1
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Dansu DK, Selcen I, Sauma S, Prentice E, Huang D, Li M, Moyon S, Casaccia P. Histone H4 acetylation differentially modulates proliferation in adult oligodendrocyte progenitors. J Cell Biol 2024; 223:e202308064. [PMID: 39133301 DOI: 10.1083/jcb.202308064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 06/18/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024] Open
Abstract
Adult oligodendrocyte progenitors (aOPCs) generate myelinating oligodendrocytes like neonatal progenitors (nOPCs), and they also display unique functional features. Here, using unbiased histone proteomics analysis and ChIP sequencing analysis of PDGFRα+ OPCs sorted from neonatal and adult Pdgfra-H2B-EGFP reporter mice, we identify the activating H4K8ac histone mark as enriched in the aOPCs. We detect increased occupancy of the H4K8ac activating mark at chromatin locations corresponding to genes related to the progenitor state (e.g., Hes5, Gpr17), metabolic processes (e.g., Txnip, Ptdgs), and myelin components (e.g., Cnp, Mog). aOPCs showed higher levels of transcripts related to lipid metabolism and myelin, and lower levels of transcripts related to cell cycle and proliferation compared with nOPCs. In addition, pharmacological inhibition of histone acetylation decreased the expression of the H4K8ac target genes in aOPCs and decreased their proliferation. Overall, this study identifies acetylation of the histone H4K8 as a regulator of the proliferative capacity of aOPCs.
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Affiliation(s)
- David K Dansu
- Neuroscience Initiative, Advanced Science Research Center at the City University of New York, New York, NY, USA
- Graduate Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY, USA
| | - Ipek Selcen
- Neuroscience Initiative, Advanced Science Research Center at the City University of New York, New York, NY, USA
- Graduate Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY, USA
| | - Sami Sauma
- Neuroscience Initiative, Advanced Science Research Center at the City University of New York, New York, NY, USA
- Graduate Program in Biology, The Graduate Center of The City University of New York, New York, NY, USA
| | - Emily Prentice
- Neuroscience Initiative, Advanced Science Research Center at the City University of New York, New York, NY, USA
- Graduate Program in Biology, The Graduate Center of The City University of New York, New York, NY, USA
| | - Dennis Huang
- Neuroscience Initiative, Advanced Science Research Center at the City University of New York, New York, NY, USA
- Graduate Program in Biology, The Graduate Center of The City University of New York, New York, NY, USA
| | - Meng Li
- Norris Medical Library, University of Southern California, Los Angeles, CA, USA
| | - Sarah Moyon
- Neuroscience Initiative, Advanced Science Research Center at the City University of New York, New York, NY, USA
- Institute of NeuroPhysiopathology (INP) UMR7051, Aix-Marseille University, CNRS, Marseille, France
| | - Patrizia Casaccia
- Neuroscience Initiative, Advanced Science Research Center at the City University of New York, New York, NY, USA
- Graduate Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY, USA
- Graduate Program in Biology, The Graduate Center of The City University of New York, New York, NY, USA
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2
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Sun H, Gao Y, Ma X, Deng Y, Bi L, Li L. Mechanism and application of feedback loops formed by mechanotransduction and histone modifications. Genes Dis 2024; 11:101061. [PMID: 39071110 PMCID: PMC11282412 DOI: 10.1016/j.gendis.2023.06.030] [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: 10/03/2022] [Revised: 03/24/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2024] Open
Abstract
Mechanical stimulation is the key physical factor in cell environment. Mechanotransduction acts as a fundamental regulator of cell behavior, regulating cell proliferation, differentiation, apoptosis, and exhibiting specific signature alterations during the pathological process. As research continues, the role of epigenetic science in mechanotransduction is attracting attention. However, the molecular mechanism of the synergistic effect between mechanotransduction and epigenetics in physiological and pathological processes has not been clarified. We focus on how histone modifications, as important components of epigenetics, are coordinated with multiple signaling pathways to control cell fate and disease progression. Specifically, we propose that histone modifications can form regulatory feedback loops with signaling pathways, that is, histone modifications can not only serve as downstream regulators of signaling pathways for target gene transcription but also provide feedback to regulate signaling pathways. Mechanotransduction and epigenetic changes could be potential markers and therapeutic targets in clinical practice.
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Affiliation(s)
- Han Sun
- Department of Hematology and Oncology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130021, China
| | - Yafang Gao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Xinyu Ma
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Yizhou Deng
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Lintao Bi
- Department of Hematology and Oncology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130021, China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
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3
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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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4
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Bi S, Huang L, Chen Y, Hu Z, Li S, Wang Y, Huang B, Zhang L, Huang Y, Dai B, Du L, Tu Z, Wang Y, Xu D, Xu X, Sun W, Kzhyshkowska J, Wang H, Chen D, Wang F, Zhang S. KAT8-mediated H4K16ac is essential for sustaining trophoblast self-renewal and proliferation via regulating CDX2. Nat Commun 2024; 15:5602. [PMID: 38961108 PMCID: PMC11222414 DOI: 10.1038/s41467-024-49930-6] [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: 12/04/2023] [Accepted: 06/24/2024] [Indexed: 07/05/2024] Open
Abstract
Abnormal trophoblast self-renewal and differentiation during early gestation is the major cause of miscarriage, yet the underlying regulatory mechanisms remain elusive. Here, we show that trophoblast specific deletion of Kat8, a MYST family histone acetyltransferase, leads to extraembryonic ectoderm abnormalities and embryonic lethality. Employing RNA-seq and CUT&Tag analyses on trophoblast stem cells (TSCs), we further discover that KAT8 regulates the transcriptional activation of the trophoblast stemness marker, CDX2, via acetylating H4K16. Remarkably, CDX2 overexpression partially rescues the defects arising from Kat8 knockout. Moreover, increasing H4K16ac via using deacetylase SIRT1 inhibitor, EX527, restores CDX2 levels and promoted placental development. Clinical analysis shows reduced KAT8, CDX2 and H4K16ac expression are associated with recurrent pregnancy loss (RPL). Trophoblast organoids derived from these patients exhibit impaired TSC self-renewal and growth, which are significantly ameliorated with EX527 treatment. These findings suggest the therapeutic potential of targeting the KAT8-H4K16ac-CDX2 axis for mitigating RPL, shedding light on early gestational abnormalities.
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Affiliation(s)
- Shilei Bi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Lijun Huang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yongjie Chen
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, Beijing, 100026, China
| | - Zhenhua Hu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Shanze Li
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Yifan Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Baoying Huang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Lizi Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yuanyuan Huang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Beibei Dai
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Lili Du
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zhaowei Tu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yijing Wang
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Dan Xu
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Xiaotong Xu
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Wen Sun
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Julia Kzhyshkowska
- Institute of Transfusion Medicine and Immunology, Mannheim Institute of Innate Immunosciences (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- German Red Cross Blood Service Baden-Württemberg-Hessen, 68167, Mannheim, Germany
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russia
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Dunjin Chen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
| | - Shuang Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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5
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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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Aguado-Alvaro LP, Garitano N, Pelacho B. Fibroblast Diversity and Epigenetic Regulation in Cardiac Fibrosis. Int J Mol Sci 2024; 25:6004. [PMID: 38892192 PMCID: PMC11172550 DOI: 10.3390/ijms25116004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Cardiac fibrosis, a process characterized by excessive extracellular matrix (ECM) deposition, is a common pathological consequence of many cardiovascular diseases (CVDs) normally resulting in organ failure and death. Cardiac fibroblasts (CFs) play an essential role in deleterious cardiac remodeling and dysfunction. In response to injury, quiescent CFs become activated and adopt a collagen-secreting phenotype highly contributing to cardiac fibrosis. In recent years, studies have been focused on the exploration of molecular and cellular mechanisms implicated in the activation process of CFs, which allow the development of novel therapeutic approaches for the treatment of cardiac fibrosis. Transcriptomic analyses using single-cell RNA sequencing (RNA-seq) have helped to elucidate the high cellular diversity and complex intercellular communication networks that CFs establish in the mammalian heart. Furthermore, a significant body of work supports the critical role of epigenetic regulation on the expression of genes involved in the pathogenesis of cardiac fibrosis. The study of epigenetic mechanisms, including DNA methylation, histone modification, and chromatin remodeling, has provided more insights into CF activation and fibrotic processes. Targeting epigenetic regulators, especially DNA methyltransferases (DNMT), histone acetylases (HAT), or histone deacetylases (HDAC), has emerged as a promising approach for the development of novel anti-fibrotic therapies. This review focuses on recent transcriptomic advances regarding CF diversity and molecular and epigenetic mechanisms that modulate the activation process of CFs and their possible clinical applications for the treatment of cardiac fibrosis.
