1
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Chen HR, Sun Y, Mittler G, Rumpf T, Shvedunova M, Grosschedl R, Akhtar A. MOF-mediated PRDX1 acetylation regulates inflammatory macrophage activation. Cell Rep 2024; 43:114682. [PMID: 39207899 DOI: 10.1016/j.celrep.2024.114682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 06/27/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
Signaling-dependent changes in protein phosphorylation are critical to enable coordination of transcription and metabolism during macrophage activation. However, the role of acetylation in signal transduction during macrophage activation remains obscure. Here, we identify the redox signaling regulator peroxiredoxin 1 (PRDX1) as a substrate of the lysine acetyltransferase MOF. MOF acetylates PRDX1 at lysine 197, preventing hyperoxidation and thus maintaining its activity under stress. PRDX1 K197ac responds to inflammatory signals, decreasing rapidly in mouse macrophages stimulated with bacterial lipopolysaccharides (LPSs) but not with interleukin (IL)-4 or IL-10. The LPS-induced decrease of PRDX1 K197ac elevates cellular hydrogen peroxide accumulation and augments ERK1/2, but not p38 or AKT, phosphorylation. Concomitantly, diminished PRDX1 K197ac stimulates glycolysis, potentiates H3 serine 28 phosphorylation, and ultimately enhances the production of pro-inflammatory mediators such as IL-6. Our work reveals a regulatory role for redox protein acetylation in signal transduction and coordinating metabolic and transcriptional programs during inflammatory macrophage activation.
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Affiliation(s)
- Hui-Ru Chen
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Baden-Württemberg, Germany; Albert-Ludwigs-University Freiburg, Faculty of Biology, Freiburg, Baden-Württemberg, Germany
| | - Yidan Sun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Baden-Württemberg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Baden-Württemberg, Germany
| | - Tobias Rumpf
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Baden-Württemberg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Baden-Württemberg, Germany
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Baden-Württemberg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Baden-Württemberg, Germany.
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2
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Lascaux P, Hoslett G, Tribble S, Trugenberger C, Antičević I, Otten C, Torrecilla I, Koukouravas S, Zhao Y, Yang H, Aljarbou F, Ruggiano A, Song W, Peron C, Deangeli G, Domingo E, Bancroft J, Carrique L, Johnson E, Vendrell I, Fischer R, Ng AWT, Ngeow J, D'Angiolella V, Raimundo N, Maughan T, Popović M, Milošević I, Ramadan K. TEX264 drives selective autophagy of DNA lesions to promote DNA repair and cell survival. Cell 2024:S0092-8674(24)00911-5. [PMID: 39265577 DOI: 10.1016/j.cell.2024.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 06/04/2024] [Accepted: 08/10/2024] [Indexed: 09/14/2024]
Abstract
DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that lysosomes process topoisomerase 1 cleavage complexes (TOP1cc) DNA lesions in vertebrates. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival at clinically relevant doses of topoisomerase 1 inhibitors. TOP1cc are exported from the nucleus to lysosomes through a transient alteration of the nuclear envelope and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating the delivery of TOP1cc to lysosomes in an MRE11-nuclease- and ATR-kinase-dependent manner. We found an evolutionarily conserved role for selective autophagy in DNA repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients.
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Affiliation(s)
- Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sara Tribble
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Camilla Trugenberger
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ivan Antičević
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Cecile Otten
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Stelios Koukouravas
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Yichen Zhao
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hongbin Yang
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Cristiano Peron
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Giulio Deangeli
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 2PY, UK
| | - Enric Domingo
- Department of Oncology, Medical Sciences Division, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - James Bancroft
- Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK
| | - Loïc Carrique
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK
| | - Errin Johnson
- Dunn School Bioimaging Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK
| | - Alvin Wei Tian Ng
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Vincenzo D'Angiolella
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Nuno Raimundo
- Penn State College of Medicine, Department of Cellular and Molecular Physiology, Hershey, PA 17033, USA; Multidisciplinary Institute for Aging, Center for Innovation in Biomedicine and Biotechnology, University of Coimbra, Coimbra 3000-370, Portugal
| | - Tim Maughan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - Marta Popović
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Ira Milošević
- Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK; Multidisciplinary Institute for Aging, Center for Innovation in Biomedicine and Biotechnology, University of Coimbra, Coimbra 3000-370, Portugal
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore.
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3
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Wang J, Chao B, Piesner J, Kelly F, Petrie SK, Xiao X, Li BX. CG-SLENP: A Chemical Genetics Strategy To Selectively Label Existing Proteins and Newly Synthesized Proteins. JACS AU 2024; 4:3146-3156. [PMID: 39211582 PMCID: PMC11350722 DOI: 10.1021/jacsau.4c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 09/04/2024]
Abstract
Protein synthesis and subsequent delivery to the target locations in cells are essential for their proper functions. Methods to label and distinguish newly synthesized proteins from existing ones are critical to assess their differential properties, but such methods are lacking. We describe the first chemical genetics-based approach for selective labeling of existing and newly synthesized proteins that we termed as CG-SLENP. Using HaloTag in-frame fusion with lamin A (LA), we demonstrate that the two pools of proteins can be selectively labeled using CG-SLENP in living cells. We further employ our recently developed selective small molecule ligand LBL1 for LA to probe the potential differences between newly synthesized and existing LA. Our results show that LBL1 can differentially modulate these two pools of LA. These results indicate that the assembly states of newly synthesized LA are distinct from existing LA in living cells. The CG-SLENP method is potentially generalizable to study any cellular proteins.
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Affiliation(s)
- Jian Wang
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Bo Chao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Jake Piesner
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Felice Kelly
- Advanced
Light Microscopy Shared Resource, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Stefanie Kaech Petrie
- Department
of Neurology, Knight Cancer Institute, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Xiangshu Xiao
- Department
of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Bingbing X. Li
- Department
of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, United States
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4
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Phongbunchoo Y, Braikia FZ, Pessoa-Rodrigues C, Ramamoorthy S, Ramachandran H, Grosschedl A, Ma F, Cauchy P, Akhtar A, Sen R, Mittler G, Grosschedl R. YY1-mediated enhancer-promoter communication in the immunoglobulin μ locus is regulated by MSL/MOF recruitment. Cell Rep 2024; 43:114456. [PMID: 38990722 DOI: 10.1016/j.celrep.2024.114456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/02/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
The rearrangement and expression of the immunoglobulin μ heavy chain (Igh) gene require communication of the intragenic Eμ and 3' regulatory region (RR) enhancers with the variable (VH) gene promoter. Eμ binding of the transcription factor YY1 has been implicated in enhancer-promoter communication, but the YY1 protein network remains obscure. By analyzing the comprehensive proteome of the 1-kb Eμ wild-type enhancer and that of Eμ lacking the YY1 binding site, we identified the male-specific lethal (MSL)/MOF complex as a component of the YY1 protein network. We found that MSL2 recruitment depends on YY1 and that gene knockout of Msl2 in primary pre-B cells reduces μ gene expression and chromatin looping of Eμ to the 3' RR enhancer and VH promoter. Moreover, Mof heterozygosity in mice impaired μ expression and early B cell differentiation. Together, these data suggest that the MSL/MOF complex regulates Igh gene expression by augmenting YY1-mediated enhancer-promoter communication.
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Affiliation(s)
- Yutthaphong Phongbunchoo
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fatima-Zohra Braikia
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cecilia Pessoa-Rodrigues
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Haribaskar Ramachandran
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Anna Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fei Ma
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Pierre Cauchy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Ranjan Sen
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA.
| | - Gerhard Mittler
- Proteomics Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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5
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Karayol R, Borroto MC, Haghshenas S, Namasivayam A, Reilly J, Levy MA, Relator R, Kerkhof J, McConkey H, Shvedunova M, Petersen AK, Magnussen K, Zweier C, Vasileiou G, Reis A, Savatt JM, Mulligan MR, Bicknell LS, Poke G, Abu-El-Haija A, Duis J, Hannig V, Srivastava S, Barkoudah E, Hauser NS, van den Born M, Hamiel U, Henig N, Baris Feldman H, McKee S, Krapels IPC, Lei Y, Todorova A, Yordanova R, Atemin S, Rogac M, McConnell V, Chassevent A, Barañano KW, Shashi V, Sullivan JA, Peron A, Iascone M, Canevini MP, Friedman J, Reyes IA, Kierstein J, Shen JJ, Ahmed FN, Mao X, Almoguera B, Blanco-Kelly F, Platzer K, Treu AB, Quilichini J, Bourgois A, Chatron N, Januel L, Rougeot C, Carere DA, Monaghan KG, Rousseau J, Myers KA, Sadikovic B, Akhtar A, Campeau PM. MSL2 variants lead to a neurodevelopmental syndrome with lack of coordination, epilepsy, specific dysmorphisms, and a distinct episignature. Am J Hum Genet 2024; 111:1330-1351. [PMID: 38815585 PMCID: PMC11267526 DOI: 10.1016/j.ajhg.2024.05.001] [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: 09/23/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
Epigenetic dysregulation has emerged as an important etiological mechanism of neurodevelopmental disorders (NDDs). Pathogenic variation in epigenetic regulators can impair deposition of histone post-translational modifications leading to aberrant spatiotemporal gene expression during neurodevelopment. The male-specific lethal (MSL) complex is a prominent multi-subunit epigenetic regulator of gene expression and is responsible for histone 4 lysine 16 acetylation (H4K16ac). Using exome sequencing, here we identify a cohort of 25 individuals with heterozygous de novo variants in MSL complex member MSL2. MSL2 variants were associated with NDD phenotypes including global developmental delay, intellectual disability, hypotonia, and motor issues such as coordination problems, feeding difficulties, and gait disturbance. Dysmorphisms and behavioral and/or psychiatric conditions, including autism spectrum disorder, and to a lesser extent, seizures, connective tissue disease signs, sleep disturbance, vision problems, and other organ anomalies, were observed in affected individuals. As a molecular biomarker, a sensitive and specific DNA methylation episignature has been established. Induced pluripotent stem cells (iPSCs) derived from three members of our cohort exhibited reduced MSL2 levels. Remarkably, while NDD-associated variants in two other members of the MSL complex (MOF and MSL3) result in reduced H4K16ac, global H4K16ac levels are unchanged in iPSCs with MSL2 variants. Regardless, MSL2 variants altered the expression of MSL2 targets in iPSCs and upon their differentiation to early germ layers. Our study defines an MSL2-related disorder as an NDD with distinguishable clinical features, a specific blood DNA episignature, and a distinct, MSL2-specific molecular etiology compared to other MSL complex-related disorders.
