1
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Palikyras S, Sofiadis K, Stavropoulou A, Danieli‐Mackay A, Varamogianni‐Mamatsi V, Hörl D, Nasiscionyte S, Zhu Y, Papadionysiou I, Papadakis A, Josipovic N, Zirkel A, O'Connell A, Loughran G, Keane J, Michel A, Wagner W, Beyer A, Harz H, Leonhardt H, Lukinavicius G, Nikolaou C, Papantonis A. Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor. Aging Cell 2024; 23:e14083. [PMID: 38196311 PMCID: PMC11019153 DOI: 10.1111/acel.14083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/07/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Cellular senescence is acknowledged as a key contributor to organismal ageing and late-life disease. Though popular, the study of senescence in vitro can be complicated by the prolonged and asynchronous timing of cells committing to it and by its paracrine effects. To address these issues, we repurposed a small molecule inhibitor, inflachromene (ICM), to induce senescence to human primary cells. Within 6 days of treatment with ICM, senescence hallmarks, including the nuclear eviction of HMGB1 and -B2, are uniformly induced across IMR90 cell populations. By generating and comparing various high throughput datasets from ICM-induced and replicative senescence, we uncovered a high similarity of the two states. Notably though, ICM suppresses the pro-inflammatory secretome associated with senescence, thus alleviating most paracrine effects. In summary, ICM rapidly and synchronously induces a senescent-like phenotype thereby allowing the study of its core regulatory program without confounding heterogeneity.
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Affiliation(s)
- Spiros Palikyras
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Konstantinos Sofiadis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Present address:
Oncode InstituteHubrecht Institute‐KNAW and University Medical Center UtrechtUtrechtThe Netherlands
| | - Athanasia Stavropoulou
- Institute for BioinnovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Adi Danieli‐Mackay
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Clinical Research Unit 5002University Medical Center GöttingenGöttingenGermany
| | | | - David Hörl
- Faculty of BiologyLudwig Maximilians University MunichMunichGermany
| | | | - Yajie Zhu
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | | | - Antonis Papadakis
- Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Natasa Josipovic
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Present address:
Single Cell DiscoveriesUtrechtThe Netherlands
| | - Anne Zirkel
- Center for Molecular Medicine CologneUniversity and University Hospital of CologneCologneGermany
| | | | | | | | | | - Wolfgang Wagner
- Helmholtz‐Institute for Biomedical EngineeringRWTH Aachen University Medical SchoolAachenGermany
- Institute for Stem Cell BiologyRWTH Aachen University Medical SchoolAachenGermany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Hartmann Harz
- Faculty of BiologyLudwig Maximilians University MunichMunichGermany
| | | | - Grazvydas Lukinavicius
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Christoforos Nikolaou
- Institute for BioinnovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Argyris Papantonis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Clinical Research Unit 5002University Medical Center GöttingenGöttingenGermany
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2
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Debès C, Papadakis A, Grönke S, Karalay Ö, Tain LS, Mizi A, Nakamura S, Hahn O, Weigelt C, Josipovic N, Zirkel A, Brusius I, Sofiadis K, Lamprousi M, Lu YX, Huang W, Esmaillie R, Kubacki T, Späth MR, Schermer B, Benzing T, Müller RU, Antebi A, Partridge L, Papantonis A, Beyer A. Ageing-associated changes in transcriptional elongation influence longevity. Nature 2023; 616:814-821. [PMID: 37046086 PMCID: PMC10132977 DOI: 10.1038/s41586-023-05922-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/07/2023] [Indexed: 04/14/2023]
Abstract
Physiological homeostasis becomes compromised during ageing, as a result of impairment of cellular processes, including transcription and RNA splicing1-4. However, the molecular mechanisms leading to the loss of transcriptional fidelity are so far elusive, as are ways of preventing it. Here we profiled and analysed genome-wide, ageing-related changes in transcriptional processes across different organisms: nematodes, fruitflies, mice, rats and humans. The average transcriptional elongation speed (RNA polymerase II speed) increased with age in all five species. Along with these changes in elongation speed, we observed changes in splicing, including a reduction of unspliced transcripts and the formation of more circular RNAs. Two lifespan-extending interventions, dietary restriction and lowered insulin-IGF signalling, both reversed most of these ageing-related changes. Genetic variants in RNA polymerase II that reduced its speed in worms5 and flies6 increased their lifespan. Similarly, reducing the speed of RNA polymerase II by overexpressing histone components, to counter age-associated changes in nucleosome positioning, also extended lifespan in flies and the division potential of human cells. Our findings uncover fundamental molecular mechanisms underlying animal ageing and lifespan-extending interventions, and point to possible preventive measures.