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Affiliation(s)
- Laura Pilar Aguado-Alvaro
- Department of Biochemistry and Genetics, University of Navarra, 31008 Pamplona, Spain; (L.P.A.-A.); (N.G.)
- Program of Cardiovascular Disease, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Nerea Garitano
- Department of Biochemistry and Genetics, University of Navarra, 31008 Pamplona, Spain; (L.P.A.-A.); (N.G.)
- Program of Cardiovascular Disease, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Beatriz Pelacho
- Department of Biochemistry and Genetics, University of Navarra, 31008 Pamplona, Spain; (L.P.A.-A.); (N.G.)
- Program of Cardiovascular Disease, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
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7
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de Talhouët C, Esteras N, Soutar MPM, O'Callaghan B, Plun-Favreau H. KAT8 compound inhibition inhibits the initial steps of PINK1-dependant mitophagy. Sci Rep 2024; 14:11721. [PMID: 38777823 PMCID: PMC11111795 DOI: 10.1038/s41598-024-60602-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
It has recently been shown that KAT8, a genome-wide association study candidate risk gene for Parkinson's Disease, is involved in PINK1/Parkin-dependant mitophagy. The KAT8 gene encodes a lysine acetyltransferase and represents the catalytically active subunit of the non-specific lethal epigenetic remodelling complex. In the current study, we show that contrary to KAT5 inhibition, dual inhibition of KAT5 and KAT8 via the MG149 compound inhibits the initial steps of the PINK1-dependant mitophagy process. More specifically, our study shows that following mitochondrial depolarisation induced by mitochondrial toxins, MG149 treatment inhibits PINK1-dependant mitophagy initiation by impairing PINK1 activation, and subsequent phosphorylation of Parkin and ubiquitin. While this inhibitory effect of MG149 on PINK1-activation is potent, MG149 treatment in the absence of mitochondrial toxins is sufficient to depolarise the mitochondrial membrane, recruit PINK1 and promote partial downstream recruitment of the autophagy receptor p62, leading to an increase in mitochondrial delivery to the lysosomes. Altogether, our study provides additional support for KAT8 as a regulator of mitophagy and autophagy processes.
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Affiliation(s)
- Capucine de Talhouët
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Noemi Esteras
- Department of Biochemistry and Molecular Biology, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Marc P M Soutar
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Benjamin O'Callaghan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Helene Plun-Favreau
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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8
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Kiss AE, Venkatasubramani AV, Pathirana D, Krause S, Sparr A, Hasenauer J, Imhof A, Müller M, Becker P. Processivity and specificity of histone acetylation by the male-specific lethal complex. Nucleic Acids Res 2024; 52:4889-4905. [PMID: 38407474 PMCID: PMC11109948 DOI: 10.1093/nar/gkae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies had yielded inconclusive results about the selectivity of MOF to acetylate the H4 N-terminus. We used targeted mass spectrometry to examine the activity of MOF in the male-specific lethal core (4-MSL) complex on nucleosome array substrates. This complex is part of the Dosage Compensation Complex (DCC) that activates X-chromosomal genes in male Drosophila. During short reaction times, MOF acetylated H4K16 efficiently and with excellent selectivity. Upon longer incubation, the enzyme progressively acetylated lysines 12, 8 and 5, leading to a mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains substrate-bound and continues to acetylate more N-terminal H4 lysines in a processive manner. The 4-MSL complex lacks non-coding roX RNA, a critical component of the DCC. Remarkably, addition of RNA to the reaction non-specifically suppressed H4 oligo-acetylation in favor of specific H4K16 acetylation. Because RNA destabilizes the MSL-nucleosome interaction in vitro we speculate that RNA accelerates enzyme-substrate turn-over in vivo, thus limiting the processivity of MOF, thereby increasing specific H4K16 acetylation.
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Affiliation(s)
- Anna E Kiss
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Anuroop V Venkatasubramani
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Dilan Pathirana
- Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Silke Krause
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Aline Campos Sparr
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Jan Hasenauer
- Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Axel Imhof
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Marisa Müller
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
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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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Li P, Yang L, Park SY, Liu F, Li AH, Zhu Y, Sui H, Gao F, Li L, Ye L, Zou Y, Tian Z, Zhao Y, Costa M, Sun H, Zhao X. Stabilization of MOF (KAT8) by USP10 promotes esophageal squamous cell carcinoma proliferation and metastasis through epigenetic activation of ANXA2/Wnt signaling. Oncogene 2024; 43:899-917. [PMID: 38317006 DOI: 10.1038/s41388-024-02955-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
Dysregulation of MOF (also known as MYST1, KAT8), a highly conserved H4K16 acetyltransferase, plays important roles in human cancers. However, its expression and function in esophageal squamous cell carcinoma (ESCC) remain unknown. Here, we report that MOF is highly expressed in ESCC tumors and predicts a worse prognosis. Depletion of MOF in ESCC significantly impedes tumor growth and metastasis both in vitro and in vivo, whereas ectopic expression of MOF but not catalytically inactive mutant (MOF-E350Q) promotes ESCC progression, suggesting that MOF acetyltransferase activity is crucial for its oncogenic activity. Further analysis reveals that USP10, a deubiquitinase highly expressed in ESCC, binds to and deubiquitinates MOF at lysine 410, which protects it from proteosome-dependent protein degradation. MOF stabilization by USP10 promotes H4K16ac enrichment in the ANXA2 promoter to stimulate ANXA2 transcription in a JUN-dependent manner, which subsequently activates Wnt/β-Catenin signaling to facilitate ESCC progression. Our findings highlight a novel USP10/MOF/ANXA2 axis as a promising therapeutic target for ESCC.
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Affiliation(s)
- Peichao Li
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Chest Cancer, The Second Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Lingxiao Yang
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Sun Young Park
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, 10010, USA
| | - Fanrong Liu
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Alex H Li
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, 10010, USA
| | - Yilin Zhu
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huacong Sui
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Fengyuan Gao
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Lingbing Li
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Lan Ye
- Cancer Center, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yongxin Zou
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Zhongxian Tian
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Chest Cancer, The Second Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Yunpeng Zhao
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Max Costa
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, 10010, USA
| | - Hong Sun
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, 10010, USA.
| | - Xiaogang Zhao
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Chest Cancer, The Second Hospital, Shandong University, Jinan, Shandong, 250012, China.
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12
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Liu TW, Zhao YM, Jin KY, Wang JX, Zhao XF. KAT8 is upregulated and recruited to the promoter of Atg8 by FOXO to induce H4 acetylation for autophagy under 20-hydroxyecdysone regulation. J Biol Chem 2024; 300:105704. [PMID: 38309506 PMCID: PMC10904276 DOI: 10.1016/j.jbc.2024.105704] [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: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 02/05/2024] Open
Abstract
Selective gene expression in cells in physiological or pathological conditions is important for the growth and development of organisms. Acetylation of histone H4 at K16 (H4K16ac) catalyzed by histone acetyltransferase 8 (KAT8) is known to promote gene transcription; however, the regulation of KAT8 transcription and the mechanism by which KAT8 acetylates H4K16ac to promote specific gene expression are unclear. Using the lepidopteran insect Helicoverpa armigera as a model, we reveal that the transcription factor FOXO promotes KAT8 expression and recruits KAT8 to the promoter region of autophagy-related gene 8 (Atg8) to increase H4 acetylation at that location, enabling Atg8 transcription under the steroid hormone 20-hydroxyecdysone (20E) regulation. H4K16ac levels are increased in the midgut during metamorphosis, which is consistent with the expression profiles of KAT8 and ATG8. Knockdown of Kat8 using RNA interference results in delayed pupation and repression of midgut autophagy and decreases H4K16ac levels. Overexpression of KAT8-GFP promotes autophagy and increases H4K16ac levels. FOXO, KAT8, and H4K16ac colocalized at the FOXO-binding region to promote Atg8 transcription under 20E regulation. Acetylated FOXO at K180 and K183 catalyzed by KAT8 promotes gene transcription for autophagy. 20E via FOXO promotes Kat8 transcription. Knockdown or overexpression of FOXO appeared to give similar results as knockdown or overexpression of KAT8. Therefore, FOXO upregulates KAT8 expression and recruits KAT8 to the promoter region of Atg8, where the KAT8 induces H4 acetylation to promote Atg8 transcription for autophagy under 20E regulation. This study reveals the mechanism that KAT8 promotes transcription of a specific gene.