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Affiliation(s)
- Remzi Karayol
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Carla Borroto
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Anoja Namasivayam
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jack Reilly
- Department of Pediatrics, Clinical Neurological Sciences and Epidemiology, Western University, London, ON N6A 3K7, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Maria Shvedunova
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Andrea K Petersen
- Department of Genetics and Metabolism, Randall Children's and Legacy Emanuel Hospitals, Portland, OR 97227, USA
| | - Kari Magnussen
- Department of Genetics and Metabolism, Randall Children's and Legacy Emanuel Hospitals, Portland, OR 97227, USA
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Meghan R Mulligan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington, New Zealand
| | - Aya Abu-El-Haija
- Division of Genetics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Jessica Duis
- Section of Genetics & Metabolism, Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Vickie Hannig
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Siddharth Srivastava
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Natalie S Hauser
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA 22042, USA
| | - Myrthe van den Born
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Uri Hamiel
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center & Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Noa Henig
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Hagit Baris Feldman
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center & Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast BT9 7AB, UK
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Albena Todorova
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria; Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
| | - Ralitsa Yordanova
- Department of pediatrics "Prof. Ivan Andreev", Medical university - Plovdiv, Plovdiv, Bulgaria; Department of Pediatrics, University Hospital "St. George", Plovdiv, Bulgaria
| | - Slavena Atemin
- Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
| | - Mihael Rogac
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vivienne McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast BT9 7AB, UK
| | - Anna Chassevent
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Kristin W Barañano
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Angela Peron
- SOC Genetica Medica, Meyer Children's Hospital IRCCS, Florence, Italy; Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", Università degli Studi di Firenze, Florence, Italy
| | - Maria Iascone
- Department of Medical Genetics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Maria P Canevini
- Epilepsy Center - Sleep Medicine Center, Childhood and Adolescence Neuropsychiatry Unit, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy; Department of Health Sciences, University of Milan, Milan, Italy
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California, San Diego, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine and Rady Children's Hospital, San Diego, CA, USA
| | - Iris A Reyes
- Rady Children's Institute for Genomic Medicine and Rady Children's Hospital, San Diego, CA, USA
| | - Janell Kierstein
- Section of Genetics & Metabolism, Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Joseph J Shen
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, UC Davis, Sacramento, CA 95817, USA
| | - Faria N Ahmed
- Division of Genomic Medicine, Department of Pediatrics, UC Davis, Sacramento, CA 95817, USA
| | - Xiao Mao
- National Health Commission Key Laboratory of Birth Defects Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Hunan, China; Nanhua University, Chiayi County, Taiwan
| | - Berta Almoguera
- Department of Genetics and Genomics, Fundacion Jimenez Diaz University Hospital, Health Research Institute-Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics and Genomics, Fundacion Jimenez Diaz University Hospital, Health Research Institute-Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, German
| | | | - Juliette Quilichini
- Service de Médecine Génomique des maladies de système et d'organe, APHP, Centre Université Paris Cité, Paris, France
| | - Alexia Bourgois
- Normandy University, UNICAEN, Caen University Hospital, Department of Genetics, UR 7450 BioTARGen, FHU G4 Genomics, Caen, France
| | - Nicolas Chatron
- Department of Genetics, Lyon University Hospital, Lyon, France; Pathophysiology and Genetics of Neuron and Muscle (PGNM, UCBL - CNRS UMR5261 - INSERM U1315), Université Claude Bernard Lyon 1, Lyon, France
| | - Louis Januel
- Department of Genetics, Lyon University Hospital, Lyon, France
| | | | | | | | - Justine Rousseau
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Kenneth A Myers
- Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada.
| | - Asifa Akhtar
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Philippe M Campeau
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H3T 1C5, Canada
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6
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Li Y, Huang M, Wang M, Wang Y, Deng P, Li C, Huang J, Chen H, Wei Z, Ouyang Q, Zhao J, Lu Y, Su S. Tumor cells impair immunological synapse formation via central nervous system-enriched metabolite. Cancer Cell 2024; 42:985-1002.e18. [PMID: 38821061 DOI: 10.1016/j.ccell.2024.05.006] [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: 07/04/2023] [Revised: 02/22/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
Abstract
Tumors employ various strategies to evade immune surveillance. Central nervous system (CNS) has multiple features to restrain immune response. Whether tumors and CNS share similar programs of immunosuppression is elusive. Here, we analyze multi-omics data of tumors from HER2+ breast cancer patients receiving trastuzumab and anti-PD-L1 antibody and find that CNS-enriched N-acetyltransferase 8-like (NAT8L) and its metabolite N-acetylaspartate (NAA) are overexpressed in resistant tumors. In CNS, NAA is released during brain inflammation. NAT8L attenuates brain inflammation and impairs anti-tumor immunity by inhibiting cytotoxicity of natural killer (NK) cells and CD8+ T cells via NAA. NAA disrupts the formation of immunological synapse by promoting PCAF-induced acetylation of lamin A-K542, which inhibits the integration between lamin A and SUN2 and impairs polarization of lytic granules. We uncover that tumor cells mimic the anti-inflammatory mechanism of CNS to evade anti-tumor immunity and NAT8L is a potential target to enhance efficacy of anti-cancer agents.
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Affiliation(s)
- Yihong Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Min Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Minger Wang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yi Wang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Peng Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Chunni Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jingying Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Hui Chen
- Guangdong Provincial Key Laboratory of Liver Disease Research the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
| | - Zhihao Wei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Qian Ouyang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jinghua Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yiwen Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
| | - Shicheng Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Biotherapy Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
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7
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Keuper K, Bartek J, Maya-Mendoza A. The nexus of nuclear envelope dynamics, circular economy and cancer cell pathophysiology. Eur J Cell Biol 2024; 103:151394. [PMID: 38340500 DOI: 10.1016/j.ejcb.2024.151394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
The nuclear envelope (NE) is a critical component in maintaining the function and structure of the eukaryotic nucleus. The NE and lamina are disassembled during each cell cycle to enable an open mitosis. Nuclear architecture construction and deconstruction is a prime example of a circular economy, as it fulfills a highly efficient recycling program bound to continuous assessment of the quality and functionality of the building blocks. Alterations in the nuclear dynamics and lamina structure have emerged as important contributors to both oncogenic transformation and cancer progression. However, the knowledge of the NE breakdown and reassembly is still limited to a fraction of participating proteins and complexes. As cancer cells contain highly diverse nuclei in terms of DNA content, but also in terms of nuclear number, size, and shape, it is of great interest to understand the intricate relationship between these nuclear features in cancer cell pathophysiology. In this review, we provide insights into how those NE dynamics are regulated, and how lamina destabilization processes may alter the NE circular economy. Moreover, we expand the knowledge of the lamina-associated domain region by using strategic algorithms, including Artificial Intelligence, to infer protein associations, assess their function and location, and predict cancer-type specificity with implications for the future of cancer diagnosis, prognosis and treatment. Using this approach we identified NUP98 and MECP2 as potential proteins that exhibit upregulation in Acute Myeloid Leukemia (LAML) patients with implications for early diagnosis.
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Affiliation(s)
- Kristina Keuper
- DNA Replication and Cancer Group, Danish Cancer Institute, Copenhagen, Denmark; Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SciLifeLab, Stockholm, Sweden
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8
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Xie M, Zhou L, Li T, Lin Y, Zhang R, Zheng X, Zeng C, Zheng L, Zhong L, Huang X, Zou Y, Kang T, Wu Y. Targeting the KAT8/YEATS4 Axis Represses Tumor Growth and Increases Cisplatin Sensitivity in Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310146. [PMID: 38526153 PMCID: PMC11165526 DOI: 10.1002/advs.202310146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/13/2024] [Indexed: 03/26/2024]
Abstract
Bladder cancer (BC) is one of the most common tumors characterized by a high rate of relapse and a lack of targeted therapy. Here, YEATS domain-containing protein 4 (YEATS4) is an essential gene for BC cell viability using CRISPR-Cas9 library screening is reported, and that HUWE1 is an E3 ligase responsible for YEATS4 ubiquitination and proteasomal degradation by the Protein Stability Regulators Screening Assay. KAT8-mediated acetylation of YEATS4 impaired its interaction with HUWE1 and consequently prevented its ubiquitination and degradation. The protein levels of YEATS4 and KAT8 are positively correlated and high levels of these two proteins are associated with poor overall survival in BC patients. Importantly, suppression of YEATS4 acetylation with the KAT8 inhibitor MG149 decreased YEATS4 acetylation, reduced cell viability, and sensitized BC cells to cisplatin treatment. The findings reveal a critical role of the KAT8/YEATS4 axis in both tumor growth and cisplatin sensitivity in BC cells, potentially generating a novel therapeutic strategy for BC patients.
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Affiliation(s)
- Miner Xie
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Department of HematologyGuangzhou First People's HospitalSouth China University of TechnologyGuangzhou510060P. R. China
| | - Liwen Zhou
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ting Li
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yujie Lin
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Xianchong Zheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Cuiling Zeng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Li Zhong
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Center of Digestive DiseaseScientific Research CenterThe Seventh Affiliated HospitalSun Yat‐sen UniversityShenzhen518107P. R. China
| | - Xiaodan Huang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yezi Zou
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- School of MedicineShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
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9
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Yoo L, Mendoza D, Richard AJ, Stephens JM. KAT8 beyond Acetylation: A Survey of Its Epigenetic Regulation, Genetic Variability, and Implications for Human Health. Genes (Basel) 2024; 15:639. [PMID: 38790268 PMCID: PMC11121512 DOI: 10.3390/genes15050639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Lysine acetyltransferase 8, also known as KAT8, is an enzyme involved in epigenetic regulation, primarily recognized for its ability to modulate histone acetylation. This review presents an overview of KAT8, emphasizing its biological functions, which impact many cellular processes and range from chromatin remodeling to genetic and epigenetic regulation. In many model systems, KAT8's acetylation of histone H4 lysine 16 (H4K16) is critical for chromatin structure modification, which influences gene expression, cell proliferation, differentiation, and apoptosis. Furthermore, this review summarizes the observed genetic variability within the KAT8 gene, underscoring the implications of various single nucleotide polymorphisms (SNPs) that affect its functional efficacy and are linked to diverse phenotypic outcomes, ranging from metabolic traits to neurological disorders. Advanced insights into the structural biology of KAT8 reveal its interaction with multiprotein assemblies, such as the male-specific lethal (MSL) and non-specific lethal (NSL) complexes, which regulate a wide range of transcriptional activities and developmental functions. Additionally, this review focuses on KAT8's roles in cellular homeostasis, stem cell identity, DNA damage repair, and immune response, highlighting its potential as a therapeutic target. The implications of KAT8 in health and disease, as evidenced by recent studies, affirm its importance in cellular physiology and human pathology.