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Affiliation(s)
- Cédric Debès
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Antonios Papadakis
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Özlem Karalay
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Luke S Tain
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Shuhei Nakamura
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Oliver Hahn
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Carina Weigelt
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Anne Zirkel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Isabell Brusius
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Konstantinos Sofiadis
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Mantha Lamprousi
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Yu-Xuan Lu
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Wenming Huang
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Reza Esmaillie
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Torsten Kubacki
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin R Späth
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Bernhard Schermer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Benzing
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Roman-Ulrich Müller
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Adam Antebi
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Linda Partridge
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, UCL, London, UK.
| | - Argyris Papantonis
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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3
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Rinzema NJ, Sofiadis K, Tjalsma SJD, Verstegen MJAM, Oz Y, Valdes-Quezada C, Felder AK, Filipovska T, van der Elst S, de Andrade Dos Ramos Z, Han R, Krijger PHL, de Laat W. Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes. Nat Struct Mol Biol 2022; 29:563-574. [PMID: 35710842 PMCID: PMC9205769 DOI: 10.1038/s41594-022-00787-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/25/2022] [Indexed: 12/14/2022]
Abstract
Developmental gene expression is often controlled by distal regulatory DNA elements called enhancers. Distant enhancer action is restricted to structural chromosomal domains that are flanked by CTCF-associated boundaries and formed through cohesin chromatin loop extrusion. To better understand how enhancers, genes and CTCF boundaries together form structural domains and control expression, we used a bottom-up approach, building series of active regulatory landscapes in inactive chromatin. We demonstrate here that gene transcription levels and activity over time reduce with increased enhancer distance. The enhancer recruits cohesin to stimulate domain formation and engage flanking CTCF sites in loop formation. It requires cohesin exclusively for the activation of distant genes, not of proximal genes, with nearby CTCF boundaries supporting efficient long-range enhancer action. Our work supports a dual activity model for enhancers: its classic role of stimulating transcription initiation and elongation from target gene promoters and a role of recruiting cohesin for the creation of chromosomal domains, the engagement of CTCF sites in chromatin looping and the activation of distal target genes.