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Affiliation(s)
- Tian-Wen Liu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Yu-Meng Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Ke-Yan Jin
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China.
| | - Xiao-Fan Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China.
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13
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White J, Derheimer FA, Jensen-Pergakes K, O'Connell S, Sharma S, Spiegel N, Paul TA. Histone lysine acetyltransferase inhibitors: an emerging class of drugs for cancer therapy. Trends Pharmacol Sci 2024; 45:243-254. [PMID: 38383216 DOI: 10.1016/j.tips.2024.01.010] [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: 01/05/2024] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
Lysine acetyltransferases (KATs) are a family of epigenetic enzymes involved in the regulation of gene expression; they represent a promising class of emerging drug targets. The frequent molecular dysregulation of these enzymes, as well as their mechanistic links to biological functions that are crucial to cancer, have led to exploration around the development of small-molecule inhibitors against KATs. Despite early challenges, recent advances have led to the development of potent and selective enzymatic and bromodomain (BRD) KAT inhibitors. In this review we discuss the discovery and development of new KAT inhibitors and their application as oncology therapeutics. Additionally, new chemically induced proximity approaches are presented, offering opportunities for unique target selectivity profiles and tissue-specific targeting of KATs. Emerging clinical data for CREB binding protein (CREBBP)/EP300 BRD inhibitors and KAT6 catalytic inhibitors indicate the promise of this target class in cancer therapeutics.
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Affiliation(s)
- Jeffrey White
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA
| | | | | | - Shawn O'Connell
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA
| | - Shikhar Sharma
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA
| | - Noah Spiegel
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA
| | - Thomas A Paul
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA.
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14
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Xie B, Zhang M, Li J, Cui J, Zhang P, Liu F, Wu Y, Deng W, Ma J, Li X, Pan B, Zhang B, Zhang H, Luo A, Xu Y, Li M, Pu Y. KAT8-catalyzed lactylation promotes eEF1A2-mediated protein synthesis and colorectal carcinogenesis. Proc Natl Acad Sci U S A 2024; 121:e2314128121. [PMID: 38359291 PMCID: PMC10895275 DOI: 10.1073/pnas.2314128121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/18/2023] [Indexed: 02/17/2024] Open
Abstract
Aberrant lysine lactylation (Kla) is associated with various diseases which are caused by excessive glycolysis metabolism. However, the regulatory molecules and downstream protein targets of Kla remain largely unclear. Here, we observed a global Kla abundance profile in colorectal cancer (CRC) that negatively correlates with prognosis. Among lactylated proteins detected in CRC, lactylation of eEF1A2K408 resulted in boosted translation elongation and enhanced protein synthesis which contributed to tumorigenesis. By screening eEF1A2 interacting proteins, we identified that KAT8, a lysine acetyltransferase that acted as a pan-Kla writer, was responsible for installing Kla on many protein substrates involving in diverse biological processes. Deletion of KAT8 inhibited CRC tumor growth, especially in a high-lactic tumor microenvironment. Therefore, the KAT8-eEF1A2 Kla axis is utilized to meet increased translational requirements for oncogenic adaptation. As a lactyltransferase, KAT8 may represent a potential therapeutic target for CRC.
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Affiliation(s)
- Bingteng Xie
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing100081, China
| | - Mengdi Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Physiology, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Jie Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing10091, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing10091, China
| | - Jianxin Cui
- Department of General Surgery & Institute of General Surgery, the First Medical Center of Chinese People’s Liberation Army General Hospital, Beijing100583, China
| | - Pengju Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Physiology, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Fangming Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Physiology, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Yuxi Wu
- Department of Chemistry, University of Virginia, Charlottesville, VA22904
| | - Weiwei Deng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Physiology, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Jihong Ma
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing10091, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing10091, China
| | - Xinyu Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing10091, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing10091, China
| | - Bingchen Pan
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing100081, China
| | - Baohui Zhang
- Department of Physiology, School of Life Science, China Medical University, Shenyang110122, China
| | - Hongbing Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Physiology, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Aiqin Luo
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing100081, China
| | - Yinzhe Xu
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Center of Chinese People’s Liberation Army General Hospital, Beijing100583, China
| | - Mo Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing10091, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing10091, China
| | - Yang Pu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Physiology, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
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15
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Dansu DK, Sauma S, Huang D, Li M, Moyon S, Casaccia P. The epigenetic landscape of oligodendrocyte progenitors changes with time. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579145. [PMID: 38501119 PMCID: PMC10946295 DOI: 10.1101/2024.02.06.579145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
SUMMARY Dansu et al. identify distinct histone H4 modifications as potential mechanism underlying the functional differences between adult and neonatal progenitors. While H4K8ac favors the expression of differentiation genes, their expression is halted by H4K20me3. Adult oligodendrocyte progenitors (aOPCs) generate myelinating oligodendrocytes, like neonatal progenitors (nOPCs), but they also display unique functional features. Here, using RNA-sequencing, unbiased histone proteomics analysis and ChIP-sequencing, we define the transcripts and histone marks underlying the unique properties of aOPCs. We describe the lower proliferative capacity and higher levels of expression of oligodendrocyte specific genes in aOPCs compared to nOPCs, as well as the greater levels of H4 histone marks. We also report increased occupancy of the H4K8ac mark at chromatin locations corresponding to oligodendrocyte-specific transcription factors and lipid metabolism genes. Pharmacological inhibition of H4K8ac deposition reduces the levels of these transcripts in aOPCs, rendering their transcriptome more similar to nOPCs. The repressive H4K20me3 mark is also higher in aOPCs compared to nOPCs and pharmacological inhibition of its deposition results in increased levels of genes related to the mature oligodendrocyte state. Overall, this study identifies two histone marks which are important for the unique transcriptional and functional identity of aOPCs.
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16
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Berthias F, Bilgin N, Mecinović J, Jensen ON. Top-down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms. Proteomics 2024; 24:e2200471. [PMID: 38282202 DOI: 10.1002/pmic.202200471] [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: 07/09/2023] [Revised: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024]
Abstract
Enzymatic catalysis is one of the fundamental processes that drives the dynamic landscape of post-translational modifications (PTMs), expanding the structural and functional diversity of proteins. Here, we assessed enzyme specificity using a top-down ion mobility spectrometry (IMS) and tandem mass spectrometry (MS/MS) workflow. We successfully applied trapped IMS (TIMS) to investigate site-specific N-ε-acetylation of lysine residues of full-length histone H4 catalyzed by histone lysine acetyltransferase KAT8. We demonstrate that KAT8 exhibits a preference for N-ε-acetylation of residue K16, while also adding acetyl groups on residues K5 and K8 as the first degree of acetylation. Achieving TIMS resolving power values of up to 300, we fully separated mono-acetylated regioisomers (H4K5ac, H4K8ac, and H4K16ac). Each of these separated regioisomers produce unique MS/MS fragment ions, enabling estimation of their individual mobility distributions and the exact localization of the N-ε-acetylation sites. This study highlights the potential of top-down TIMS-MS/MS for conducting enzymatic assays at the intact protein level and, more generally, for separation and identification of intact isomeric proteoforms and precise PTM localization.