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Affiliation(s)
- Lindsey Yoo
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - David Mendoza
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Allison J. Richard
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
| | - Jacqueline M. Stephens
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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10
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Chander A, Mager J. Loss of KANSL3 leads to defective inner cell mass and early embryonic lethality. Mol Reprod Dev 2024; 91:e23760. [PMID: 38769918 PMCID: PMC11244731 DOI: 10.1002/mrd.23760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
e-Lysine acetylation is a prominent histone mark found at transcriptionally active loci. Among many lysine acetyl transferases, nonspecific lethal complex (NSL) members are known to mediate the modification of histone H4. In addition to histone modifications, the KAT8 regulatory complex subunit 3 gene (Kansl3), a core member of NSL complex, has been shown to be involved in several other cellular processes such as mitosis and mitochondrial activity. Although functional studies have been performed on NSL complex members, none of the four core proteins, including Kansl3, have been studied during early mouse development. Here we show that homozygous knockout Kansl3 embryos are lethal at peri-implantation stages, failing to hatch out of the zona pellucida. When the zona pellucida is removed in vitro, Kansl3 null embryos form an abnormal outgrowth with significantly disrupted inner cell mass (ICM) morphology. We document lineage-specific defects at the blastocyst stage with significantly reduced ICM cell number but no difference in trophectoderm cell numbers. Both epiblast and primitive endoderm lineages are altered with reduced cell numbers in null mutants. These results show that Kansl3 is indispensable during early mouse embryonic development and with defects in both ICM and trophectoderm lineages.
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Affiliation(s)
- Ashmita Chander
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Veterinary and Animal Sciences, University of Massachusetts-Amherst, 661 North Pleasant Street, Amherst, Massachusetts, USA
| | - Jesse Mager
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Veterinary and Animal Sciences, University of Massachusetts-Amherst, 661 North Pleasant Street, Amherst, Massachusetts, USA
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11
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Molenberghs F, Verschuuren M, Vandeweyer L, Peeters S, Bogers JJ, Novo CP, Vanden Berghe W, De Reu H, Cools N, Schelhaas M, De Vos WH. Lamin B1 curtails early human papillomavirus infection by safeguarding nuclear compartmentalization and autophagic capacity. Cell Mol Life Sci 2024; 81:141. [PMID: 38485766 PMCID: PMC10940392 DOI: 10.1007/s00018-024-05194-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
Human papillomavirus (HPV) infection is a primary cause of cervical and head-and-neck cancers. The HPV genome enters the nucleus during mitosis when the nuclear envelope disassembles. Given that lamins maintain nuclear integrity during interphase, we asked to what extent their loss would affect early HPV infection. To address this question, we infected human cervical cancer cells and keratinocytes lacking the major lamins with a HPV16 pseudovirus (HP-PsV) encoding an EGFP reporter. We found that a sustained reduction or complete loss of lamin B1 significantly increased HP-PsV infection rate. A corresponding greater nuclear HP-PsV load in LMNB1 knockout cells was directly related to their prolonged mitotic window and extensive nuclear rupture propensity. Despite the increased HP-PsV presence, EGFP transcript levels remained virtually unchanged, indicating an additional defect in protein turnover. Further investigation revealed that LMNB1 knockout led to a substantial decrease in autophagic capacity, possibly linked to the persistent activation of cGAS by cytoplasmic chromatin exposure. Thus, the attrition of lamin B1 increases nuclear perviousness and attenuates autophagic capacity, creating an environment conducive to unrestrained accumulation of HPV capsids. Our identification of lower lamin B1 levels and nuclear BAF foci in the basal epithelial layer of several human cervix samples suggests that this pathway may contribute to an increased individual susceptibility to HPV infection.
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Affiliation(s)
- Freya Molenberghs
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Marlies Verschuuren
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Lauran Vandeweyer
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Sarah Peeters
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Johannes J Bogers
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Claudina Perez Novo
- Cell Death Signaling Lab, Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Cell Death Signaling Lab, Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Hans De Reu
- Laboratory of Experimental Hematology, Faculty Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Nathalie Cools
- Laboratory of Experimental Hematology, Faculty Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Mario Schelhaas
- Institute of Cellular Virology, University of Münster, Münster, Germany
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
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12
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Mestres I, Atabay A, Escolano JC, Arndt S, Schmidtke K, Einsiedel M, Patsonis M, Bolaños-Castro LA, Yun M, Bernhardt N, Taubenberger A, Calegari F. Manipulation of the nuclear envelope-associated protein SLAP during mammalian brain development affects cortical lamination and exploratory behavior. Biol Open 2024; 13:bio060359. [PMID: 38466184 PMCID: PMC10958201 DOI: 10.1242/bio.060359] [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: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/12/2024] Open
Abstract
Here, we report the first characterization of the effects resulting from the manipulation of Soluble-Lamin Associated Protein (SLAP) expression during mammalian brain development. We found that SLAP localizes to the nuclear envelope and when overexpressed causes changes in nuclear morphology and lengthening of mitosis. SLAP overexpression in apical progenitors of the developing mouse brain altered asymmetric cell division, neurogenic commitment and neuronal migration ultimately resulting in unbalance in the proportion of upper, relative to deeper, neuronal layers. Several of these effects were also recapitulated upon Cas9-mediated knockdown. Ultimately, SLAP overexpression during development resulted in a reduction in subcortical projections of young mice and, notably, reduced their exploratory behavior. Our study shows the potential relevance of the previously uncharacterized nuclear envelope protein SLAP in neurodevelopmental disorders.
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Affiliation(s)
- Ivan Mestres
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Azra Atabay
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Joan-Carles Escolano
- Biotechnology Center, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Solveig Arndt
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Klara Schmidtke
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Maximilian Einsiedel
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Melina Patsonis
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Lizbeth Airais Bolaños-Castro
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Maximina Yun
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Nadine Bernhardt
- Department of Psychiatry and Psychotherapy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Anna Taubenberger
- Biotechnology Center, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Federico Calegari
- CRTD-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
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13
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Guhathakurta S, Erdogdu NU, Hoffmann JJ, Grzadzielewska I, Schendzielorz A, Seyfferth J, Mårtensson CU, Corrado M, Karoutas A, Warscheid B, Pfanner N, Becker T, Akhtar A. COX17 acetylation via MOF-KANSL complex promotes mitochondrial integrity and function. Nat Metab 2023; 5:1931-1952. [PMID: 37813994 PMCID: PMC10663164 DOI: 10.1038/s42255-023-00904-w] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/06/2023] [Indexed: 10/11/2023]
Abstract
Reversible acetylation of mitochondrial proteins is a regulatory mechanism central to adaptive metabolic responses. Yet, how such functionally relevant protein acetylation is achieved remains unexplored. Here we reveal an unprecedented role of the MYST family lysine acetyltransferase MOF in energy metabolism via mitochondrial protein acetylation. Loss of MOF-KANSL complex members leads to mitochondrial defects including fragmentation, reduced cristae density and impaired mitochondrial electron transport chain complex IV integrity in primary mouse embryonic fibroblasts. We demonstrate COX17, a complex IV assembly factor, as a bona fide acetylation target of MOF. Loss of COX17 or expression of its non-acetylatable mutant phenocopies the mitochondrial defects observed upon MOF depletion. The acetylation-mimetic COX17 rescues these defects and maintains complex IV activity even in the absence of MOF, suggesting an activatory role of mitochondrial electron transport chain protein acetylation. Fibroblasts from patients with MOF syndrome who have intellectual disability also revealed respiratory defects that could be restored by alternative oxidase, acetylation-mimetic COX17 or mitochondrially targeted MOF. Overall, our findings highlight the critical role of MOF-KANSL complex in mitochondrial physiology and provide new insights into MOF syndrome.
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Affiliation(s)
- Sukanya Guhathakurta
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Juliane J Hoffmann
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Iga Grzadzielewska
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Christoph U Mårtensson
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mauro Corrado
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Adam Karoutas
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bettina Warscheid
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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14
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Buchwalter A. Intermediate, but not average: The unusual lives of the nuclear lamin proteins. Curr Opin Cell Biol 2023; 84:102220. [PMID: 37619289 DOI: 10.1016/j.ceb.2023.102220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
The nuclear lamins are polymeric intermediate filament proteins that scaffold the nucleus and organize the genome in nearly all eukaryotic cells. This review focuses on the dynamic regulation of lamin filaments through their biogenesis, assembly, disassembly, and degradation. The lamins are unusually long-lived proteins under homeostatic conditions, but their turnover can be induced in select contexts that are highlighted in this review. Finally, we discuss recent investigations into the influence of laminopathy-linked mutations on the assembly, folding, and stability of the nuclear lamins.
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Affiliation(s)
- Abigail Buchwalter
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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15
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Tsang TH, Wiese M, Helmstädter M, Stehle T, Seyfferth J, Shvedunova M, Holz H, Walz G, Akhtar A. Transcriptional regulation by the NSL complex enables diversification of IFT functions in ciliated versus nonciliated cells. SCIENCE ADVANCES 2023; 9:eadh5598. [PMID: 37624894 PMCID: PMC10456878 DOI: 10.1126/sciadv.adh5598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Members of the NSL histone acetyltransferase complex are involved in multiorgan developmental syndromes. While the NSL complex is known for its importance in early development, its role in fully differentiated cells remains enigmatic. Using a kidney-specific model, we discovered that deletion of NSL complex members KANSL2 or KANSL3 in postmitotic podocytes led to catastrophic kidney dysfunction. Systematic comparison of two primary differentiated cell types reveals the NSL complex as a master regulator of intraciliary transport genes in both dividing and nondividing cells. NSL complex ablation led to loss of cilia and impaired sonic hedgehog pathway in ciliated fibroblasts. By contrast, nonciliated podocytes responded with altered microtubule dynamics and obliterated podocyte functions. Finally, overexpression of wild-type but not a double zinc finger (ZF-ZF) domain mutant of KANSL2 rescued the transcriptional defects, revealing a critical function of this domain in NSL complex assembly and function. Thus, the NSL complex exhibits bifurcation of functions to enable diversity of specialized outcomes in differentiated cells.
