lamin A involvement in ageing processes. Ageing Res Rev 2020; 62:101073. [PMID: 32446955 DOI: 10.1016/j.arr.2020.101073] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 03/05/2020] [Accepted: 04/11/2020] [Indexed: 12/29/2022]
Abstract
Lamin A, a main constituent of the nuclear lamina, is the major splicing product of the LMNA gene, which also encodes lamin C, lamin A delta 10 and lamin C2. Involvement of lamin A in the ageing process became clear after the discovery that a group of progeroid syndromes, currently referred to as progeroid laminopathies, are caused by mutations in LMNA gene. Progeroid laminopathies include Hutchinson-Gilford Progeria, Mandibuloacral Dysplasia, Atypical Progeria and atypical-Werner syndrome, disabling and life-threatening diseases with accelerated ageing, bone resorption, lipodystrophy, skin abnormalities and cardiovascular disorders. Defects in lamin A post-translational maturation occur in progeroid syndromes and accumulated prelamin A affects ageing-related processes, such as mTOR signaling, epigenetic modifications, stress response, inflammation, microRNA activation and mechanosignaling. In this review, we briefly describe the role of these pathways in physiological ageing and go in deep into lamin A-dependent mechanisms that accelerate the ageing process. Finally, we propose that lamin A acts as a sensor of cell intrinsic and environmental stress through transient prelamin A accumulation, which triggers stress response mechanisms. Exacerbation of lamin A sensor activity due to stably elevated prelamin A levels contributes to the onset of a permanent stress response condition, which triggers accelerated ageing.
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Affiliation(s)
- Vittoria Cenni
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Cristina Capanni
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Elisabetta Mattioli
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Elisa Schena
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Stefano Squarzoni
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge, University Hospital, Stockholm, Sweden
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Interdepartmental Center Alma Mater Research Institute on Global Challenges and Climate Changes, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
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46
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Hu H, Ji Q, Song M, Ren J, Liu Z, Wang Z, Liu X, Yan K, Hu J, Jing Y, Wang S, Zhang W, Liu GH, Qu J. ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin. Nucleic Acids Res 2020; 48:6001-6018. [PMID: 32427330 PMCID: PMC7293006 DOI: 10.1093/nar/gkaa425] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/13/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Zinc finger protein with KRAB and SCAN domains 3 (ZKSCAN3) has long been known as a master transcriptional repressor of autophagy. Here, we identify a novel role for ZKSCAN3 in alleviating senescence that is independent of its autophagy-related activity. Downregulation of ZKSCAN3 is observed in aged human mesenchymal stem cells (hMSCs) and depletion of ZKSCAN3 accelerates senescence of these cells. Mechanistically, ZKSCAN3 maintains heterochromatin stability via interaction with heterochromatin-associated proteins and nuclear lamina proteins. Further study shows that ZKSCAN3 deficiency results in the detachment of genomic lamina-associated domains (LADs) from the nuclear lamina, loss of heterochromatin, a more accessible chromatin status and consequently, aberrant transcription of repetitive sequences. Overexpression of ZKSCAN3 not only rescues premature senescence phenotypes in ZKSCAN3-deficient hMSCs but also rejuvenates physiologically and pathologically senescent hMSCs. Together, these data reveal for the first time that ZKSCAN3 functions as an epigenetic modulator to maintain heterochromatin organization and thereby attenuate cellular senescence. Our findings establish a new functional link among ZKSCAN3, epigenetic regulation, and stem cell aging.