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Affiliation(s)
- Niels J Rinzema
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Konstantinos Sofiadis
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sjoerd J D Tjalsma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Yuva Oz
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Christian Valdes-Quezada
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anna-Karina Felder
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Teodora Filipovska
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan van der Elst
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Zaria de Andrade Dos Ramos
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ruiqi Han
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
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4
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Zampetidis CP, Galanos P, Angelopoulou A, Zhu Y, Polyzou A, Karamitros T, Kotsinas A, Lagopati N, Mourkioti I, Mirzazadeh R, Polyzos A, Garnerone S, Mizi A, Gusmao EG, Sofiadis K, Gál Z, Larsen DH, Pefani DE, Demaria M, Tsirigos A, Crosetto N, Maya-Mendoza A, Papaspyropoulos A, Evangelou K, Bartek J, Papantonis A, Gorgoulis VG. A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization. Mol Cell 2021; 81:4907-4923.e8. [PMID: 34793711 DOI: 10.1016/j.molcel.2021.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/14/2021] [Accepted: 10/16/2021] [Indexed: 12/12/2022]
Abstract
Oncogene-induced senescence (OIS) is an inherent and important tumor suppressor mechanism. However, if not removed timely via immune surveillance, senescent cells also have detrimental effects. Although this has mostly been attributed to the senescence-associated secretory phenotype (SASP) of these cells, we recently proposed that "escape" from the senescent state is another unfavorable outcome. The mechanism underlying this phenomenon remains elusive. Here, we exploit genomic and functional data from a prototypical human epithelial cell model carrying an inducible CDC6 oncogene to identify an early-acquired recurrent chromosomal inversion that harbors a locus encoding the circadian transcription factor BHLHE40. This inversion alone suffices for BHLHE40 activation upon CDC6 induction and driving cell cycle re-entry of senescent cells, and malignant transformation. Ectopic overexpression of BHLHE40 prevented induction of CDC6-triggered senescence. We provide strong evidence in support of replication stress-induced genomic instability being a causative factor underlying "escape" from oncogene-induced senescence.
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Affiliation(s)
- Christos P Zampetidis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece
| | - Panagiotis Galanos
- Genome Integrity Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.
| | - Andriani Angelopoulou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece
| | - Yajie Zhu
- Translational Epigenetics Group, Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Aikaterini Polyzou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece
| | - Timokratis Karamitros
- Unit of Bioinformatics and Applied Genomics, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Athanassios Kotsinas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece
| | - Nefeli Lagopati
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece
| | - Ioanna Mourkioti
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece
| | - Reza Mirzazadeh
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Solna, Stockholm, Sweden
| | - Alexandros Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Silvano Garnerone
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Solna, Stockholm, Sweden
| | - Athanasia Mizi
- Translational Epigenetics Group, Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Eduardo G Gusmao
- Translational Epigenetics Group, Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Konstantinos Sofiadis
- Translational Epigenetics Group, Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | | | - Marco Demaria
- University of Groningen (RUG), European Research Institute for the Biology of Aging (ERIBA), University Medical Center Groningen (UMCG), 9713 AV Groningen, the Netherlands
| | | | - Nicola Crosetto
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Solna, Stockholm, Sweden
| | - Apolinar Maya-Mendoza
- DNA Replication and Cancer Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Angelos Papaspyropoulos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece
| | - Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Solna, Stockholm, Sweden.
| | - Argyris Papantonis
- Translational Epigenetics Group, Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, 11527 Athens, Greece; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, University of Manchester, M20 4GJ Manchester, UK; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Faculty of Health and Medical Sciences, University of Surrey, Surrey GU2 7YH, UK.
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5
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Sofiadis K, Josipovic N, Nikolic M, Kargapolova Y, Übelmesser N, Varamogianni-Mamatsi V, Zirkel A, Papadionysiou I, Loughran G, Keane J, Michel A, Gusmao EG, Becker C, Altmüller J, Georgomanolis T, Mizi A, Papantonis A. HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence. Mol Syst Biol 2021; 17:e9760. [PMID: 34166567 PMCID: PMC8224457 DOI: 10.15252/msb.20209760] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/15/2022] Open
Abstract
Spatial organization and gene expression of mammalian chromosomes are maintained and regulated in conjunction with cell cycle progression. This is perturbed once cells enter senescence and the highly abundant HMGB1 protein is depleted from nuclei to act as an extracellular proinflammatory stimulus. Despite its physiological importance, we know little about the positioning of HMGB1 on chromatin and its nuclear roles. To address this, we mapped HMGB1 binding genome‐wide in two primary cell lines. We integrated ChIP‐seq and Hi‐C with graph theory to uncover clustering of HMGB1‐marked topological domains that harbor genes involved in paracrine senescence. Using simplified Cross‐Linking and Immuno‐Precipitation and functional tests, we show that HMGB1 is also a bona fide RNA‐binding protein (RBP) binding hundreds of mRNAs. It presents an interactome rich in RBPs implicated in senescence regulation. The mRNAs of many of these RBPs are directly bound by HMGB1 and regulate availability of SASP‐relevant transcripts. Our findings reveal a broader than hitherto assumed role for HMGB1 in coordinating chromatin folding and RNA homeostasis as part of a regulatory loop controlling cell‐autonomous and paracrine senescence.