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Affiliation(s)
- Tsz Hong Tsang
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), 79108 Freiburg, Germany
| | - Meike Wiese
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Martin Helmstädter
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Thomas Stehle
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Gerd Walz
- Department of Medicine IV, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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16
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Pande S, Ghosh DK. Nuclear proteostasis imbalance in laminopathy-associated premature aging diseases. FASEB J 2023; 37:e23116. [PMID: 37498235 DOI: 10.1096/fj.202300878r] [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: 05/02/2023] [Revised: 06/15/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
Laminopathies are a group of rare genetic disorders with heterogeneous clinical phenotypes such as premature aging, cardiomyopathy, lipodystrophy, muscular dystrophy, microcephaly, epilepsy, and so on. The cellular phenomena associated with laminopathy invariably show disruption of nucleoskeleton of lamina due to deregulated expression, localization, function, and interaction of mutant lamin proteins. Impaired spatial and temporal tethering of lamin proteins to the lamina or nucleoplasmic aggregation of lamins are the primary molecular events that can trigger nuclear proteotoxicity by modulating differential protein-protein interactions, sequestering quality control proteins, and initiating a cascade of abnormal post-translational modifications. Clearly, laminopathic cells exhibit moderate to high nuclear proteotoxicity, raising the question of whether an imbalance in nuclear proteostasis is involved in laminopathic diseases, particularly in diseases of early aging such as HGPS and laminopathy-associated premature aging. Here, we review nuclear proteostasis and its deregulation in the context of lamin proteins and laminopathies.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Debasish Kumar Ghosh
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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17
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Papathanasiou S, Mynhier NA, Liu S, Brunette G, Stokasimov E, Jacob E, Li L, Comenho C, van Steensel B, Buenrostro JD, Zhang CZ, Pellman D. Heritable transcriptional defects from aberrations of nuclear architecture. Nature 2023; 619:184-192. [PMID: 37286600 PMCID: PMC10322708 DOI: 10.1038/s41586-023-06157-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Transcriptional heterogeneity due to plasticity of the epigenetic state of chromatin contributes to tumour evolution, metastasis and drug resistance1-3. However, the mechanisms that cause this epigenetic variation are incompletely understood. Here we identify micronuclei and chromosome bridges, aberrations in the nucleus common in cancer4,5, as sources of heritable transcriptional suppression. Using a combination of approaches, including long-term live-cell imaging and same-cell single-cell RNA sequencing (Look-Seq2), we identified reductions in gene expression in chromosomes from micronuclei. With heterogeneous penetrance, these changes in gene expression can be heritable even after the chromosome from the micronucleus has been re-incorporated into a normal daughter cell nucleus. Concomitantly, micronuclear chromosomes acquire aberrant epigenetic chromatin marks. These defects may persist as variably reduced chromatin accessibility and reduced gene expression after clonal expansion from single cells. Persistent transcriptional repression is strongly associated with, and may be explained by, markedly long-lived DNA damage. Epigenetic alterations in transcription may therefore be inherently coupled to chromosomal instability and aberrations in nuclear architecture.
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Affiliation(s)
- Stamatis Papathanasiou
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Institute of Molecular Biology, Mainz, Germany.
| | - Nikos A Mynhier
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shiwei Liu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gregory Brunette
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ema Stokasimov
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Etai Jacob
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- AstraZeneca, Waltham, MA, USA
| | - Lanting Li
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Caroline Comenho
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cheng-Zhong Zhang
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - David Pellman
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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18
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Fan JR, Chang SN, Chu CT, Chen HC. AKT2-mediated nuclear deformation leads to genome instability during epithelial-mesenchymal transition. iScience 2023; 26:106992. [PMID: 37378334 PMCID: PMC10291577 DOI: 10.1016/j.isci.2023.106992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/04/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Nuclear deformation has been observed in some cancer cells for decades, but its underlying mechanism and biological significance remain elusive. To address these questions, we employed human lung cancer A549 cell line as a model in context with transforming growth factor β (TGFβ)-induced epithelial-mesenchymal transition. Here, we report that nuclear deformation induced by TGFβ is concomitant with increased phosphorylation of lamin A at Ser390, defective nuclear lamina and genome instability. AKT2 and Smad3 serve as the downstream effectors for TGFβ to induce nuclear deformation. AKT2 directly phosphorylates lamin A at Ser390, whereas Smad3 is required for AKT2 activation upon TGFβ stimulation. Expression of the lamin A mutant with a substitution of Ser390 to Ala or suppression of AKT2 or Smad3 prevents nuclear deformation and genome instability induced by TGFβ. These findings reveal a molecular mechanism for TGFβ-induced nuclear deformation and establish a role of nuclear deformation in genome instability during epithelial-mesenchymal transition.
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Affiliation(s)
- Jia-Rong Fan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Sung-Nian Chang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ching-Tung Chu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Hong-Chen Chen
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
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19
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Schibler AC, Jevtic P, Pegoraro G, Levy DL, Misteli T. Identification of epigenetic modulators as determinants of nuclear size and shape. eLife 2023; 12:e80653. [PMID: 37219077 PMCID: PMC10259489 DOI: 10.7554/elife.80653] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
The shape and size of the human cell nucleus is highly variable among cell types and tissues. Changes in nuclear morphology are associated with disease, including cancer, as well as with premature and normal aging. Despite the very fundamental nature of nuclear morphology, the cellular factors that determine nuclear shape and size are not well understood. To identify regulators of nuclear architecture in a systematic and unbiased fashion, we performed a high-throughput imaging-based siRNA screen targeting 867 nuclear proteins including chromatin-associated proteins, epigenetic regulators, and nuclear envelope components. Using multiple morphometric parameters, and eliminating cell cycle effectors, we identified a set of novel determinants of nuclear size and shape. Interestingly, most identified factors altered nuclear morphology without affecting the levels of lamin proteins, which are known prominent regulators of nuclear shape. In contrast, a major group of nuclear shape regulators were modifiers of repressive heterochromatin. Biochemical and molecular analysis uncovered a direct physical interaction of histone H3 with lamin A mediated via combinatorial histone modifications. Furthermore, disease-causing lamin A mutations that result in disruption of nuclear shape inhibited lamin A-histone H3 interactions. Oncogenic histone H3.3 mutants defective for H3K27 methylation resulted in nuclear morphology abnormalities. Altogether, our results represent a systematic exploration of cellular factors involved in determining nuclear morphology and they identify the interaction of lamin A with histone H3 as an important contributor to nuclear morphology in human cells.
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Affiliation(s)
| | - Predrag Jevtic
- Department of Molecular Biology, University of WyomingLaramieUnited States
| | - Gianluca Pegoraro
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIHBethesdaUnited States
| | - Daniel L Levy
- Department of Molecular Biology, University of WyomingLaramieUnited States
| | - Tom Misteli
- National Cancer InstituteBethesdaUnited States
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20
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Fan Q, Li XM, Zhai C, Li B, Li ST, Dong MQ. Somatic nuclear blebbing in Caenorhabditis elegans is not a feature of organismal aging but a potential indicator of germline proliferation in early adulthood. G3 (BETHESDA, MD.) 2023; 13:jkad029. [PMID: 36735812 PMCID: PMC10085788 DOI: 10.1093/g3journal/jkad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Abnormal nuclear morphology is suggested to be a hallmark of aging and one such abnormality is nuclear blebbing. However, little is known about whether and how nuclear blebbing participates in animal aging, and what regulates it. In this study, we show that the frequency of nuclear blebbing in the hypodermis increases during aging in wild-type C. elegans. These nuclear blebs are enveloped by the nuclear lamina, the inner and the outer nuclear membrane, and 42% of them contain chromatin. Although nuclear blebbing could lead to DNA loss if chromatin-containing blebs detach and fuse with lysosomes, we find by time-lapse imaging that nuclear blebs rarely detach, and the estimated lifetime of a nuclear bleb is 772 h or 32 days. The amount of DNA lost through nuclear blebbing is estimated to be about 0.1% of the total DNA loss by adult Day 11. Furthermore, the frequency of nuclear blebbing does not correlate with the rate of aging in C. elegans. Old age does not necessarily induce nuclear blebbing, neither does starvation, heat stress, or oxidative stress. Intriguingly, we find that proliferation of germ cells promotes nuclear blebbing.
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Affiliation(s)
- Qiang Fan
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Xue-Mei Li
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Chao Zhai
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Bin Li
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Shang-Tong Li
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Meng-Qiu Dong
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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21
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Disrupting the phase separation of KAT8-IRF1 diminishes PD-L1 expression and promotes antitumor immunity. NATURE CANCER 2023; 4:382-400. [PMID: 36894639 PMCID: PMC10042735 DOI: 10.1038/s43018-023-00522-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/02/2023] [Indexed: 03/11/2023]
Abstract
Immunotherapies targeting the PD-1/PD-L1 axis have become first-line treatments in multiple cancers. However, only a limited subset of individuals achieves durable benefits because of the elusive mechanisms regulating PD-1/PD-L1. Here, we report that in cells exposed to interferon-γ (IFNγ), KAT8 undergoes phase separation with induced IRF1 and forms biomolecular condensates to upregulate PD-L1. Multivalency from both the specific and promiscuous interactions between IRF1 and KAT8 is required for condensate formation. KAT8-IRF1 condensation promotes IRF1 K78 acetylation and binding to the CD247 (PD-L1) promoter and further enriches the transcription apparatus to promote transcription of PD-L1 mRNA. Based on the mechanism of KAT8-IRF1 condensate formation, we identified the 2142-R8 blocking peptide, which disrupts KAT8-IRF1 condensate formation and consequently inhibits PD-L1 expression and enhances antitumor immunity in vitro and in vivo. Our findings reveal a key role of KAT8-IRF1 condensates in PD-L1 regulation and provide a competitive peptide to enhance antitumor immune responses.
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22
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Shen S, Rui Y, Wang Y, Su J, Yu X. SARS-CoV-2, HIV, and HPV: Convergent evolution of selective regulation of cGAS-STING signaling. J Med Virol 2023; 95:e28220. [PMID: 36229923 PMCID: PMC9874546 DOI: 10.1002/jmv.28220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/21/2022] [Accepted: 10/11/2022] [Indexed: 01/27/2023]
Abstract
Recognizing aberrant cytoplasmic double-stranded DNA and stimulating innate immunity is essential for the host's defense against viruses and tumors. Cyclic GMP-AMP (cGAMP) synthase (cGAS) is a cytosolic DNA sensor that synthesizes the second messenger 2'3'-cGAMP and subsequently activates stimulator of interferon genes (STING)-mediated activation of TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3) and the production of type I interferon (IFN-I). Both the cGAS-STING-mediated IFN-I antiviral defense and the countermeasures developed by diverse viruses have been extensively studied. However, recent studies have revealed a convergent evolutionary feature of severe acute respiratory syndrome coronavirus 2 and human immunodeficiency virus (HIV) viral proteins in terms of the selective regulation of cGAS-STING-mediated nuclear factor-κB (NF-κB) signaling without any effect on cGAS-STING-mediated TBK1/IRF3 activation and IFN production. The potential beneficial effect of this cGAS-STING-mediated, NF-κB-dependent antiviral effect, and the possible detrimental effect of IFN-I in the pathogenesis of coronavirus disease 2019 and HIV infection deserve more attention and future investigation.