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Affiliation(s)
- Francis Berthias
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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17
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Sun D, Chang Q, Lu F. Immunomodulation in diabetic wounds healing: The intersection of macrophage reprogramming and immunotherapeutic hydrogels. J Tissue Eng 2024; 15:20417314241265202. [PMID: 39071896 PMCID: PMC11283672 DOI: 10.1177/20417314241265202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/12/2024] [Indexed: 07/30/2024] Open
Abstract
Diabetic wound healing presents a significant clinical challenge due to the interplay of systemic metabolic disturbances and local inflammation, which hinder the healing process. Macrophages undergo a phenotypic shift from M1 to M2 during wound healing, a transition pivotal for effective tissue repair. However, in diabetic wounds, the microenvironment disrupts this phenotypic polarization, perpetuating inflammation, and impeding healing. Reprograming macrophages to restore their M2 phenotype offers a potential avenue for modulating the wound immune microenvironment and promoting healing. This review elucidates the mechanisms underlying impaired macrophage polarization toward the M2 phenotype in diabetic wounds and discusses novel strategies, including epigenetic and metabolic interventions, to promote macrophage conversion to M2. Hydrogels, with their hydrated 3D cross-linked structure, closely resemble the physiological extracellular matrix and offer advantageous properties such as biocompatibility, tunability, and versatility. These characteristics make hydrogels promising candidates for developing immunomodulatory materials aimed at addressing diabetic wounds. Understanding the role of hydrogels in immunotherapy, particularly in the context of macrophage reprograming, is essential for the development of advanced wound care solutions. This review also highlights recent advancements in immunotherapeutic hydrogels as a step toward precise and effective treatments for diabetic wounds.
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Affiliation(s)
- Dan Sun
- Department of Plastic and Aesthetic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qiang Chang
- Department of Plastic and Aesthetic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Feng Lu
- Department of Plastic and Aesthetic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
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18
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An HM, Dai YF, Zhu J, Liu W, Wang XP. MYST family histone acetyltransferases regulate reproductive diapause initiation. Int J Biol Macromol 2024; 256:128269. [PMID: 38029912 DOI: 10.1016/j.ijbiomac.2023.128269] [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: 10/08/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023]
Abstract
Histone acetylation, a crucial epigenetic mechanism, has been suggested to play a role in diapause regulation, but this has not been confirmed through gene loss-of-function studies. In this work, we investigated the involvement of MYST family genes, which are key writers of histone acetylation, in initiating reproductive diapause using the cabbage beetle Colaphellus bowringi as a model. We identified C. bowringi orthologs of MYST, including Tip60, KAT6A, KAT7, and KAT8, from previous transcriptomes. Analyses of phylogenetic trees and protein domains indicated that these MYST proteins are structurally conserved across animal species. Expression of these MYST genes was found to be enriched in heads and ovaries of C. bowringi. Under reproductive photoperiod conditions, RNAi targeting MYST genes, especially KAT8, suppressed ovarian growth and yolk deposition, resembling the characteristics of diapausing ovaries. Additionally, KAT8 knockdown led to the upregulation of diapause-related genes, such as heat shock proteins and diapause protein 1, and the emergence of diapause-like guts. Moreover, KAT8 knockdown reduced the expression of a crucial enzyme involved in juvenile hormone (JH) biosynthesis, likely due to decreased H4K16ac levels. Consequently, our findings suggest that MYST family genes, specifically KAT8, influence the JH signal, thereby regulating the initiation of reproductive diapause.
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Affiliation(s)
- Hao-Min An
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Fei Dai
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Zhu
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wen Liu
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Ping Wang
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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19
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Hicks AR, Reynolds RH, O’Callaghan B, García-Ruiz S, Gil-Martínez AL, Botía J, Plun-Favreau H, Ryten M. The non-specific lethal complex regulates genes and pathways genetically linked to Parkinson's disease. Brain 2023; 146:4974-4987. [PMID: 37522749 PMCID: PMC10689904 DOI: 10.1093/brain/awad246] [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: 01/31/2023] [Revised: 05/12/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023] Open
Abstract
Genetic variants conferring risks for Parkinson's disease have been highlighted through genome-wide association studies, yet exploration of their specific disease mechanisms is lacking. Two Parkinson's disease candidate genes, KAT8 and KANSL1, identified through genome-wide studies and a PINK1-mitophagy screen, encode part of the histone acetylating non-specific lethal complex. This complex localizes to the nucleus, where it plays a role in transcriptional activation, and to mitochondria, where it has been suggested to have a role in mitochondrial transcription. In this study, we sought to identify whether the non-specific lethal complex has potential regulatory relationships with other genes associated with Parkinson's disease in human brain. Correlation in the expression of non-specific lethal genes and Parkinson's disease-associated genes was investigated in primary gene co-expression networks using publicly-available transcriptomic data from multiple brain regions (provided by the Genotype-Tissue Expression Consortium and UK Brain Expression Consortium), whilst secondary networks were used to examine cell type specificity. Reverse engineering of gene regulatory networks generated regulons of the complex, which were tested for heritability using stratified linkage disequilibrium score regression. Prioritized gene targets were then validated in vitro using a QuantiGene multiplex assay and publicly-available chromatin immunoprecipitation-sequencing data. Significant clustering of non-specific lethal genes was revealed alongside Parkinson's disease-associated genes in frontal cortex primary co-expression modules, amongst other brain regions. Both primary and secondary co-expression modules containing these genes were enriched for mainly neuronal cell types. Regulons of the complex contained Parkinson's disease-associated genes and were enriched for biological pathways genetically linked to disease. When examined in a neuroblastoma cell line, 41% of prioritized gene targets showed significant changes in mRNA expression following KANSL1 or KAT8 perturbation. KANSL1 and H4K8 chromatin immunoprecipitation-sequencing data demonstrated non-specific lethal complex activity at many of these genes. In conclusion, genes encoding the non-specific lethal complex are highly correlated with and regulate genes associated with Parkinson's disease. Overall, these findings reveal a potentially wider role for this protein complex in regulating genes and pathways implicated in Parkinson's disease.
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Affiliation(s)
- Amy R Hicks
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Regina H Reynolds
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
| | - Benjamin O’Callaghan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sonia García-Ruiz
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
| | - Ana Luisa Gil-Martínez
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
- Department of Information and Communication Engineering, University of Murcia, Murcia 30100, Spain
| | - Juan Botía
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Department of Information and Communication Engineering, University of Murcia, Murcia 30100, Spain
| | - Hélène Plun-Favreau
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Mina Ryten
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
- NIHR GOSH Biomedical Research Centre, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
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20
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Sun Y, Wiese M, Hmadi R, Karayol R, Seyfferth J, Martinez Greene JA, Erdogdu NU, Deboutte W, Arrigoni L, Holz H, Renschler G, Hirsch N, Foertsch A, Basilicata MF, Stehle T, Shvedunova M, Bella C, Pessoa Rodrigues C, Schwalb B, Cramer P, Manke T, Akhtar A. MSL2 ensures biallelic gene expression in mammals. Nature 2023; 624:173-181. [PMID: 38030723 PMCID: PMC10700137 DOI: 10.1038/s41586-023-06781-3] [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: 05/29/2022] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA1,2. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders1,3. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear. MSL2 is known for dosage compensation of the male X chromosome in flies. Here we identify a role of MSL2 in regulating allelic expression in mammals. Allele-specific bulk and single-cell analyses in mouse neural progenitor cells revealed that, in addition to the targets showing biallelic downregulation, a class of genes transitions from biallelic to monoallelic expression after MSL2 loss. Many of these genes are haploinsufficient. In the absence of MSL2, one allele remains active, retaining active histone modifications and transcription factor binding, whereas the other allele is silenced, exhibiting loss of promoter-enhancer contacts and the acquisition of DNA methylation. Msl2-knockout mice show perinatal lethality and heterogeneous phenotypes during embryonic development, supporting a role for MSL2 in regulating gene dosage. The role of MSL2 in preserving biallelic expression of specific dosage-sensitive genes sets the stage for further investigation of other factors that are involved in allelic dosage compensation in mammalian cells, with considerable implications for human disease.