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Affiliation(s)
| | - Natasa Josipovic
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Milos Nikolic
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Yulia Kargapolova
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Nadine Übelmesser
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Anne Zirkel
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | | | | | - James Keane
- Ribomaps, Cork, Ireland.,Cork Institute of Technology, Cork, Ireland
| | | | - Eduardo G Gusmao
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Theodore Georgomanolis
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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6
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Kargapolova Y, Rehimi R, Kayserili H, Brühl J, Sofiadis K, Zirkel A, Palikyras S, Mizi A, Li Y, Yigit G, Hoischen A, Frank S, Russ N, Trautwein J, van Bon B, Gilissen C, Laugsch M, Gusmao EG, Josipovic N, Altmüller J, Nürnberg P, Längst G, Kaiser FJ, Watrin E, Brunner H, Rada-Iglesias A, Kurian L, Wollnik B, Bouazoune K, Papantonis A. Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology. Nat Commun 2021; 12:3014. [PMID: 34021162 PMCID: PMC8140133 DOI: 10.1038/s41467-021-23327-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 12/18/2022] Open
Abstract
Members of the chromodomain-helicase-DNA binding (CHD) protein family are chromatin remodelers implicated in human pathologies, with CHD6 being one of its least studied members. We discovered a de novo CHD6 missense mutation in a patient clinically presenting the rare Hallermann-Streiff syndrome (HSS). We used genome editing to generate isogenic iPSC lines and model HSS in relevant cell types. By combining genomics with functional in vivo and in vitro assays, we show that CHD6 binds a cohort of autophagy and stress response genes across cell types. The HSS mutation affects CHD6 protein folding and impairs its ability to recruit co-remodelers in response to DNA damage or autophagy stimulation. This leads to accumulation of DNA damage burden and senescence-like phenotypes. We therefore uncovered a molecular mechanism explaining HSS onset via chromatin control of autophagic flux and genotoxic stress surveillance.
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Affiliation(s)
- Yulia Kargapolova
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Heart Center, University Hospital Cologne, Cologne, Germany.
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Age-associated Disorders (CECAD), University of Cologne, Cologne, Germany
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine, Istanbul, Turkey
| | - Joanna Brühl
- Institute of Molecular Biology and Tumor Research, Philipps-University Marburg, Marburg, Germany
| | | | - Anne Zirkel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Spiros Palikyras
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stefan Frank
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
- Bayer AG, Wuppertal, Germany
| | - Nicole Russ
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | - Jonathan Trautwein
- Institute of Molecular Biology and Tumor Research, Philipps-University Marburg, Marburg, Germany
| | - Bregje van Bon
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Magdalena Laugsch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Eduardo Gade Gusmao
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Gernot Längst
- Biochemistry Centre Regensburg (BRC), University of Regensburg, Regensburg, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Erwan Watrin
- Research Institute of Genetics and Development, Faculté de Médecine, Rennes, France
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Age-associated Disorders (CECAD), University of Cologne, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Santander, Spain
| | - Leo Kurian
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany
| | - Karim Bouazoune
- Institute of Molecular Biology and Tumor Research, Philipps-University Marburg, Marburg, Germany.
| | - Argyris Papantonis
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.