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Affiliation(s)
- Si Shen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina,Cancer CenterZhejiang UniversityHangzhouZhejiangChina
| | - Yajuan Rui
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina,Cancer CenterZhejiang UniversityHangzhouZhejiangChina
| | - Yanpu Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina,Cancer CenterZhejiang UniversityHangzhouZhejiangChina
| | - Jiaming Su
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina,Cancer CenterZhejiang UniversityHangzhouZhejiangChina
| | - Xiao‐Fang Yu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina,Cancer CenterZhejiang UniversityHangzhouZhejiangChina
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23
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Nie Q, Huan X, Kang J, Yin J, Zhao J, Li Y, Zhang Z. MG149 Inhibits MOF-Mediated p53 Acetylation to Attenuate X-Ray Radiation-Induced Apoptosis in H9c2 Cells. Radiat Res 2022; 198:590-598. [PMID: 36481803 DOI: 10.1667/rade-22-00049.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 09/30/2022] [Indexed: 12/13/2022]
Abstract
Cardiomyocyte apoptosis is involved in the pathogenesis of radiation-induced heart disease, but the underlying epigenetic mechanism remains elusive. We evaluated the potential mediating role of males absent on the first (MOF) in the association between epigenetic activation of p53 lysine 120 (p53K120) and X-ray radiation-induced apoptosis in H9c2 cells. H9c2 cells were pretreated for 24 h with the MOF inhibitor MG149 after 4 Gy irradiation, followed by assessment of cell proliferation, injury, and apoptosis. MOF expression was upregulated by X-ray radiation. MG149 suppressed the proliferation inhibition, reduction of mitochondrial membrane potential, ROS production, and cell apoptosis. MG149 may promote the survival of H9c2 cells via inhibition of MOF-mediated p53K120 acetylation in response to X-ray radiation-induced apoptosis. Our data indicates a MOF-associated epigenetic mechanism in H9c2 cells that promotes attenuation of X-ray radiation-induced injury.
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Affiliation(s)
- Qianwen Nie
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
| | - Xuan Huan
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
| | - Jing Kang
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
| | - Jiangyan Yin
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
| | - Jiahui Zhao
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China
| | - Yi Li
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - ZhengYi Zhang
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
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24
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Kalukula Y, Stephens AD, Lammerding J, Gabriele S. Mechanics and functional consequences of nuclear deformations. Nat Rev Mol Cell Biol 2022; 23:583-602. [PMID: 35513718 PMCID: PMC9902167 DOI: 10.1038/s41580-022-00480-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 02/08/2023]
Abstract
As the home of cellular genetic information, the nucleus has a critical role in determining cell fate and function in response to various signals and stimuli. In addition to biochemical inputs, the nucleus is constantly exposed to intrinsic and extrinsic mechanical forces that trigger dynamic changes in nuclear structure and morphology. Emerging data suggest that the physical deformation of the nucleus modulates many cellular and nuclear functions. These functions have long been considered to be downstream of cytoplasmic signalling pathways and dictated by gene expression. In this Review, we discuss an emerging perspective on the mechanoregulation of the nucleus that considers the physical connections from chromatin to nuclear lamina and cytoskeletal filaments as a single mechanical unit. We describe key mechanisms of nuclear deformations in time and space and provide a critical review of the structural and functional adaptive responses of the nucleus to deformations. We then consider the contribution of nuclear deformations to the regulation of important cellular functions, including muscle contraction, cell migration and human disease pathogenesis. Collectively, these emerging insights shed new light on the dynamics of nuclear deformations and their roles in cellular mechanobiology.
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Affiliation(s)
- Yohalie Kalukula
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Sylvain Gabriele
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
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25
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Divisato G, Chiariello AM, Esposito A, Zoppoli P, Zambelli F, Elia MA, Pesole G, Incarnato D, Passaro F, Piscitelli S, Oliviero S, Nicodemi M, Parisi S, Russo T. Hmga2 protein loss alters nuclear envelope and 3D chromatin structure. BMC Biol 2022; 20:171. [PMID: 35918713 PMCID: PMC9344646 DOI: 10.1186/s12915-022-01375-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The high-mobility group Hmga family of proteins are non-histone chromatin-interacting proteins which have been associated with a number of nuclear functions, including heterochromatin formation, replication, recombination, DNA repair, transcription, and formation of enhanceosomes. Due to its role based on dynamic interaction with chromatin, Hmga2 has a pathogenic role in diverse tumors and has been mainly studied in a cancer context; however, whether Hmga2 has similar physiological functions in normal cells remains less explored. Hmga2 was additionally shown to be required during the exit of embryonic stem cells (ESCs) from the ground state of pluripotency, to allow their transition into epiblast-like cells (EpiLCs), and here, we use that system to gain further understanding of normal Hmga2 function. RESULTS We demonstrated that Hmga2 KO pluripotent stem cells fail to develop into EpiLCs. By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. Accordingly, a sustained expression of polycomb repressive complex 2 (PRC2), responsible for H3K27me3 deposition, was observed in KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. Starting from this observation, we demonstrated that nuclear lamina underwent severe alterations when Hmga2 KO or KD cells were induced to exit from the naïve state and this phenomenon is accompanied by a mislocalization of the heterochromatin mark H3K9me3 within the nucleus. As nuclear lamina (NL) is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of Hi-C data in wt and Hmga2 KO cells allowed us to observe that inter-TAD (topologically associated domains) interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina. CONCLUSIONS Overall, our results indicate that Hmga2 interacts with heterochromatic lamin-associated domains, and highlight a role for Hmga2 in the crosstalk between chromatin and nuclear lamina, affecting the establishment of inter-TAD interactions.
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Affiliation(s)
- Giuseppina Divisato
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Naples, Italy
| | - Pietro Zoppoli
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Federico Zambelli
- Dipartimento di Bioscienze, Università di Milano Statale, Milan, Italy
| | - Maria Antonietta Elia
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Graziano Pesole
- Dipartimento Di Bioscienze, Biotecnologie e Biofarmaceutica, Università di Bari A. Moro and IBIOM CNR, Bari, Italy
| | - Danny Incarnato
- University of Groningen, GBB Institute, Groningen, The Netherlands
| | - Fabiana Passaro
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Silvia Piscitelli
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino and IIGM Candiolo, Turin, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Naples, Italy.,Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany.,CNR-SPIN, Naples, Italy
| | - Silvia Parisi
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy.
| | - Tommaso Russo
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy.
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26
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Selezneva A, Gibb AJ, Willis D. The Nuclear Envelope as a Regulator of Immune Cell Function. Front Immunol 2022; 13:840069. [PMID: 35757775 PMCID: PMC9226455 DOI: 10.3389/fimmu.2022.840069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/10/2022] [Indexed: 01/07/2023] Open
Abstract
The traditional view of the nuclear envelope (NE) was that it represented a relatively inert physical barrier within the cell, whose main purpose was to separate the nucleoplasm from the cytoplasm. However, recent research suggests that this is far from the case, with new and important cellular functions being attributed to this organelle. In this review we describe research suggesting an important contribution of the NE and its constituents in regulating the functions of cells of the innate and adaptive immune system. One of the standout properties of immune cells is their ability to migrate around the body, allowing them to carry out their physiological/pathophysiology cellular role at the appropriate location. This together with the physiological role of the tissue, changes in tissue matrix composition due to disease and aging, and the activation status of the immune cell, all result in immune cells being subjected to different mechanical forces. We report research which suggests that the NE may be an important sensor/transducer of these mechanical signals and propose that the NE is an integrator of both mechanical and chemical signals, allowing the cells of the innate immune system to precisely regulate gene transcription and functionality. By presenting this overview we hope to stimulate the interests of researchers into this often-overlooked organelle and propose it should join the ranks of mitochondria and phagosome, which are important organelles contributing to immune cell function.
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Affiliation(s)
- Anna Selezneva
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, United Kingdom
| | - Alasdair J Gibb
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, United Kingdom
| | - Dean Willis
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, United Kingdom
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27
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A Nuclear Belt Fastens on Neural Cell Fate. Cells 2022; 11:cells11111761. [PMID: 35681456 PMCID: PMC9179901 DOI: 10.3390/cells11111761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/22/2022] Open
Abstract
Successful embryonic and adult neurogenesis require proliferating neural stem and progenitor cells that are intrinsically and extrinsically guided into a neuronal fate. In turn, migration of new-born neurons underlies the complex cytoarchitecture of the brain. Proliferation and migration are therefore essential for brain development, homeostasis and function in adulthood. Among several tightly regulated processes involved in brain formation and function, recent evidence points to the nuclear envelope (NE) and NE-associated components as critical new contributors. Classically, the NE was thought to merely represent a barrier mediating selective exchange between the cytoplasm and nucleoplasm. However, research over the past two decades has highlighted more sophisticated and diverse roles for NE components in progenitor fate choice and migration of their progeny by tuning gene expression via interactions with chromatin, transcription factors and epigenetic factors. Defects in NE components lead to neurodevelopmental impairments, whereas age-related changes in NE components are proposed to influence neurodegenerative diseases. Thus, understanding the roles of NE components in brain development, maintenance and aging is likely to reveal new pathophysiological mechanisms for intervention. Here, we review recent findings for the previously underrepresented contribution of the NE in neuronal commitment and migration, and envision future avenues for investigation.
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28
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Zheng M, Jin G, Zhou Z. Post-Translational Modification of Lamins: Mechanisms and Functions. Front Cell Dev Biol 2022; 10:864191. [PMID: 35656549 PMCID: PMC9152177 DOI: 10.3389/fcell.2022.864191] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/17/2022] [Indexed: 12/22/2022] Open
Abstract
Lamins are the ancient type V intermediate filament proteins contributing to diverse biological functions, such as the maintenance of nuclear morphology, stabilization of chromatin architecture, regulation of cell cycle progression, regulation of spatial-temporal gene expressions, and transduction of mechano-signaling. Deregulation of lamins is associated with abnormal nuclear morphology and chromatin disorganization, leading to a variety of diseases such as laminopathy and premature aging, and might also play a role in cancer. Accumulating evidence indicates that lamins are functionally regulated by post-translational modifications (PTMs) including farnesylation, phosphorylation, acetylation, SUMOylation, methylation, ubiquitination, and O-GlcNAcylation that affect protein stabilization and the association with chromatin or associated proteins. The mechanisms by which these PTMs are modified and the relevant functionality become increasingly appreciated as understanding of these changes provides new insights into the molecular mechanisms underlying the laminopathies concerned and novel strategies for the management. In this review, we discussed a range of lamin PTMs and their roles in both physiological and pathological processes, as well as potential therapeutic strategies by targeting lamin PTMs.
