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Dalcher D, Tan JY, Bersaglieri C, Peña‐Hernández R, Vollenweider E, Zeyen S, Schmid MW, Bianchi V, Butz S, Roganowicz M, Kuzyakiv R, Baubec T, Marques AC, Santoro R. BAZ2A safeguards genome architecture of ground-state pluripotent stem cells. EMBO J 2020; 39:e105606. [PMID: 33433018 PMCID: PMC7705451 DOI: 10.15252/embj.2020105606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 05/12/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground-state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. On ESC chromatin, BAZ2A interacts with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. BAZ2A associates with chromatin sub-domains within the active A compartment, which intersect through long-range contacts. We found that ground-state chromatin selectively requires BAZ2A to limit the invasion of active domains into repressive compartments. BAZ2A depletion increases chromatin accessibility at B compartments. Furthermore, BAZ2A regulates H3K27me3 genome occupancy in a TOP2A-dependent manner. Finally, ground-state ESCs require BAZ2A for growth, differentiation, and correct expression of developmental genes. Our results uncover the propensity of open chromatin domains to invade repressive domains, which is counteracted by chromatin remodeling to establish genome partitioning and preserve cell identity.
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Affiliation(s)
- Damian Dalcher
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Jennifer Yihong Tan
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Rodrigo Peña‐Hernández
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Eva Vollenweider
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Stefan Zeyen
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Marc W Schmid
- Service and Support for Science ITUniversity of ZurichZurichSwitzerland
| | - Valerio Bianchi
- Oncode InstituteHubrecht Institute‐KNAWUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Stefan Butz
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Marcin Roganowicz
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Rostyslav Kuzyakiv
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Service and Support for Science ITUniversity of ZurichZurichSwitzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
| | - Ana Claudia Marques
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
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Reichmuth ML, Hömke R, Zürcher K, Sander P, Avihingsanon A, Collantes J, Loiseau C, Borrell S, Reinhard M, Wilkinson RJ, Yotebieng M, Fenner L, Böttger EC, Gagneux S, Egger M, Keller PM. Natural Polymorphisms in Mycobacterium tuberculosis Conferring Resistance to Delamanid in Drug-Naive Patients. Antimicrob Agents Chemother 2020; 64:e00513-20. [PMID: 32868333 PMCID: PMC7577131 DOI: 10.1128/aac.00513-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 04/09/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Mutations in the genes of the F420 signaling pathway of Mycobacterium tuberculosis complex, including dnn, fgd1, fbiA, fbiB, fbiC, and fbiD, can lead to delamanid resistance. We searched for such mutations among 129 M. tuberculosis strains from Asia, South America, and Africa using whole-genome sequencing; 70 (54%) strains had at least one mutation in one of the genes. For 10 strains with mutations, we determined the MIC of delamanid. We found one strain from a delamanid-naive patient carrying the natural polymorphism Tyr29del (ddn) that was associated with a critical delamanid MIC.
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Affiliation(s)
- Martina L Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Rico Hömke
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Kathrin Zürcher
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Peter Sander
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Anchalee Avihingsanon
- The HIV Netherlands Australia Thailand (HIV-NAT) Research Collaboration, Thai Red Cross AIDS Research Centre and Tuberculosis Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jimena Collantes
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, Republic of South Africa
- Department of Infectious Diseases, Imperial College, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Marcel Yotebieng
- National TB Lab, Kinshasa, Democratic Republic of the Congo
- Albert Einstein College of Medicine, New York, New York, USA