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Affiliation(s)
- Yidan Sun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Meike Wiese
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Raed Hmadi
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Remzi Karayol
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Juan Alfonso Martinez Greene
- 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
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gina Renschler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Naama Hirsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Arion Foertsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Thomas Stehle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Chiara Bella
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bjoern Schwalb
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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21
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Li Z, Deeks SG, Ott M, Greene WC. Comprehensive synergy mapping links a BAF- and NSL-containing "supercomplex" to the transcriptional silencing of HIV-1. Cell Rep 2023; 42:113055. [PMID: 37682714 PMCID: PMC10591912 DOI: 10.1016/j.celrep.2023.113055] [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: 12/09/2022] [Revised: 05/26/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
Host repressors mediate HIV latency, but how they interactively silence the virus remains unclear. Here, we develop "reiterative enrichment and authentication of CRISPRi targets for synergies (REACTS)" to probe the genome for synergies between HIV transcription repressors. Using eight known host repressors as queries, we identify 32 synergies involving eleven repressors, including BCL7C, KANSL2, and SIRT2. Overexpression of these three proteins reduces HIV reactivation in Jurkat T cells and in CD4 T cells from people living with HIV on antiretroviral therapy (ART). We show that the BCL7C-containing BAF complex and the KANSL2-containing NSL complex form a "supercomplex" that increases inhibitory histone acetylation of the HIV long-terminal repeat (LTR) and its occupancy by the short variant of the acetyl-lysine reader Brd4. Collectively, we provide a validated platform for defining gene synergies genome wide, and the BAF-NSL "supercomplex" represents a potential target for overcoming HIV rebound after ART cessation.
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Affiliation(s)
- Zichong Li
- Gladstone Institute of Virology, San Francisco, CA 94158, USA.
| | - Steven G Deeks
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute of Virology, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA
| | - Warner C Greene
- Gladstone Institute of Virology, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA.
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22
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Romhányi D, Szabó K, Kemény L, Groma G. Histone and Histone Acetylation-Related Alterations of Gene Expression in Uninvolved Psoriatic Skin and Their Effects on Cell Proliferation, Differentiation, and Immune Responses. Int J Mol Sci 2023; 24:14551. [PMID: 37833997 PMCID: PMC10572426 DOI: 10.3390/ijms241914551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Psoriasis is a chronic immune-mediated skin disease in which the symptom-free, uninvolved skin carries alterations in gene expression, serving as a basis for lesion formation. Histones and histone acetylation-related processes are key regulators of gene expression, controlling cell proliferation and immune responses. Dysregulation of these processes is likely to play an important role in the pathogenesis of psoriasis. To gain a complete overview of these potential alterations, we performed a meta-analysis of a psoriatic uninvolved skin dataset containing differentially expressed transcripts from nearly 300 individuals and screened for histones and histone acetylation-related molecules. We identified altered expression of the replication-dependent histones HIST2H2AA3 and HIST2H4A and the replication-independent histones H2AFY, H2AFZ, and H3F3A/B. Eight histone chaperones were also identified. Among the histone acetyltransferases, ELP3 and KAT5 and members of the ATAC, NSL, and SAGA acetyltransferase complexes are affected in uninvolved skin. Histone deacetylation-related alterations were found to affect eight HDACs and members of the NCOR/SMRT, NURD, SIN3, and SHIP HDAC complexes. In this article, we discuss how histone and histone acetylation-related expression changes may affect proliferation and differentiation, as well as innate, macrophage-mediated, and T cell-mediated pro- and anti-inflammatory responses, which are known to play a central role in the development of psoriasis.
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Affiliation(s)
- Dóra Romhányi
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
| | - Kornélia Szabó
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- Hungarian Centre of Excellence for Molecular Medicine-University of Szeged Skin Research Group (HCEMM-USZ Skin Research Group), H-6720 Szeged, Hungary
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Lajos Kemény
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- Hungarian Centre of Excellence for Molecular Medicine-University of Szeged Skin Research Group (HCEMM-USZ Skin Research Group), H-6720 Szeged, Hungary
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Gergely Groma
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
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23
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Kelly K, Lewis PA, Plun-Favreau H, Manzoni C. Protein network analysis links the NSL complex to Parkinson's disease via mitochondrial and nuclear biology. Mol Omics 2023; 19:668-679. [PMID: 37427757 DOI: 10.1039/d2mo00325b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Whilst the majority of Parkinson's Disease (PD) cases are sporadic, much of our understanding of the pathophysiological basis of the disease can be traced back to the study of rare, monogenic forms of PD. In the past decade, the availability of genome-wide association studies (GWAS) has facilitated a shift in focus, toward identifying common risk variants conferring increased risk of developing PD across the population. A recent mitophagy screening assay of GWAS candidates has functionally implicated the non-specific lethal (NSL) complex in the regulation of PINK1-mitophagy. Here, a bioinformatics approach has been taken to investigate the proteome of the NSL complex, to unpick its relevance to PD pathogenesis. The NSL interactome has been built, using 3 online tools: PINOT, HIPPIE and MIST, to mine curated, literature-derived protein-protein interaction (PPI) data. We built (i) the 'mitochondrial' NSL interactome exploring its relevance to PD genetics and (ii) the PD-oriented NSL interactome to uncover biological pathways underpinning the NSL/PD association. In this study, we find the mitochondrial NSL interactome to be significantly enriched for the protein products of PD-associated genes, including the Mendelian PD genes LRRK2 and VPS35. In addition, we find nuclear processes to be amongst those most significantly enriched within the PD-associated NSL interactome. These findings strengthen the role of the NSL complex in sporadic and familial PD, mediated by both its mitochondrial and nuclear functions.
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Affiliation(s)
- Katie Kelly
- UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Patrick A Lewis
- UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
- Royal Veterinary College, University of London, Royal College Street, Camden, NW1 0TU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Helene Plun-Favreau
- UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Claudia Manzoni
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- UCL School of Pharmacy, Brunswick Square, London, WC1N 1AX, UK.
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24
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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: 0] [Impact Index Per Article: 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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25
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Wang D, Li H, Chandel NS, Dou Y, Yi R. MOF-mediated histone H4 Lysine 16 acetylation governs mitochondrial and ciliary functions by controlling gene promoters. Nat Commun 2023; 14:4404. [PMID: 37479688 PMCID: PMC10362062 DOI: 10.1038/s41467-023-40108-0] [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: 11/11/2022] [Accepted: 07/11/2023] [Indexed: 07/23/2023] Open
Abstract
Histone H4 lysine 16 acetylation (H4K16ac), governed by the histone acetyltransferase MOF, orchestrates gene expression regulation and chromatin interaction. However, the roles of MOF and H4K16ac in controlling cellular function and regulating mammalian tissue development remain unclear. Here we show that conditional deletion of Mof in the skin, but not Kansl1, causes severe defects in the self-renewal of basal epithelial progenitors, epidermal differentiation, and hair follicle growth, resulting in barrier defects and perinatal lethality. MOF-regulated genes are highly enriched for essential functions in the mitochondria and cilia. Genetic deletion of Uqcrq, an essential subunit for the electron transport chain (ETC) Complex III, in the skin, recapitulates the defects in epidermal differentiation and hair follicle growth observed in MOF knockout mouse. Together, this study reveals the requirement of MOF-mediated epigenetic mechanism for regulating mitochondrial and ciliary gene expression and underscores the important function of the MOF/ETC axis for mammalian skin development.