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Affiliation(s)
- Mingyue Zheng
- Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Guoxiang Jin
- Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhongjun Zhou
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
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29
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Zhang L, Wang L, Hu X, Hou M, Xiao Y, Xiang J, Xie J, Chen Z, Yang T, Nie Q, Fu J, Wang Y, Zheng S, Liu Y, Gan Y, Gao Q, Bai Y, Wang J, Qi R, Zou M, Ke Q, Zhu X, Gong L, Liu Y, Li DW. MYPT1/PP1-Mediated EZH2 Dephosphorylation at S21 Promotes Epithelial-Mesenchymal Transition in Fibrosis through Control of Multiple Families of Genes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105539. [PMID: 35293697 PMCID: PMC9108659 DOI: 10.1002/advs.202105539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/24/2022] [Indexed: 05/25/2023]
Abstract
The methyltransferase EZH2 plays an important role in regulating chromatin conformation and gene transcription. Phosphorylation of EZH2 at S21 by AKT kinase suppresses its function. However, protein phosphatases responsible for the dephosphorylation of EZH2-S21 remain elusive. Here, it is demonstrated that EZH2 is highly expressed in the ocular lens, and AKT-EZH2 axis is important in TGFβ-induced epithelial-mesenchymal transition (EMT). More importantly, it is identified that MYPT1/PP1 dephosphorylates EZH2-S21 and thus modulates its functions. MYPT1 knockout accelerates EMT, but expression of the EZH2-S21A mutant suppresses EMT through control of multiple families of genes. Furthermore, the phosphorylation status and gene expression modulation of EZH2 are implicated in control of anterior subcapsular cataracts (ASC) in human and mouse eyes. Together, the results identify the specific phosphatase for EZH2-S21 and reveal EZH2 dephosphorylation control of several families of genes implicated in lens EMT and ASC pathogenesis. These results provide important novel information in EZH2 function and regulation.
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Affiliation(s)
- Lan Zhang
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Ling Wang
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Xue‐Bin Hu
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Min Hou
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Yuan Xiao
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Jia‐Wen Xiang
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Jie Xie
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Zhi‐Gang Chen
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Tian‐Heng Yang
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Qian Nie
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Jia‐Ling Fu
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Yan Wang
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Shu‐Yu Zheng
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Yun‐Fei Liu
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Yu‐Wen Gan
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Qian Gao
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Yue‐Yue Bai
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Jing‐Miao Wang
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Rui‐Li Qi
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Ming Zou
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Qin Ke
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Xing‐Fei Zhu
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Lili Gong
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - Yizhi Liu
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
| | - David Wan‐Cheng Li
- The State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen University#54 Xianlie South RoadGuangzhouGuangdong510060China
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30
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Zervopoulos SD, Boukouris AE, Saleme B, Haromy A, Tejay S, Sutendra G, Michelakis ED. MFN2-driven mitochondria-to-nucleus tethering allows a non-canonical nuclear entry pathway of the mitochondrial pyruvate dehydrogenase complex. Mol Cell 2022; 82:1066-1077.e7. [PMID: 35245450 DOI: 10.1016/j.molcel.2022.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/15/2021] [Accepted: 02/01/2022] [Indexed: 12/21/2022]
Abstract
The mitochondrial pyruvate dehydrogenase complex (PDC) translocates into the nucleus, facilitating histone acetylation by producing acetyl-CoA. We describe a noncanonical pathway for nuclear PDC (nPDC) import that does not involve nuclear pore complexes (NPCs). Mitochondria cluster around the nucleus in response to proliferative stimuli and tether onto the nuclear envelope (NE) via mitofusin-2 (MFN2)-enriched contact points. A decrease in nuclear MFN2 levels decreases mitochondria tethering and nPDC levels. Mitochondrial PDC crosses the NE and interacts with lamin A, forming a ring below the NE before crossing through the lamin layer into the nucleoplasm, in areas away from NPCs. Effective blockage of NPC trafficking does not decrease nPDC levels. The PDC-lamin interaction is maintained during cell division, when lamin depolymerizes and disassembles before reforming daughter nuclear envelopes, providing another pathway for nPDC entry during mitosis. Our work provides a different angle to understanding mitochondria-to-nucleus communication and nuclear metabolism.
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Affiliation(s)
| | | | - Bruno Saleme
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Alois Haromy
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Saymon Tejay
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Gopinath Sutendra
- Department of Medicine, University of Alberta, Edmonton, AB, Canada.
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31
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Mammel AE, Hatch EM. Genome instability from nuclear catastrophe and DNA damage. Semin Cell Dev Biol 2022; 123:131-139. [PMID: 33839019 PMCID: PMC8494860 DOI: 10.1016/j.semcdb.2021.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/29/2021] [Indexed: 11/28/2022]
Abstract
The nuclear envelope compartmentalizes the eukaryotic genome, provides mechanical resistance, and regulates access to the chromatin. However, recent studies have identified several conditions where the nuclear membrane ruptures during interphase, breaking down this compartmentalization leading to DNA damage, chromothripsis, and kataegis. This review discusses three major circumstances that promote nuclear membrane rupture, nuclear deformation, chromatin bridges, and micronucleation, and how each of these nuclear catastrophes results in DNA damage. In addition, we highlight recent studies that demonstrate a single chromosome missegregation can initiate a cascade of events that lead to accumulating damage and even multiple rounds of chromothripsis.
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Affiliation(s)
- Anna E. Mammel
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Emily M. Hatch
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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32
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Chen YJC, Koutelou E, Dent SY. Now open: Evolving insights to the roles of lysine acetylation in chromatin organization and function. Mol Cell 2022; 82:716-727. [PMID: 35016034 PMCID: PMC8857060 DOI: 10.1016/j.molcel.2021.12.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
Protein acetylation is conserved across phylogeny and has been recognized as one of the most prominent post-translational modifications since its discovery nearly 60 years ago. Histone acetylation is an active mark characteristic of open chromatin, but acetylation on specific lysine residues and histone variants occurs in different biological contexts and can confer various outcomes. The significance of acetylation events is indicated by the associations of lysine acetyltransferases, deacetylases, and acetyl-lysine readers with developmental disorders and pathologies. Recent advances have uncovered new roles of acetylation regulators in chromatin-centric events, which emphasize the complexity of these functional networks. In this review, we discuss mechanisms and dynamics of acetylation in chromatin organization and DNA-templated processes, including gene transcription and DNA repair and replication.
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Affiliation(s)
- Ying-Jiun C. Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sharon Y.R. Dent
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Correspondence:
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33
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Varga JK, Diffley K, Welker Leng KR, Fierke CA, Schueler-Furman O. Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates. Sci Rep 2022; 12:1788. [PMID: 35110592 PMCID: PMC8810773 DOI: 10.1038/s41598-022-05681-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/17/2022] [Indexed: 01/25/2023] Open
Abstract
Histone deacetylases play important biological roles well beyond the deacetylation of histone tails. In particular, HDAC6 is involved in multiple cellular processes such as apoptosis, cytoskeleton reorganization, and protein folding, affecting substrates such as ɑ-tubulin, Hsp90 and cortactin proteins. We have applied a biochemical enzymatic assay to measure the activity of HDAC6 on a set of candidate unlabeled peptides. These served for the calibration of a structure-based substrate prediction protocol, Rosetta FlexPepBind, previously used for the successful substrate prediction of HDAC8 and other enzymes. A proteome-wide screen of reported acetylation sites using our calibrated protocol together with the enzymatic assay provide new peptide substrates and avenues to novel potential functional regulatory roles of this promiscuous, multi-faceted enzyme. In particular, we propose novel regulatory roles of HDAC6 in tumorigenesis and cancer cell survival via the regulation of EGFR/Akt pathway activation. The calibration process and comparison of the results between HDAC6 and HDAC8 highlight structural differences that explain the established promiscuity of HDAC6.
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Affiliation(s)
- Julia K Varga
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University of Jerusalem, Faculty of Medicine, POB 12272, 9112102, Jerusalem, Israel
| | - Kelsey Diffley
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - Katherine R Welker Leng
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - Carol A Fierke
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University of Jerusalem, Faculty of Medicine, POB 12272, 9112102, Jerusalem, Israel.
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34
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Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 292] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
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Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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35
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Chi YH, Wang WP, Hung MC, Liou GG, Wang JY, Chao PHG. Deformation of the nucleus by TGFβ1 via the remodeling of nuclear envelope and histone isoforms. Epigenetics Chromatin 2022; 15:1. [PMID: 34983624 PMCID: PMC8725468 DOI: 10.1186/s13072-021-00434-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022] Open
Abstract
The cause of nuclear shape abnormalities which are often seen in pre-neoplastic and malignant tissues is not clear. In this study we report that deformation of the nucleus can be induced by TGFβ1 stimulation in several cell lines including Huh7. In our results, the upregulated histone H3.3 expression downstream of SMAD signaling contributed to TGFβ1-induced nuclear deformation, a process of which requires incorporation of the nuclear envelope (NE) proteins lamin B1 and SUN1. During this process, the NE constitutively ruptured and reformed. Contrast to lamin B1 which was relatively stationary around the nucleus, the upregulated lamin A was highly mobile, clustering at the nuclear periphery and reintegrating into the nucleoplasm. The chromatin regions that lost NE coverage formed a supra-nucleosomal structure characterized by elevated histone H3K27me3 and histone H1, the formation of which depended on the presence of lamin A. These results provide evidence that shape of the nucleus can be modulated through TGFβ1-induced compositional changes in the chromatin and nuclear lamina.