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7
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Zirkel A, Nikolic M, Sofiadis K, Mallm JP, Brackley CA, Gothe H, Drechsel O, Becker C, Altmüller J, Josipovic N, Georgomanolis T, Brant L, Franzen J, Koker M, Gusmao EG, Costa IG, Ullrich RT, Wagner W, Roukos V, Nürnberg P, Marenduzzo D, Rippe K, Papantonis A. HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types. Mol Cell 2018; 70:730-744.e6. [PMID: 29706538 DOI: 10.1016/j.molcel.2018.03.030] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 02/19/2018] [Accepted: 03/25/2018] [Indexed: 11/30/2022]
Abstract
Processes like cellular senescence are characterized by complex events giving rise to heterogeneous cell populations. However, the early molecular events driving this cascade remain elusive. We hypothesized that senescence entry is triggered by an early disruption of the cells' three-dimensional (3D) genome organization. To test this, we combined Hi-C, single-cell and population transcriptomics, imaging, and in silico modeling of three distinct cells types entering senescence. Genes involved in DNA conformation maintenance are suppressed upon senescence entry across all cell types. We show that nuclear depletion of the abundant HMGB2 protein occurs early on the path to senescence and coincides with the dramatic spatial clustering of CTCF. Knocking down HMGB2 suffices for senescence-induced CTCF clustering and for loop reshuffling, while ectopically expressing HMGB2 rescues these effects. Our data suggest that HMGB2-mediated genomic reorganization constitutes a primer for the ensuing senescent program.
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Affiliation(s)
- Anne Zirkel
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Milos Nikolic
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Konstantinos Sofiadis
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Jan-Philipp Mallm
- German Cancer Research Center and Bioquant, 69120 Heidelberg, Germany
| | - Chris A Brackley
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Henrike Gothe
- Institute of Molecular Biology, 55128 Mainz, Germany
| | | | - Christian Becker
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Natasa Josipovic
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | | | - Lilija Brant
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Julia Franzen
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Mirjam Koker
- Clinic I of Internal Medicine and Center for Integrated Oncology, University Hospital Cologne, 50931 Cologne, Germany
| | - Eduardo G Gusmao
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Interdisciplinary Centre for Clinical Research, RWTH Aachen University Medical School, 52062 Aachen, Germany
| | - Ivan G Costa
- Interdisciplinary Centre for Clinical Research, RWTH Aachen University Medical School, 52062 Aachen, Germany
| | - Roland T Ullrich
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Clinic I of Internal Medicine and Center for Integrated Oncology, University Hospital Cologne, 50931 Cologne, Germany
| | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | | | - Peter Nürnberg
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Karsten Rippe
- German Cancer Research Center and Bioquant, 69120 Heidelberg, Germany
| | - Argyris Papantonis
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany.
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8
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Georgomanolis T, Sofiadis K, Papantonis A. Cutting a Long Intron Short: Recursive Splicing and Its Implications. Front Physiol 2016; 7:598. [PMID: 27965595 PMCID: PMC5126111 DOI: 10.3389/fphys.2016.00598] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
Over time eukaryotic genomes have evolved to host genes carrying multiple exons separated by increasingly larger intronic, mostly non-protein-coding, sequences. Initially, little attention was paid to these intronic sequences, as they were considered not to contain regulatory information. However, advances in molecular biology, sequencing, and computational tools uncovered that numerous segments within these genomic elements do contribute to the regulation of gene expression. Introns are differentially removed in a cell type-specific manner to produce a range of alternatively-spliced transcripts, and many span tens to hundreds of kilobases. Recent work in human and fruitfly tissues revealed that long introns are extensively processed cotranscriptionally and in a stepwise manner, before their two flanking exons are spliced together. This process, called "recursive splicing," often involves non-canonical splicing elements positioned deep within introns, and different mechanisms for its deployment have been proposed. Still, the very existence and widespread nature of recursive splicing offers a new regulatory layer in the transcript maturation pathway, which may also have implications in human disease.
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Affiliation(s)
- Theodore Georgomanolis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
| | - Konstantinos Sofiadis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
| | - Argyris Papantonis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
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