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Affiliation(s)
- Dongmei Wang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Haimin Li
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Navdeep S Chandel
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Yali Dou
- Department of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Rui Yi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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26
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Pal D, Patel M, Boulet F, Sundarraj J, Grant OA, Branco MR, Basu S, Santos SDM, Zabet NR, Scaffidi P, Pradeepa MM. H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function. Nat Struct Mol Biol 2023; 30:935-947. [PMID: 37308596 PMCID: PMC10352135 DOI: 10.1038/s41594-023-01016-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 05/05/2023] [Indexed: 06/14/2023]
Abstract
Mammalian genomes harbor abundant transposable elements (TEs) and their remnants, with numerous epigenetic repression mechanisms enacted to silence TE transcription. However, TEs are upregulated during early development, neuronal lineage, and cancers, although the epigenetic factors contributing to the transcription of TEs have yet to be fully elucidated. Here, we demonstrate that the male-specific lethal (MSL)-complex-mediated histone H4 acetylation at lysine 16 (H4K16ac) is enriched at TEs in human embryonic stem cells (hESCs) and cancer cells. This in turn activates transcription of subsets of full-length long interspersed nuclear elements (LINE1s, L1s) and endogenous retrovirus (ERV) long terminal repeats (LTRs). Furthermore, we show that the H4K16ac-marked L1 and LTR subfamilies display enhancer-like functions and are enriched in genomic locations with chromatin features associated with active enhancers. Importantly, such regions often reside at boundaries of topologically associated domains and loop with genes. CRISPR-based epigenetic perturbation and genetic deletion of L1s reveal that H4K16ac-marked L1s and LTRs regulate the expression of genes in cis. Overall, TEs enriched with H4K16ac contribute to the cis-regulatory landscape at specific genomic locations by maintaining an active chromatin landscape at TEs.
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Affiliation(s)
- Debosree Pal
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Manthan Patel
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Fanny Boulet
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jayakumar Sundarraj
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
- Bhabha Atomic Research Centre, Mumbai, India
| | - Olivia A Grant
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
- School of Life Sciences, University of Essex, Colchester, UK
| | - Miguel R Branco
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Nicolae Radu Zabet
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Paola Scaffidi
- Francis Crick Institute, London, UK
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Madapura M Pradeepa
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK.
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27
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Edwards DM, Davies P, Hebenstreit D. Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting. Genome Biol 2023; 24:138. [PMID: 37328900 PMCID: PMC10276402 DOI: 10.1186/s13059-023-02977-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/25/2023] [Indexed: 06/18/2023] Open
Abstract
Despite the recent rise of RNA-seq datasets combining single-cell (sc) resolution with 4-thiouridine (4sU) labelling, analytical methods exploiting their power to dissect transcriptional bursting are lacking. Here, we present a mathematical model and Bayesian inference implementation to facilitate genome-wide joint parameter estimation and confidence quantification (R package: burstMCMC). We demonstrate that, unlike conventional scRNA-seq, 4sU scRNA-seq resolves temporal parameters and furthermore boosts inference of dimensionless parameters via a synergy between single-cell resolution and 4sU labelling. We apply our method to published 4sU scRNA-seq data and linked with ChIP-seq data, we uncover previously obscured associations between different parameters and histone modifications.
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Affiliation(s)
| | - Philip Davies
- School of Life Sciences, University of Warwick, Coventry, UK
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28
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Fiorentino F, Sementilli S, Menna M, Turrisi F, Tomassi S, Pellegrini FR, Iuzzolino A, D'Acunzo F, Feoli A, Wapenaar H, Taraglio S, Fraschetti C, Del Bufalo D, Sbardella G, Dekker FJ, Paiardini A, Trisciuoglio D, Mai A, Rotili D. First-in-Class Selective Inhibitors of the Lysine Acetyltransferase KAT8. J Med Chem 2023; 66:6591-6616. [PMID: 37155735 DOI: 10.1021/acs.jmedchem.2c01937] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
KAT8 is a lysine acetyltransferase primarily catalyzing the acetylation of Lys16 of histone H4 (H4K16). KAT8 dysregulation is linked to the development and metastatization of many cancer types, including non-small cell lung cancer (NSCLC) and acute myeloid leukemia (AML). Few KAT8 inhibitors have been reported so far, none of which displaying selective activity. Based on the KAT3B/KDAC inhibitor C646, we developed a series of N-phenyl-5-pyrazolone derivatives and identified compounds 19 and 34 as low-micromolar KAT8 inhibitors selective over a panel of KATs and KDACs. Western blot, immunofluorescence, and CETSA experiments demonstrated that both inhibitors selectively target KAT8 in cells. Moreover, 19 and 34 exhibited mid-micromolar antiproliferative activity in different cancer cell lines, including NSCLC and AML, without impacting the viability of nontransformed cells. Overall, these compounds are valuable tools for elucidating KAT8 biology, and their simple structures make them promising candidates for future optimization studies.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Sara Sementilli
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Via degli Apuli 4, Rome 00185, Italy
| | - Martina Menna
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Federica Turrisi
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Via degli Apuli 4, Rome 00185, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", via Domenico Montesano 49, Naples 80131, Italy
| | - Francesca Romana Pellegrini
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Via degli Apuli 4, Rome 00185, Italy
| | - Angela Iuzzolino
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Via degli Apuli 4, Rome 00185, Italy
| | - Francesca D'Acunzo
- Institute of Biological Systems (ISB), Italian National Research Council (CNR), Sezione Meccanismi di Reazione, c/o Department of Chemistry, Sapienza University of Rome, P. le A. Moro 5, Rome 00185, Italy
| | - Alessandra Feoli
- Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, Fisciano (SA) 84084, Italy
| | - Hannah Wapenaar
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Sophie Taraglio
- Department of Biochemical Sciences, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Caterina Fraschetti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Donatella Del Bufalo
- Preclinical Models and New Therapeutic Agents Unit, IRCCS-Regina Elena National Cancer Institute, Via Elio Chianesi 53, Rome 00144, Italy
| | - Gianluca Sbardella
- Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, Fisciano (SA) 84084, Italy
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Alessandro Paiardini
- Department of Biochemical Sciences, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Daniela Trisciuoglio
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Via degli Apuli 4, Rome 00185, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
- Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
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29
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Morgan MA, Shilatifard A. Epigenetic moonlighting: Catalytic-independent functions of histone modifiers in regulating transcription. SCIENCE ADVANCES 2023; 9:eadg6593. [PMID: 37083523 PMCID: PMC10121172 DOI: 10.1126/sciadv.adg6593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The past three decades have yielded a wealth of information regarding the chromatin regulatory mechanisms that control transcription. The "histone code" hypothesis-which posits that distinct combinations of posttranslational histone modifications are "read" by downstream effector proteins to regulate gene expression-has guided chromatin research to uncover fundamental mechanisms relevant to many aspects of biology. However, recent molecular and genetic studies revealed that the function of many histone-modifying enzymes extends independently and beyond their catalytic activities. In this review, we highlight original and recent advances in the understanding of noncatalytic functions of histone modifiers. Many of the histone modifications deposited by these enzymes-previously considered to be required for transcriptional activation-have been demonstrated to be dispensable for gene expression in living organisms. This perspective aims to prompt further examination of these enigmatic chromatin modifications by inspiring studies to define the noncatalytic "epigenetic moonlighting" functions of chromatin-modifying enzymes.
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30
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Mehta S, Buyanbat A, Orkin S, Nabet B. High-efficiency knock-in of degradable tags (dTAG) at endogenous loci in cell lines. Methods Enzymol 2023; 681:1-22. [PMID: 36764753 DOI: 10.1016/bs.mie.2022.08.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The dTAG system is a versatile strategy for tunable control of protein abundance and facilitates the time-resolved assessment of disease-associated protein function. A "co-opted" fusion-based degron peptide, the "dTAG" facilitates the study of endogenous protein function when knocked-in at the endogenous genetic loci of proteins of interest. We combine CRISPR/Cas9 mediated induction of double-strand breaks (DSB) with the delivery of a single-stranded DNA HDR-donor-template via crude preparations of recombinant adeno-associated virus (rAAV). Our approach to knock-in of large (1-2kb) DNA fragments via crude-rAAV mediated HDR donor delivery is rapid and inexpensive. It facilitates genetic modification of a variety of human as well as mouse cell lines at high efficiency and precision.
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Affiliation(s)
- Stuti Mehta
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, United States
| | - Altantsetseg Buyanbat
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, United States
| | - Stuart Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, United States
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, United States.