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Affiliation(s)
- Ya-Hui Chi
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan. .,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan.
| | - Wan-Ping Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan
| | - Ming-Chun Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan
| | - Gunn-Guang Liou
- National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Jing-Ya Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan
| | - Pen-Hsiu Grace Chao
- Department of Biomedical Engineering, School of Medicine and School of Engineering, National Taiwan University, Taipei, 10617, Taiwan
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36
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Shellard A, Mayor R. Collective durotaxis along a self-generated stiffness gradient in vivo. Nature 2021; 600:690-694. [PMID: 34880503 DOI: 10.1038/s41586-021-04210-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/02/2021] [Indexed: 02/07/2023]
Abstract
Collective cell migration underlies morphogenesis, wound healing and cancer invasion1,2. Most directed migration in vivo has been attributed to chemotaxis, whereby cells follow a chemical gradient3-5. Cells can also follow a stiffness gradient in vitro, a process called durotaxis3,4,6-8, but evidence for durotaxis in vivo is lacking6. Here we show that in Xenopus laevis the neural crest-an embryonic cell population-self-generates a stiffness gradient in the adjacent placodal tissue, and follows this gradient by durotaxis. The gradient moves with the neural crest, which is continually pursuing a retreating region of high substrate stiffness. Mechanistically, the neural crest induces the gradient due to N-cadherin interactions with the placodes and senses the gradient through cell-matrix adhesions, resulting in polarized Rac activity and actomyosin contractility, which coordinates durotaxis. Durotaxis synergizes with chemotaxis, cooperatively polarizing actomyosin machinery of the cell group to prompt efficient directional collective cell migration in vivo. These results show that durotaxis and dynamic stiffness gradients exist in vivo, and gradients of chemical and mechanical signals cooperate to achieve efficient directional cell migration.
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Affiliation(s)
- Adam Shellard
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Roberto Mayor
- Department of Cell and Developmental Biology, University College London, London, UK.
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37
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Popova LV, Nagarajan P, Lovejoy CM, Sunkel B, Gardner M, Wang M, Freitas M, Stanton B, Parthun M. Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones. Nucleic Acids Res 2021; 49:12136-12151. [PMID: 34788845 PMCID: PMC8643632 DOI: 10.1093/nar/gkab1044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/20/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
A central component of the epigenome is the pattern of histone post-translational modifications that play a critical role in the formation of specific chromatin states. Following DNA replication, nascent chromatin is a 1:1 mixture of parental and newly synthesized histones and the transfer of modification patterns from parental histones to new histones is a fundamental step in epigenetic inheritance. Here we report that loss of HAT1, which acetylates lysines 5 and 12 of newly synthesized histone H4 during replication-coupled chromatin assembly, results in the loss of accessibility of large domains of heterochromatin, termed HAT1-dependent Accessibility Domains (HADs). HADs are mega base-scale domains that comprise ∼10% of the mouse genome. HAT1 globally represses H3 K9 me3 levels and HADs correspond to the regions of the genome that display HAT1-dependent increases in H3 K9me3 peak density. HADs display a high degree of overlap with a subset of Lamin-Associated Domains (LADs). HAT1 is required to maintain nuclear structure and integrity. These results indicate that HAT1 and the acetylation of newly synthesized histones may be critical regulators of the epigenetic inheritance of heterochromatin and suggest a new mechanism for the epigenetic regulation of nuclear lamina-heterochromatin interactions.
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Affiliation(s)
- Liudmila V Popova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Prabakaran Nagarajan
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Callie M Lovejoy
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin D Sunkel
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Miranda L Gardner
- Campus Chemical Instrument Center, Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH 43210, USA
| | - Meng Wang
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Z Stanton
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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38
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Zhou Z, Zhang X, Lei X, Xiao X, Jiao T, Ma R, Dong X, Jiang Q, Wang W, Shi Y, Zheng T, Rao J, Xiang Z, Ren L, Deng T, Jiang Z, Dou Z, Wei W, Wang J. Sensing of cytoplasmic chromatin by cGAS activates innate immune response in SARS-CoV-2 infection. Signal Transduct Target Ther 2021; 6:382. [PMID: 34732709 PMCID: PMC8564796 DOI: 10.1038/s41392-021-00800-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 01/07/2023] Open
Abstract
The global coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive-sense RNA virus. How the host immune system senses and responds to SARS-CoV-2 infection remain largely unresolved. Here, we report that SARS-CoV-2 infection activates the innate immune response through the cytosolic DNA sensing cGAS-STING pathway. SARS-CoV-2 infection induces the cellular level of 2′3′-cGAMP associated with STING activation. cGAS recognizes chromatin DNA shuttled from the nucleus as a result of cell-to-cell fusion upon SARS-CoV-2 infection. We further demonstrate that the expression of spike protein from SARS-CoV-2 and ACE2 from host cells is sufficient to trigger cytoplasmic chromatin upon cell fusion. Furthermore, cytoplasmic chromatin-cGAS-STING pathway, but not MAVS-mediated viral RNA sensing pathway, contributes to interferon and pro-inflammatory gene expression upon cell fusion. Finally, we show that cGAS is required for host antiviral responses against SARS-CoV-2, and a STING-activating compound potently inhibits viral replication. Together, our study reported a previously unappreciated mechanism by which the host innate immune system responds to SARS-CoV-2 infection, mediated by cytoplasmic chromatin from the infected cells. Targeting the cytoplasmic chromatin-cGAS-STING pathway may offer novel therapeutic opportunities in treating COVID-19. In addition, these findings extend our knowledge in host defense against viral infection by showing that host cells’ self-nucleic acids can be employed as a “danger signal” to alarm the immune system.
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Affiliation(s)
- Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
| | - Xinyi Zhang
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiaobo Lei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China.,Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Xia Xiao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Tao Jiao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Ruiyi Ma
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Xiaojing Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Qi Jiang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Wenjing Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Yujin Shi
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Tian Zheng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Jian Rao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Zichun Xiang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China.,Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China.,Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China
| | - Tao Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhengfan Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Pseking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Zhixun Dou
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China. .,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China. .,Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, P.R. China.
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39
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Pessoa Rodrigues C, Chatterjee A, Wiese M, Stehle T, Szymanski W, Shvedunova M, Akhtar A. Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice. Nat Commun 2021; 12:6212. [PMID: 34707105 PMCID: PMC8551339 DOI: 10.1038/s41467-021-26277-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 09/21/2021] [Indexed: 12/26/2022] Open
Abstract
Noncommunicable diseases (NCDs) account for over 70% of deaths world-wide. Previous work has linked NCDs such as type 2 diabetes (T2D) to disruption of chromatin regulators. However, the exact molecular origins of these chronic conditions remain elusive. Here, we identify the H4 lysine 16 acetyltransferase MOF as a critical regulator of central carbon metabolism. High-throughput metabolomics unveil a systemic amino acid and carbohydrate imbalance in Mof deficient mice, manifesting in T2D predisposition. Oral glucose tolerance testing (OGTT) reveals defects in glucose assimilation and insulin secretion in these animals. Furthermore, Mof deficient mice are resistant to diet-induced fat gain due to defects in glucose uptake in adipose tissue. MOF-mediated H4K16ac deposition controls expression of the master regulator of glucose metabolism, Pparg and the entire downstream transcriptional network. Glucose uptake and lipid storage can be reconstituted in MOF-depleted adipocytes in vitro by ectopic Glut4 expression, PPARγ agonist thiazolidinedione (TZD) treatment or SIRT1 inhibition. Hence, chronic imbalance in H4K16ac promotes a destabilisation of metabolism triggering the development of a metabolic disorder, and its maintenance provides an unprecedented regulatory epigenetic mechanism controlling diet-induced obesity.
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Affiliation(s)
- Cecilia Pessoa Rodrigues
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Aindrila Chatterjee
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Meike Wiese
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Thomas Stehle
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Witold Szymanski
- Proteomics Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany.
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany.
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40
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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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41
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Zhang W, Tan X, Lin S, Gou Y, Han C, Zhang C, Ning W, Wang C, Xue Y. CPLM 4.0: an updated database with rich annotations for protein lysine modifications. Nucleic Acids Res 2021; 50:D451-D459. [PMID: 34581824 PMCID: PMC8728254 DOI: 10.1093/nar/gkab849] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/31/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Here, we reported the compendium of protein lysine modifications (CPLM 4.0, http://cplm.biocuckoo.cn/), a data resource for various post-translational modifications (PTMs) specifically occurred at the side-chain amino group of lysine residues in proteins. From the literature and public databases, we collected 450 378 protein lysine modification (PLM) events, and combined them with the existing data of our previously developed protein lysine modification database (PLMD 3.0). In total, CPLM 4.0 contained 592 606 experimentally identified modification events on 463 156 unique lysine residues of 105 673 proteins for up to 29 types of PLMs across 219 species. Furthermore, we carefully annotated the data using the knowledge from 102 additional resources that covered 13 aspects, including variation and mutation, disease-associated information, protein-protein interaction, protein functional annotation, DNA & RNA element, protein structure, chemical-target relation, mRNA expression, protein expression/proteomics, subcellular localization, biological pathway annotation, functional domain annotation, and physicochemical property. Compared to PLMD 3.0 and other existing resources, CPLM 4.0 achieved a >2-fold increase in collection of PLM events, with a data volume of ∼45GB. We anticipate that CPLM 4.0 can serve as a more useful database for further study of PLMs.
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Affiliation(s)
- Weizhi Zhang
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaodan Tan
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaofeng Lin
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yujie Gou
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Cheng Han
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chi Zhang
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wanshan Ning
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chenwei Wang
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu 210031, China
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42
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Mejia-Ramirez E, Geiger H, Florian MC. Loss of epigenetic polarity is a hallmark of hematopoietic stem cell aging. Hum Mol Genet 2021; 29:R248-R254. [PMID: 32821941 DOI: 10.1093/hmg/ddaa189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023] Open
Abstract
Changes of polarity in somatic stem cells upon aging or disease lead to a functional deterioration of stem cells and consequently loss of tissue homeostasis, likely due to changes in the mode (symmetry versus asymmetry) of stem cell divisions. Changes in polarity of epigenetic markers (or 'epi-polarity') in stem cells, which are linked to alterations in chromatin architecture, might explain how a decline in the frequency of epipolar stem cells can have a long-lasting impact on the function of especially aging stem cells. The drift in epipolarity might represent a novel therapeutic target to improve stem cell function upon aging or disease. Here we review basic biological principles of epigenetic polarity, with a special focus on epipolarity and aging of hematopoietic stem cells.
