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Separovich RJ, Karakatsanis NM, Gao K, Fuh D, Hamey JJ, Wilkins MR. Proline-directed yeast and human MAP kinases phosphorylate the Dot1p/DOT1L histone H3K79 methyltransferase. FEBS J 2024. [PMID: 38270553 DOI: 10.1111/febs.17062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/24/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Disruptor of telomeric silencing 1 (Dot1p) is an exquisitely conserved histone methyltransferase and is the sole enzyme responsible for H3K79 methylation in the budding yeast Saccharomyces cerevisiae. It has been shown to be highly phosphorylated in vivo; however, the upstream kinases that act on Dot1p are almost entirely unknown in yeast and all other eukaryotes. Here, we used in vitro and in vivo kinase discovery approaches to show that mitogen-activated protein kinase HOG1 (Hog1p) is a bona fide kinase of the Dot1p methyltransferase. In vitro kinase assays showed that Hog1p phosphorylates Dot1p at multiple sites, including at several proline-adjacent sites that are consistent with known Hog1p substrate preferences. The activity of Hog1p was specifically enhanced at these proline-adjacent sites on Dot1p upon Hog1p activation by the osmostress-responsive MAP kinase kinase PBS2 (Pbs2p). Genomic deletion of HOG1 reduced phosphorylation at specific sites on Dot1p in vivo, providing further evidence for Hog1p kinase activity on Dot1p in budding yeast cells. Phenotypic analysis of knockout and phosphosite mutant yeast strains revealed the importance of Hog1p-catalysed phosphorylation of Dot1p for cellular responses to ultraviolet-induced DNA damage. In mammalian systems, this kinase-substrate relationship was found to be conserved: human DOT1L (the ortholog of yeast Dot1p) can be phosphorylated by the proline-directed kinase p38β (also known as MAPK11; the ortholog of yeast Hog1p) at multiple sites in vitro. Taken together, our findings establish Hog1p and p38β as newly identified upstream kinases of the Dot1p/DOT1L H3K79 methyltransferase enzymes in eukaryotes.
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Affiliation(s)
- Ryan J Separovich
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Nicola M Karakatsanis
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Kelley Gao
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - David Fuh
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Joshua J Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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3
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Nil Z, Deshwar AR, Huang Y, Barish S, Zhang X, Choufani S, Le Quesne Stabej P, Hayes I, Yap P, Haldeman-Englert C, Wilson C, Prescott T, Tveten K, Vøllo A, Haynes D, Wheeler PG, Zon J, Cytrynbaum C, Jobling R, Blyth M, Banka S, Afenjar A, Mignot C, Robin-Renaldo F, Keren B, Kanca O, Mao X, Wegner DJ, Sisco K, Shinawi M, Wangler MF, Weksberg R, Yamamoto S, Costain G, Bellen HJ. Rare de novo gain-of-function missense variants in DOT1L are associated with developmental delay and congenital anomalies. Am J Hum Genet 2023; 110:1919-1937. [PMID: 37827158 PMCID: PMC10645550 DOI: 10.1016/j.ajhg.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Abstract
Misregulation of histone lysine methylation is associated with several human cancers and with human developmental disorders. DOT1L is an evolutionarily conserved gene encoding a lysine methyltransferase (KMT) that methylates histone 3 lysine-79 (H3K79) and was not previously associated with a Mendelian disease in OMIM. We have identified nine unrelated individuals with seven different de novo heterozygous missense variants in DOT1L through the Undiagnosed Disease Network (UDN), the SickKids Complex Care genomics project, and GeneMatcher. All probands had some degree of global developmental delay/intellectual disability, and most had one or more major congenital anomalies. To assess the pathogenicity of the DOT1L variants, functional studies were performed in Drosophila and human cells. The fruit fly DOT1L ortholog, grappa, is expressed in most cells including neurons in the central nervous system. The identified DOT1L variants behave as gain-of-function alleles in flies and lead to increased H3K79 methylation levels in flies and human cells. Our results show that human DOT1L and fly grappa are required for proper development and that de novo heterozygous variants in DOT1L are associated with a Mendelian disease.