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Affiliation(s)
- Huifang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zehua Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianli Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaobin Jing
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Si Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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47
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Forsberg F, Brunet A, Ali TML, Collas P. Interplay of lamin A and lamin B LADs on the radial positioning of chromatin. Nucleus 2020; 10:7-20. [PMID: 30663495 PMCID: PMC6363278 DOI: 10.1080/19491034.2019.1570810] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Immunosuppressive drugs such as cyclosporin A (CsA) can elicit hepatotoxicity by affecting gene expression. Here, we address the link between CsA and large-scale chromatin organization in HepG2 hepatocarcinoma cells. We show the existence of lamina-associated domains (LADs) interacting with lamin A, lamin B, or both. These ‘A-B’, ‘A-only’ and ‘B-only’ LADs display distinct fates after CsA treatment: A-B LADs remain constitutive or lose A, A-only LADs mainly lose A or switch to B, and B-only LADs remain B-only or acquire A. LAD rearrangement is overall uncoupled from changes in gene expression. Three-dimensional (3D) genome modeling predicts changes in radial positioning of LADs as LADs switch identities, which are corroborated by fluorescence in situ hybridization. Our results reveal interplay between A- and B-type lamins on radial locus positioning, suggesting complementary contributions to large-scale genome architecture. The data also unveil a hitherto unsuspected impact of cytotoxic drugs on genome conformation.Abbreviations: ChIP-seq: chromatin immunoprecipitation sequencing; CsA: cyclosporin A; FISH; fluorescence in situ hybridization; ICMT: isoprenylcysteine methyltransferase; LAD: lamina-associated domain; TAD: topologically-associated domain
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Affiliation(s)
- Frida Forsberg
- a Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , Oslo , Norway
| | - Annaël Brunet
- a Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , Oslo , Norway
| | - Tharvesh M Liyakat Ali
- a Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , Oslo , Norway
| | - Philippe Collas
- a Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , Oslo , Norway.,b Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine , Oslo University Hospital , Oslo , Norway
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Abstract
At the nuclear periphery, associations of chromatin with the nuclear lamina through lamina-associated domains (LADs) aid functional organization of the genome. We review the organization of LADs and provide evidence of LAD heterogeneity from cell ensemble and single-cell data. LADs are typically repressive environments in the genome; nonetheless, we discuss findings of lamin interactions with regulatory elements of active genes, and the role lamins may play in genome regulation. We address the relationship between LADs and other genome organizers, and the involvement of LADs in laminopathies. The current data lay the basis for future studies on the significance of lamin-chromatin interactions in health and disease.
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Affiliation(s)
- Nolwenn Briand
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway.
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway.
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4D Genome Rewiring during Oncogene-Induced and Replicative Senescence. Mol Cell 2020; 78:522-538.e9. [PMID: 32220303 PMCID: PMC7208559 DOI: 10.1016/j.molcel.2020.03.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/20/2019] [Accepted: 03/04/2020] [Indexed: 12/26/2022]
Abstract
To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene expression profiles from cells entering replicative senescence (RS) or upon oncogene-induced senescence (OIS). We identify senescence-associated heterochromatin domains (SAHDs). Differential intra- versus inter-SAHD interactions lead to the formation of senescence-associated heterochromatin foci (SAHFs) in OIS but not in RS. This OIS-specific configuration brings active genes located in genomic regions adjacent to SAHDs in close spatial proximity and favors their expression. We also identify DNMT1 as a factor that induces SAHFs by promoting HMGA2 expression. Upon DNMT1 depletion, OIS cells transition to a 3D genome conformation akin to that of cells in replicative senescence. These data show how multi-omics and imaging can identify critical features of RS and OIS and discover determinants of acute senescence and SAHF formation. Deep multi-omics characterization of replicative and oncogene-induced senescence Senescence-associated heterochromatin domains (SAHDs) form SAHFs via 3D changes DNMT1 is required for SAHF formation via regulation of HMGA2 expression SAHF formation leads to expression of SAHF-adjacent genes via 3D chromatin contacts
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Paluvai H, Di Giorgio E, Brancolini C. The Histone Code of Senescence. Cells 2020; 9:cells9020466. [PMID: 32085582 PMCID: PMC7072776 DOI: 10.3390/cells9020466] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Senescence is the end point of a complex cellular response that proceeds through a set of highly regulated steps. Initially, the permanent cell-cycle arrest that characterizes senescence is a pro-survival response to irreparable DNA damage. The maintenance of this prolonged condition requires the adaptation of the cells to an unfavorable, demanding and stressful microenvironment. This adaptation is orchestrated through a deep epigenetic resetting. A first wave of epigenetic changes builds a dam on irreparable DNA damage and sustains the pro-survival response and the cell-cycle arrest. Later on, a second wave of epigenetic modifications allows the genomic reorganization to sustain the transcription of pro-inflammatory genes. The balanced epigenetic dynamism of senescent cells influences physiological processes, such as differentiation, embryogenesis and aging, while its alteration leads to cancer, neurodegeneration and premature aging. Here we provide an overview of the most relevant histone modifications, which characterize senescence, aging and the activation of a prolonged DNA damage response.
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