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31
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Soutar MPM, Melandri D, O’Callaghan B, Annuario E, Monaghan AE, Welsh NJ, D’Sa K, Guelfi S, Zhang D, Pittman A, Trabzuni D, Verboven AHA, Pan KS, Kia DA, Bictash M, Gandhi S, Houlden H, Cookson MR, Kasri NN, Wood NW, Singleton AB, Hardy J, Whiting PJ, Blauwendraat C, Whitworth AJ, Manzoni C, Ryten M, Lewis PA, Plun-Favreau H. Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson's disease at 16q11.2 and MAPT H1 loci. Brain 2022; 145:4349-4367. [PMID: 36074904 PMCID: PMC9762952 DOI: 10.1093/brain/awac325] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 02/02/2023] Open
Abstract
Parkinson's disease is a common incurable neurodegenerative disease. The identification of genetic variants via genome-wide association studies has considerably advanced our understanding of the Parkinson's disease genetic risk. Understanding the functional significance of the risk loci is now a critical step towards translating these genetic advances into an enhanced biological understanding of the disease. Impaired mitophagy is a key causative pathway in familial Parkinson's disease, but its relevance to idiopathic Parkinson's disease is unclear. We used a mitophagy screening assay to evaluate the functional significance of risk genes identified through genome-wide association studies. We identified two new regulators of PINK1-dependent mitophagy initiation, KAT8 and KANSL1, previously shown to modulate lysine acetylation. These findings suggest PINK1-mitophagy is a contributing factor to idiopathic Parkinson's disease. KANSL1 is located on chromosome 17q21 where the risk associated gene has long been considered to be MAPT. While our data do not exclude a possible association between the MAPT gene and Parkinson's disease, they provide strong evidence that KANSL1 plays a crucial role in the disease. Finally, these results enrich our understanding of physiological events regulating mitophagy and establish a novel pathway for drug targeting in neurodegeneration.
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Affiliation(s)
- Marc P M Soutar
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Daniela Melandri
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Benjamin O’Callaghan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Emily Annuario
- Department of Basic and Clinical Neuroscience, King’s College, London, UK
| | - Amy E Monaghan
- UCL Alzheimer’s Research UK, Drug Discovery Institute, London, UK
- UCL Dementia Research Institute, London, UK
| | - Natalie J Welsh
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Karishma D’Sa
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Francis Crick Institute, London, UK
| | - Sebastian Guelfi
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David Zhang
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Alan Pittman
- Genetics Research Centre, Molecular and Clinical Sciences, St Georges University, London, UK
| | - Daniah Trabzuni
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Anouk H A Verboven
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Kylie S Pan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Demis A Kia
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Magda Bictash
- UCL Alzheimer’s Research UK, Drug Discovery Institute, London, UK
- UCL Dementia Research Institute, London, UK
| | - Sonia Gandhi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Francis Crick Institute, London, UK
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands
| | - Nicholas W Wood
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- UCL Dementia Research Institute, London, UK
| | - Paul J Whiting
- UCL Alzheimer’s Research UK, Drug Discovery Institute, London, UK
- UCL Dementia Research Institute, London, UK
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Claudia Manzoni
- Department of Pharmacology, UCL School of Pharmacy, London, UK
| | - Mina Ryten
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Patrick A Lewis
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Comparative Biomedical Sciences, Royal Veterinary College, LondonUK
| | - Hélène Plun-Favreau
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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32
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Wang W, Shen Y, Zhang P, Liu L, Sha X, Li H, Wang S, Zhang H, Zhou Y, Shi J. Histone acetylation modification regulator-mediated tumor microenvironment infiltration characteristics and prognostic model of lung adenocarcinoma patients. J Thorac Dis 2022; 14:3886-3902. [PMID: 36389327 PMCID: PMC9641363 DOI: 10.21037/jtd-22-1000] [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: 07/18/2022] [Accepted: 09/16/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND The incidence rate of lung adenocarcinoma (LUAD) is rapidly increasing. Recent studies have reported that histone acetylation modification plays an important role in the occurrence and development of tumors. However, the potential role of modification of histone acetylation modification in the development of tumor immune microenvironment is still unclear. METHODS In this study, we comprehensively evaluated the acetylation modification patterns of LUAD samples obtained from various different databases based on 36 histone modification regulators, and constructed a prognostic model based on The Cancer Genome Atlas (TCGA) LUAD cohort using the Cox regression method. The close relationship between histone acetylation and tumor immune characteristics was further studied, including immune infiltration, immune escape and immunotherapy. Finally, we combined three cohort (GSE30219, GSE72094 and GSE50081) from Gene Expression Omnibus (GEO) database to verify the above results. RESULTS We analyzed the expression, mutation and interaction of 36 histone acetylation regulated genes. After Univariate Cox regression analysis and least absolute shrinkage and selection operator regression (LASSO), 5 genes (KAT2B, SIRT2, HDAC5, KAT8, HDAC2) were screened to establish the prognosis model and calculate the risk score. Then, patients in the TCGA cohort were divided into high- and low-risk groups based on the risk scores. Further analysis indicated that patients in the high-risk group exhibited significantly reduced overall survival (OS) compared with those in the low-risk group. The high- and low-risk groups exhibited significant differences in terms of tumor immune characteristics, such as immune infiltration, immune escape and immunotherapy. The high-risk group had lower immune score, less immune cell infiltration and higher clinical stage. Moreover, multivariate analysis revealed that this prognostic model might be a powerful prognostic predictor for LUAD. In addition, drugs sensitive for this classification were identified. Finally, the efficacy of the prognostic model was validated by cohort (GSE30219, GSE72094 and GSE50081) from GEO database. CONCLUSIONS Our study provided a robust signature for predicting changing prognosis of patients with LUAD. Thus, it appears to be a potentially useful prognostic tool. Moreover, the important relationship between histone acetylation and tumor immune microenvironment was revealed.
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Affiliation(s)
- Wenmiao Wang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Yao Shen
- School of Medicine, Nantong University, Nantong, China
| | - Peng Zhang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Lei Liu
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Xinyu Sha
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Houqiang Li
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Silin Wang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Youlang Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiahai Shi
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China;,School of Public Health, Nantong University, Nantong, China
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33
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Yedier-Bayram O, Gokbayrak B, Kayabolen A, Aksu AC, Cavga AD, Cingöz A, Kala EY, Karabiyik G, Günsay R, Esin B, Morova T, Uyulur F, Syed H, Philpott M, Cribbs AP, Kung SHY, Lack NA, Onder TT, Bagci-Onder T. EPIKOL, a chromatin-focused CRISPR/Cas9-based screening platform, to identify cancer-specific epigenetic vulnerabilities. Cell Death Dis 2022; 13:710. [PMID: 35973998 PMCID: PMC9381743 DOI: 10.1038/s41419-022-05146-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/24/2022] [Accepted: 07/28/2022] [Indexed: 01/21/2023]
Abstract
Dysregulation of the epigenome due to alterations in chromatin modifier proteins commonly contribute to malignant transformation. To interrogate the roles of epigenetic modifiers in cancer cells, we generated an epigenome-wide CRISPR-Cas9 knockout library (EPIKOL) that targets a wide-range of epigenetic modifiers and their cofactors. We conducted eight screens in two different cancer types and showed that EPIKOL performs with high efficiency in terms of sgRNA distribution and depletion of essential genes. We discovered novel epigenetic modifiers that regulate triple-negative breast cancer (TNBC) and prostate cancer cell fitness. We confirmed the growth-regulatory functions of individual candidates, including SS18L2 and members of the NSL complex (KANSL2, KANSL3, KAT8) in TNBC cells. Overall, we show that EPIKOL, a focused sgRNA library targeting ~800 genes, can reveal epigenetic modifiers that are essential for cancer cell fitness under in vitro and in vivo conditions and enable the identification of novel anti-cancer targets. Due to its comprehensive epigenome-wide targets and relatively high number of sgRNAs per gene, EPIKOL will facilitate studies examining functional roles of epigenetic modifiers in a wide range of contexts, such as screens in primary cells, patient-derived xenografts as well as in vivo models.
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Affiliation(s)
- Ozlem Yedier-Bayram
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Bengul Gokbayrak
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Alisan Kayabolen
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Ali Cenk Aksu
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Ayse Derya Cavga
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
- Biostatistics, Bioinformatics and Data Management Core, KUTTAM, Istanbul, Türkiye
| | - Ahmet Cingöz
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Ezgi Yagmur Kala
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Goktug Karabiyik
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Rauf Günsay
- Koç University School of Medicine, Istanbul, Türkiye
| | - Beril Esin
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
| | - Tunc Morova
- Koç University School of Medicine, Istanbul, Türkiye
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Fırat Uyulur
- Koç University Department of Computational Biology, Istanbul, Türkiye
| | - Hamzah Syed
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
- Biostatistics, Bioinformatics and Data Management Core, KUTTAM, Istanbul, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
| | - Martin Philpott
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sonia H Y Kung
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Nathan A Lack
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
- Koç University School of Medicine, Istanbul, Türkiye
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Tamer T Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye.