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Affiliation(s)
- Zelha Nil
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ashish R Deshwar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Yan Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Scott Barish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China; National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410005, China
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Polona Le Quesne Stabej
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, the University of Auckland, Auckland, New Zealand
| | - Ian Hayes
- Genetic Health Service New Zealand- Northern Hub, Auckland District Health Board, Auckland, New Zealand
| | - Patrick Yap
- Genetic Health Service New Zealand- Northern Hub, Auckland District Health Board, Auckland, New Zealand
| | | | - Carolyn Wilson
- Mission Fullerton Genetics Center, Asheville, NC 28803, USA
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Arve Vøllo
- Department of Pediatrics, Hospital of Østfold, 1714 Grålum, Norway
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children - Orlando Health, Orlando, FL, USA; Clinical Genetics Service, Guy's Hospital, Guy's and St Thomas' NHS Trust, London, England, UK
| | - Patricia G Wheeler
- Division of Genetics, Arnold Palmer Hospital for Children - Orlando Health, Orlando, FL, USA
| | - Jessica Zon
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rebekah Jobling
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Moira Blyth
- North of Scotland Regional Genetics Service, Clinical Genetics Centre, Ashgrove House, Foresterhill, Aberdeen, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, M13 9WL Manchester, UK
| | - Alexandra Afenjar
- Service de génétique, CRMR des malformations et maladies congénitales du cervelet et CRMR déficience intellectuelle, hôpital Trousseau, AP-HP, Paris, France
| | - Cyril Mignot
- Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, Paris, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
| | | | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, 75013 Paris, France
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xiao Mao
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410005, China; Clinical Research Center for Placental Medicine in Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410005, China
| | - Daniel J Wegner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kathleen Sisco
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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4
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Maksimova V, Makus J, Popova V, Prus A, Usalka O, Trapeznikova E, Zhidkova E, Belitsky G, Yakubovskaya M, Kirsanov K. Histone Methyltransferases as a New Target for Epigenetic Action of Vorinostat. Biochemistry (Mosc) 2023; 88:968-978. [PMID: 37751867 DOI: 10.1134/s000629792307009x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 09/28/2023]
Abstract
Epigenetic genome regulation during malignant cell transformation is characterized by the aberrant methylation and acetylation of histones. Vorinostat (SAHA) is an epigenetic modulator actively used in clinical oncology. The antitumor activity of vorinostat is commonly believed to be associated with the inhibition of histone deacetylases, while the impact of this drug on histone methylation has been poorly studied. Using HeLa TI cells as a test system allowing evaluation of the effect of epigenetically active compounds from the expression of the GFP reporter gene and gene knockdown by small interfering RNAs, we showed that vorinostat not only suppressed HDAC1, but also reduced the activity of EZH2, SUV39H1, SUV39H2, and SUV420H1. The ability of vorinostat to suppress expression of EZH2, SUV39H1/2, SUV420H1 was confirmed by Western blotting. Vorinostat also downregulated expression of SUV420H2 and DOT1L enzymes. The data obtained expand our understanding of the epigenetic effects of vorinostat and demonstrate the need for a large-scale analysis of its activity toward other enzymes involved in the epigenetic genome regulation. Elucidation of the mechanism underlying the epigenetic action of vorinostat will contribute to its more proper use in the treatment of tumors with an aberrant epigenetic profile.
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Affiliation(s)
- Varvara Maksimova
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Julia Makus
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
- Peoples' Friendship University of Russia, Moscow, 117198, Russia
| | - Valeriia Popova
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
- Dmitry Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russia
| | - Anzhelika Prus
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
- MIREA, Russian Technological University, Moscow, 119571, Russia
| | - Olga Usalka
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, 119991, Russia
| | - Ekaterina Trapeznikova
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, 119991, Russia
| | - Ekaterina Zhidkova
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Gennady Belitsky
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | | | - Kirill Kirsanov
- Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia.
- Peoples' Friendship University of Russia, Moscow, 117198, Russia
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5
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Zhang J, Yang T, Han M, Wang X, Yang W, Guo N, Ren Y, Cui W, Li S, Zhao Y, Zhai X, Jia L, Yang J, Wu C, Wang L. Gain-of-function mutations in the catalytic domain of DOT1L promote lung cancer malignant phenotypes via the MAPK/ERK signaling pathway. Sci Adv 2023; 9:eadc9273. [PMID: 37256945 PMCID: PMC10413674 DOI: 10.1126/sciadv.adc9273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
Lung cancer is a lethal malignancy lacking effective therapies. Emerging evidence suggests that epigenetic enzyme mutations are closely related to the malignant phenotype of lung cancer. Here, we identified a series of gain-of-function mutations in the histone methyltransferase DOT1L. The strongest of them is R231Q, located in the catalytic DOT domain. R231Q can enhance the substrate binding ability of DOT1L. Moreover, R231Q promotes cell growth and drug resistance of lung cancer cells in vitro and in vivo. Mechanistic studies also revealed that the R231Q mutant specifically activates the MAPK/ERK signaling pathway by enriching H3K79me2 on the RAF1 promoter and epigenetically regulating the expression of downstream targets. The combination of a DOT1L inhibitor (SGC0946) and a MAPK/ERK axis inhibitor (binimetinib) can effectively reverse the R231Q-induced phenomena. Our results reveal gain-of-function mutations in an epigenetic enzyme and provide promising insights for the precise treatment of lung cancer patients.
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Affiliation(s)
- Jiayu Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Ting Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Mei Han
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Xiaoxuan Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Weiming Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Ning Guo
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Yong Ren
- Department of Pathology, General Hospital of Central Theater Command of People's Liberation Army, Wuhan 430070, China
| | - Wei Cui
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shangxiao Li
- Department of Biochemistry and Molecular Biology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yongshan Zhao
- Department of Biochemistry and Molecular Biology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lina Jia
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jingyu Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chunfu Wu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lihui Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
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