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Affiliation(s)
- Eva Mejia-Ramirez
- Program of Regenerative Medicine, IDIBELL and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), Av. Granvia 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Hartmut Geiger
- Institute of Molecular Medicine, University of Ulm, James-Franck-Ring 11c, 89081, Ulm, Germany
| | - M Carolina Florian
- Program of Regenerative Medicine, IDIBELL and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), Av. Granvia 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain.,Institute of Molecular Medicine, University of Ulm, James-Franck-Ring 11c, 89081, Ulm, Germany
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43
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Chu CT, Chen YH, Chiu WT, Chen HC. Tyrosine phosphorylation of lamin A by Src promotes disassembly of nuclear lamina in interphase. Life Sci Alliance 2021; 4:4/10/e202101120. [PMID: 34385357 PMCID: PMC8362257 DOI: 10.26508/lsa.202101120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022] Open
Abstract
Lamins form the nuclear lamina, which is important for nuclear structure and activity. Although posttranslational modifications, in particular serine phosphorylation, have been shown to be important for structural properties and functions of lamins, little is known about the role of tyrosine phosphorylation in this regard. In this study, we found that the constitutively active Src Y527F mutant caused the disassembly of lamin A/C. We demonstrate that Src directly phosphorylates lamin A mainly at Tyr45 both in vitro and in intact cells. The phosphomimetic Y45D mutant was diffusively distributed in the nucleoplasm and failed to assemble into the nuclear lamina. Depletion of lamin A/C in HeLa cells induced nuclear dysmorphia and genomic instability as well as increased nuclear plasticity for cell migration, all of which were partially restored by re-expression of lamin A, but further promoted by the Y45D mutant. Together, our results reveal a novel mechanism for regulating the assembly of nuclear lamina through Src and suggest that aberrant phosphorylation of lamin A by Src may contribute to nuclear dysmorphia, genomic instability, and nuclear plasticity.
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Affiliation(s)
- Ching-Tung Chu
- Institue of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Hsuan Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Hong-Chen Chen
- Institue of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan .,Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institue of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
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44
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Creamer KM, Kolpa HJ, Lawrence JB. Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction. Mol Cell 2021; 81:3509-3525.e5. [PMID: 34320406 DOI: 10.1016/j.molcel.2021.07.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 12/17/2022]
Abstract
Nuclear chromosomes transcribe far more RNA than required to encode protein. Here we investigate whether non-coding RNA broadly contributes to cytological-scale chromosome territory architecture. We develop a procedure that depletes soluble proteins, chromatin, and most nuclear RNA from the nucleus but does not delocalize XIST, a known architectural RNA, from an insoluble chromosome "scaffold." RNA-seq analysis reveals that most RNA in the nuclear scaffold is repeat-rich, non-coding, and derived predominantly from introns of nascent transcripts. Insoluble, repeat-rich (C0T-1) RNA co-distributes with known scaffold proteins including scaffold attachment factor A (SAF-A), and distribution of these components inversely correlates with chromatin compaction in normal and experimentally manipulated nuclei. We further show that RNA is required for SAF-A to interact with chromatin and for enrichment of structurally embedded "scaffold attachment regions" prevalent in euchromatin. Collectively, the results indicate that long nascent transcripts contribute a dynamic structural role that promotes the open architecture of active chromosome territories.
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Affiliation(s)
- Kevin Michael Creamer
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Heather Jill Kolpa
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jeanne Bentley Lawrence
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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45
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Murray-Nerger LA, Cristea IM. Lamin post-translational modifications: emerging toggles of nuclear organization and function. Trends Biochem Sci 2021; 46:832-847. [PMID: 34148760 DOI: 10.1016/j.tibs.2021.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/03/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023]
Abstract
Nuclear lamins are ancient type V intermediate filaments with diverse functions that include maintaining nuclear shape, mechanosignaling, tethering and stabilizing chromatin, regulating gene expression, and contributing to cell cycle progression. Despite these numerous roles, an outstanding question has been how lamins are regulated. Accumulating work indicates that a range of lamin post-translational modifications (PTMs) control their functions both in homeostatic cells and in disease states such as progeria, muscular dystrophy, and viral infection. Here, we review the current knowledge of the diverse types of PTMs that regulate lamins in a site-specific manner. We highlight methods that can be used to characterize lamin PTMs whose functions are currently unknown and provide a perspective on the future of the lamin PTM field.
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Affiliation(s)
- Laura A Murray-Nerger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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46
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Chang R, Xiao X, Fu Y, Zhang C, Zhu X, Gao Y. ITGB1-DT Facilitates Lung Adenocarcinoma Progression via Forming a Positive Feedback Loop With ITGB1/Wnt/β-Catenin/MYC. Front Cell Dev Biol 2021; 9:631259. [PMID: 33763420 PMCID: PMC7982827 DOI: 10.3389/fcell.2021.631259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/22/2021] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the main histological type of lung cancer, which is the leading cause of cancer-related deaths. Long non-coding RNAs (lncRNAs) were recently revealed to be involved in various cancers. However, the clinical relevance and potential biological roles of most lncRNAs in LUAD remain unclear. Here, we identified a prognosis-related lncRNA ITGB1-DT in LUAD. ITGB1-DT was upregulated in LUAD and high expression of ITGB1-DT was correlated with advanced clinical stages and poor overall survival and disease-free survival. Enhanced expression of ITGB1-DT facilitated LUAD cellular proliferation, migration, and invasion, and also lung metastasis in vivo. Knockdown of ITGB1-DT repressed LUAD cellular proliferation, migration, and invasion. ITGB1-DT interacted with EZH2, repressed the binding of EZH2 to ITGB1 promoter, reduced H3K27me3 levels at ITGB1 promoter region, and therefore activated ITGB1 expression. Through upregulating ITGB1, ITGB1-DT activated Wnt/β-catenin pathway and its downstream target MYC in LUAD. The expressions of ITGB1-DT, ITGB1, and MYC were positively correlated with each other in LUAD tissues. Intriguingly, ITGB1-DT was found as a transcriptional target of MYC. MYC directly transcriptionally activated ITGB1-DT expression. Thus, ITGB1-DT formed a positive feedback loop with ITGB1/Wnt/β-catenin/MYC. The oncogenic roles of ITGB1-DT were reversed by depletion of ITGB1 or inhibition of Wnt/β-catenin pathway. In summary, these findings revealed ITGB1-DT as a prognosis-related and oncogenic lncRNA in LUAD via activating the ITGB1-DT/ITGB1/Wnt/β-catenin/MYC positive feedback loop. These results implicated ITGB1-DT as a potential prognostic biomarker and therapeutic target for LUAD.
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Affiliation(s)
- Ruimin Chang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, China
| | - Xiaoxiong Xiao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Yao Fu
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Xiaoyan Zhu
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Yang Gao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
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47
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Complex-dependent histone acetyltransferase activity of KAT8 determines its role in transcription and cellular homeostasis. Mol Cell 2021; 81:1749-1765.e8. [PMID: 33657400 DOI: 10.1016/j.molcel.2021.02.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 12/20/2022]
Abstract
Acetylation of lysine 16 on histone H4 (H4K16ac) is catalyzed by histone acetyltransferase KAT8 and can prevent chromatin compaction in vitro. Although extensively studied in Drosophila, the functions of H4K16ac and two KAT8-containing protein complexes (NSL and MSL) are not well understood in mammals. Here, we demonstrate a surprising complex-dependent activity of KAT8: it catalyzes H4K5ac and H4K8ac as part of the NSL complex, whereas it catalyzes the bulk of H4K16ac as part of the MSL complex. Furthermore, we show that MSL complex proteins and H4K16ac are not required for cell proliferation and chromatin accessibility, whereas the NSL complex is essential for cell survival, as it stimulates transcription initiation at the promoters of housekeeping genes. In summary, we show that KAT8 switches catalytic activity and function depending on its associated proteins and that, when in the NSL complex, it catalyzes H4K5ac and H4K8ac required for the expression of essential genes.
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48
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Murray-Nerger LA, Justice JL, Rekapalli P, Hutton JE, Cristea I. Lamin B1 acetylation slows the G1 to S cell cycle transition through inhibition of DNA repair. Nucleic Acids Res 2021; 49:2044-2064. [PMID: 33533922 PMCID: PMC7913768 DOI: 10.1093/nar/gkab019] [Citation(s) in RCA: 15] [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: 07/03/2020] [Revised: 01/05/2021] [Accepted: 01/13/2021] [Indexed: 12/21/2022] Open
Abstract
The integrity and regulation of the nuclear lamina is essential for nuclear organization and chromatin stability, with its dysregulation being linked to laminopathy diseases and cancer. Although numerous posttranslational modifications have been identified on lamins, few have been ascribed a regulatory function. Here, we establish that lamin B1 (LMNB1) acetylation at K134 is a molecular toggle that controls nuclear periphery stability, cell cycle progression, and DNA repair. LMNB1 acetylation prevents lamina disruption during herpesvirus type 1 (HSV-1) infection, thereby inhibiting virus production. We also demonstrate the broad impact of this site on laminar processes in uninfected cells. LMNB1 acetylation negatively regulates canonical nonhomologous end joining by impairing the recruitment of 53BP1 to damaged DNA. This defect causes a delay in DNA damage resolution and a persistent activation of the G1/S checkpoint. Altogether, we reveal LMNB1 acetylation as a mechanism for controlling DNA repair pathway choice and stabilizing the nuclear periphery.
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Affiliation(s)
- Laura A Murray-Nerger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Pranav Rekapalli
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Josiah E Hutton
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
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49
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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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50
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Marrese M, Paardekam EJ, Iannuzzi D. Indentation probe with optical fibre array-based optical coherence tomography for material deformation. J Microsc 2020; 282:205-214. [PMID: 33314150 PMCID: PMC8248032 DOI: 10.1111/jmi.12994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a new optomechanical probe for mechanical testing of soft matter. The probe consists of a micromachined cantilever equipped with an indenting sphere, and an array of 16 single‐mode optical fibres, which are connected to an optical coherence tomography (OCT) system that allows subsurface analysis of the sample during the indentation stroke. To test our device and its capability, we performed indentation on a PDMS‐based phantom. Our findings demonstrate that Common Path (CP)‐OCT via lensed optical fibres can be successfully combined with a microindentation sensor to visualise the phantom's deformation profile at different indentation depths and locations in real time. Lay Description This work presents a new approach to simultaneously perform micro‐indentation experiments and OCT imaging. An optical fiber array‐based sensor is used to develop a new hybrid tool where micro‐indentation is combined with optical coherence tomography. The sensor is therefore capable of compressing a sample with a small force and simultaneously collecting OCT depth profiles underneath and around the indentation point. This method offers the opportunity to characterize the mechanical properties of soft materials and simultaneously visualize their deformation profile. The ability to integrate OCT imaging with indentation technology is promising for the non‐invasive and precise characterization of different soft materials.
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Affiliation(s)
- Marica Marrese
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, The Netherlands
| | - E J Paardekam
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, The Netherlands
| | - Davide Iannuzzi
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, The Netherlands
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