- Koç University School of Medicine, Istanbul, Türkiye.
| | - Tugba Bagci-Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye.
- Koç University School of Medicine, Istanbul, Türkiye.
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34
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Corrochano-Fraile A, Davie A, Carboni S, Bekaert M. Evidence of multiple genome duplication events in Mytilus evolution. BMC Genomics 2022; 23:340. [PMID: 35501689 PMCID: PMC9063065 DOI: 10.1186/s12864-022-08575-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
Background Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Results Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. Conclusions The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08575-9.
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Affiliation(s)
- Ana Corrochano-Fraile
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Andrew Davie
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Stefano Carboni
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK. .,International Marine Centre, Loc. Sa Mardini snc, 09170, Torre Grande, OR, Italy.
| | - Michaël Bekaert
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
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35
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Furth N, Shema E. It's all in the combination: decoding the epigenome for cancer research and diagnostics. Curr Opin Genet Dev 2022; 73:101899. [PMID: 35091256 PMCID: PMC9168437 DOI: 10.1016/j.gde.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Genome regulation is governed by the dynamics of chromatin modifications. The extensive and diverse array of DNA and histone modifications allow multiple elements to act combinatorically and direct tissue-specific and cell-specific outcomes. Yet, our ability to elucidate these complex combinations and link them to normal genome regulation, as well as understand their deregulation in cancer, has been hindered by the lack of suitable technologies. Here, we describe recent findings indicating the importance of the combinatorial epigenome, and novel methodologies to measure and characterize these combinations. These complementary methods span multiple disciplines, providing a means to decode epigenetic combinations and link them to biological outcomes. Finally, we discuss the promise of harnessing the rich combinatorial epigenetic information to improve cancer diagnostics and monitoring.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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36
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Liu H, Wei T, Sun L, Wu T, Li F, Zhao J, Chu J, Wang F, Cai Y, Jin J. The Non-Specific Lethal (NSL) Histone Acetyltransferase Complex Transcriptionally Regulates Yin Yang 1-Mediated Cell Proliferation in Human Cells. Int J Mol Sci 2022; 23:ijms23073801. [PMID: 35409160 PMCID: PMC8998616 DOI: 10.3390/ijms23073801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
The human males absent on the first (MOF)-containing non-specific lethal (NSL) histone acetyltransferase (HAT) complex acetylates histone H4 at lysine K5, K8, and K16. This complex shares several subunits with other epigenetic regulatory enzymes, which highlights the complexity of its intracellular function. However, the effect of the NSL HAT complex on the genome and target genes in human cells is still unclear. By using a CRISPR/Cas9-mediated NSL3-knockout 293T cell line and chromatin immunoprecipitation-sequencing (ChIP-Seq) approaches, we identified more than 100 genes as NSL HAT transcriptional targets, including several transcription factors, such as Yin Yang 1 (YY1) which are mainly involved in cell proliferation, biological adhesion, and metabolic processes. We found here that the ChIP-Seq peaks of MOF and NSL3 co-localized with H4K16ac, H3K4me2, and H3K4me3 at the transcriptional start site of YY1. In addition, both the mRNA and protein expression levels of YY1 were regulated by silencing or overexpressing NSL HAT. Interestingly, the expression levels of cell division cycle 6, a downstream target gene of YY1, were regulated by MOF or NSL3. In addition, the suppressed clonogenic ability of HepG2 cells caused by siNSL3 was reversed by overexpressing YY1, suggesting the involvement of YY1 in NSL HAT functioning. Additionally, de novo motif analysis of MOF and NSL3 targets indicated that the NSL HAT complex may recognize the specific DNA-binding sites in the promoter region of target genes in order to regulate their transcription.
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Affiliation(s)
- Hongsen Liu
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
| | - Tao Wei
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
| | - Lin Sun
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
| | - Tingting Wu
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
| | - Fuqiang Li
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Jianlei Zhao
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
| | - Jinmeng Chu
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
| | - Fei Wang
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
- Correspondence: (Y.C.); (J.J.); Tel.: +86-431-8515-5132 (Y.C.); +86-431-8515-5475 (J.J.)
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun 130012, China; (H.L.); (T.W.); (L.S.); (T.W.); (F.L.); (J.Z.); (J.C.); (F.W.)
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
- Correspondence: (Y.C.); (J.J.); Tel.: +86-431-8515-5132 (Y.C.); +86-431-8515-5475 (J.J.)
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37
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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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38
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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: 271] [Impact Index Per Article: 135.5] [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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39
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Van HT, Harkins PR, Patel A, Jain AK, Lu Y, Bedford MT, Santos MA. Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression-regulating NSL complexes. J Biol Chem 2022; 298:101588. [PMID: 35033534 PMCID: PMC8867114 DOI: 10.1016/j.jbc.2022.101588] [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: 08/06/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 11/16/2022] Open
Abstract
The methyl-lysine readers plant homeodomain finger protein 20 (PHF20) and its homolog PHF20-like protein 1 (PHF20L1) are known components of the nonspecific lethal (NSL) complex that regulates gene expression through its histone acetyltransferase activity. In the current model, both PHF homologs coexist in the same NSL complex, although this was not formally tested; nor have the functions of PHF20 and PHF20L1 regarding NSL complex integrity and transcriptional regulation been investigated. Here, we perform an in-depth biochemical and functional characterization of PHF20 and PHF20L1 in the context of the NSL complex. Using mass spectrometry, genome-wide chromatin analysis, and protein-domain mapping, we identify the existence of two distinct NSL complexes that exclusively contain either PHF20 or PHF20L1. We show that the C-terminal domains of PHF20 and PHF20L1 are essential for complex formation with NSL, and the Tudor 2 domains are required for chromatin binding. The genome-wide chromatin landscape of PHF20–PHF20L1 shows that these proteins bind mostly to the same genomic regions, at promoters of highly expressed/housekeeping genes. Yet, deletion of PHF20 and PHF20L1 does not abrogate gene expression or impact the recruitment of the NSL complex to those target gene promoters, suggesting the existence of an alternative mechanism that compensates for the transcription of genes whose sustained expression is important for critical cellular functions. This work shifts the current paradigm and lays the foundation for studies on the differential roles of PHF20 and PHF20L1 in regulating NSL complex activity in physiological and diseases states.
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Affiliation(s)
- Hieu T Van
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Peter R Harkins
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Avni Patel
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Margarida A Santos
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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40
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Damhofer H, Radzisheuskaya A, Helin K. Generation of locus-specific degradable tag knock-ins in mouse and human cell lines. STAR Protoc 2021; 2:100575. [PMID: 34151298 PMCID: PMC8188616 DOI: 10.1016/j.xpro.2021.100575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Protein degradation technologies represent a powerful functional genomics tool, allowing fast and controllable target protein depletion. Establishing these systems requires a knock-in of the degradation tag into both endogenous target gene alleles. Here, we provide a step-by-step protocol for the efficient generation of biallelic degradation tag knock-ins in mouse and human cell lines using CRISPR-Cas9. We use knockin of an endogenous Kansl3 degradation tag in mouse embryonic stem (ES) cells as an example but provide modifications for application in other cell types. For complete details on the use and execution of this protocol, please refer to Radzisheuskaya et al. (2021). Efficient generation of biallelic degradation tag knock-ins in mouse and human cells Extensive advice on donor plasmid design and ligation-free vector construction Recommendations for functional validation of the degron-fused protein
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Affiliation(s)
- Helene Damhofer
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N 2200, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), University of Copenhagen, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Aliaksandra Radzisheuskaya
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N 2200, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), University of Copenhagen, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N 2200, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), University of Copenhagen, University of Copenhagen, Copenhagen N 2200, Denmark
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