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss National Center for Mycobacteria, Zurich, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Georgi F, Andriasyan V, Witte R, Murer L, Hemmi S, Yu L, Grove M, Meili N, Kuttler F, Yakimovich A, Turcatti G, Greber UF. The FDA-Approved Drug Nelfinavir Inhibits Lytic Cell-Free but Not Cell-Associated Nonlytic Transmission of Human Adenovirus. Antimicrob Agents Chemother 2020; 64:e01002-20. [PMID: 32601166 PMCID: PMC7449217 DOI: 10.1128/aac.01002-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 05/17/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Adenoviruses (AdVs) are prevalent and give rise to chronic and recurrent disease. Human AdV (HAdV) species B and C, such as HAdV-C2, -C5, and -B14, cause respiratory disease and constitute a health threat for immunocompromised individuals. HAdV-Cs are well known for lysing cells owing to the E3 CR1-β-encoded adenovirus death protein (ADP). We previously reported a high-throughput image-based screening framework and identified an inhibitor of HAdV-C2 multiround infection, nelfinavir mesylate. Nelfinavir is the active ingredient of Viracept, an FDA-approved inhibitor of human immunodeficiency virus (HIV) aspartyl protease that is used to treat AIDS. It is not effective against single-round HAdV infections. Here, we show that nelfinavir inhibits lytic cell-free transmission of HAdV, indicated by the suppression of comet-shaped infection foci in cell culture. Comet-shaped foci occur upon convection-based transmission of cell-free viral particles from an infected cell to neighboring uninfected cells. HAdV lacking ADP was insensitive to nelfinavir but gave rise to comet-shaped foci, indicating that ADP enhances but is not required for cell lysis. This was supported by the notion that HAdV-B14 and -B14p1 lacking ADP were highly sensitive to nelfinavir, although HAdV-A31, -B3, -B7, -B11, -B16, -B21, -D8, -D30, and -D37 were less sensitive. Conspicuously, nelfinavir uncovered slow-growing round HAdV-C2 foci, independent of neutralizing antibodies in the medium, indicative of nonlytic cell-to-cell transmission. Our study demonstrates the repurposing potential of nelfinavir with postexposure efficacy against different HAdVs and describes an alternative nonlytic cell-to-cell transmission mode of HAdV.
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Affiliation(s)
- Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Luca Murer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Lisa Yu
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Melanie Grove
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Nicole Meili
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Fabien Kuttler
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Artur Yakimovich
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Artificial Intelligence for Life Sciences CIC, London, United Kingdom
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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Mustazzolu A, Venturelli L, Dinarelli S, Brown K, Floto RA, Dietler G, Fattorini L, Kasas S, Girasole M, Longo G. A Rapid Unraveling of the Activity and Antibiotic Susceptibility of Mycobacteria. Antimicrob Agents Chemother 2019; 63:e02194-18. [PMID: 30602518 PMCID: PMC6395931 DOI: 10.1128/aac.02194-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 10/17/2018] [Accepted: 12/14/2018] [Indexed: 01/10/2023] Open
Abstract
The development of antibiotic-resistant bacteria is a worldwide health-related emergency that calls for new tools to study the bacterial metabolism and to obtain fast diagnoses. Indeed, the conventional analysis time scale is too long and affects our ability to fight infections. Slowly growing bacteria represent a bigger challenge, since their analysis may require up to months. Among these bacteria, Mycobacterium tuberculosis, the causative agent of tuberculosis, has caused more than 10 million new cases and 1.7 million deaths in 2016 only. We employed a particularly powerful nanomechanical oscillator, the nanomotion sensor, to characterize rapidly and in real time tuberculous and nontuberculous bacterial species, Mycobacterium bovis bacillus Calmette-Guérin and Mycobacterium abscessus, respectively, exposed to different antibiotics. Here, we show how high-speed and high-sensitivity detectors, the nanomotion sensors, can provide a rapid and reliable analysis of different mycobacterial species, obtaining qualitative and quantitative information on their responses to different drugs. This is the first application of the technique to tackle the urgent medical issue of mycobacterial infections, evaluating the dynamic response of bacteria to different antimicrobial families and the role of the replication rate in the resulting nanomotion pattern. In addition to a fast analysis, which could massively benefit patients and the overall health care system, we investigated the real-time responses of the bacteria to extract unique information on the bacterial mechanisms triggered in response to antibacterial pressure, with consequences both at the clinical level and at the microbiological level.
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Affiliation(s)
| | - L Venturelli
- LPMV-IPHYS, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | - S Dinarelli
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - K Brown
- Molecular Immunity Unit, University of Cambridge, Cambridge, United Kingdom
| | - R A Floto
- Molecular Immunity Unit, University of Cambridge, Cambridge, United Kingdom
| | - G Dietler
- LPMV-IPHYS, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | | | - S Kasas
- LPMV-IPHYS, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | - M Girasole
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - G Longo
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
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