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Huether R, Dong L, Chen X, Wu G, Parker M, Wei L, Ma J, Edmonson MN, Hedlund EK, Rusch MC, Shurtleff SA, Mulder HL, Boggs K, Vadordaria B, Cheng J, Yergeau D, Song G, Becksfort J, Lemmon G, Weber C, Cai Z, Dang J, Walsh M, Gedman AL, Faber Z, Easton J, Gruber T, Kriwacki RW, Partridge JF, Ding L, Wilson RK, Mardis ER, Mullighan CG, Gilbertson RJ, Baker SJ, Zambetti G, Ellison DW, Zhang J, Downing JR. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun 2014; 5:3630. [PMID: 24710217 DOI: 10.1038/ncomms4630] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 03/12/2014] [Indexed: 02/07/2023] Open
Abstract
Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known epigenetic regulatory proteins, in over 1,000 paediatric tumours to define the landscape of somatic mutations in epigenetic regulators in paediatric cancer. Our results demonstrate a marked variation in the frequency of gene mutations across 21 different paediatric cancer subtypes, with the highest frequency of mutations detected in high-grade gliomas, T-lineage acute lymphoblastic leukaemia and medulloblastoma, and a paucity of mutations in low-grade glioma and retinoblastoma. The most frequently mutated genes are H3F3A, PHF6, ATRX, KDM6A, SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1, NSD2, SETD2, SMC1A and ZMYM3. We identify novel loss-of-function mutations in the ubiquitin-specific processing protease 7 (USP7) in paediatric leukaemia, which result in decreased deubiquitination activity. Collectively, our results help to define the landscape of mutations in epigenetic regulatory genes in paediatric cancer and yield a valuable new database for investigating the role of epigenetic dysregulations in cancer.
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Affiliation(s)
- Robert Huether
- 1] Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2]
| | - Li Dong
- 1] Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2]
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Matthew Parker
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Lei Wei
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jing Ma
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael N Edmonson
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Erin K Hedlund
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael C Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Sheila A Shurtleff
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Heather L Mulder
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Kristy Boggs
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Bhavin Vadordaria
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinjun Cheng
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Donald Yergeau
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Guangchun Song
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jared Becksfort
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gordon Lemmon
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Catherine Weber
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Zhongling Cai
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinjun Dang
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael Walsh
- Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Amanda L Gedman
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Zachary Faber
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - John Easton
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Tanja Gruber
- 1] Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2] Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Janet F Partridge
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Li Ding
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Richard K Wilson
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Elaine R Mardis
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard J Gilbertson
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gerard Zambetti
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - James R Downing
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
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5
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Neelkantan N, Mikhaylova A, Stewart AM, Arnold R, Gjeloshi V, Kondaveeti D, Poudel MK, Kalueff AV. Perspectives on zebrafish models of hallucinogenic drugs and related psychotropic compounds. ACS Chem Neurosci 2013; 4:1137-50. [PMID: 23883191 DOI: 10.1021/cn400090q] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Among different classes of psychotropic drugs, hallucinogenic agents exert one of the most prominent effects on human and animal behaviors, markedly altering sensory, motor, affective, and cognitive responses. The growing clinical and preclinical interest in psychedelic, dissociative, and deliriant hallucinogens necessitates novel translational, sensitive, and high-throughput in vivo models and screens. Primate and rodent models have been traditionally used to study cellular mechanisms and neural circuits of hallucinogenic drugs' action. The utility of zebrafish ( Danio rerio ) in neuroscience research is rapidly growing due to their high physiological and genetic homology to humans, ease of genetic manipulation, robust behaviors, and cost effectiveness. Possessing a fully characterized genome, both adult and larval zebrafish are currently widely used for in vivo screening of various psychotropic compounds, including hallucinogens and related drugs. Recognizing the growing importance of hallucinogens in biological psychiatry, here we discuss hallucinogenic-induced phenotypes in zebrafish and evaluate their potential as efficient preclinical models of drug-induced states in humans.
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Affiliation(s)
- Nikhil Neelkantan
- Zebrafish Neuroscience Research Consortium (ZNRC) and ZENEREI Institute, 309
Palmer Court, Slidell, Louisiana 70458, United States
- Departments of Physiology and
Pharmacology, International American University College of Medicine, Vieux Fort, St. Lucia, WI
| | - Alina Mikhaylova
- Zebrafish Neuroscience Research Consortium (ZNRC) and ZENEREI Institute, 309
Palmer Court, Slidell, Louisiana 70458, United States
- Departments of Physiology and
Pharmacology, International American University College of Medicine, Vieux Fort, St. Lucia, WI
| | - Adam Michael Stewart
- Zebrafish Neuroscience Research Consortium (ZNRC) and ZENEREI Institute, 309
Palmer Court, Slidell, Louisiana 70458, United States
- Department of Neuroscience, University of Pittsburgh, A210 Langley Hall, Pittsburgh,
Pennsylvania 15260, United States
| | - Raymond Arnold
- Zebrafish Neuroscience Research Consortium (ZNRC) and ZENEREI Institute, 309
Palmer Court, Slidell, Louisiana 70458, United States
- Departments of Physiology and
Pharmacology, International American University College of Medicine, Vieux Fort, St. Lucia, WI
| | - Visar Gjeloshi
- Zebrafish Neuroscience Research Consortium (ZNRC) and ZENEREI Institute, 309
Palmer Court, Slidell, Louisiana 70458, United States
| | - Divya Kondaveeti
- Zebrafish Neuroscience Research Consortium (ZNRC) and ZENEREI Institute, 309
Palmer Court, Slidell, Louisiana 70458, United States
| | - Manoj K. Poudel
- Zebrafish Neuroscience Research Consortium (ZNRC) and ZENEREI Institute, 309
Palmer Court, Slidell, Louisiana 70458, United States
- Departments of Physiology and
Pharmacology, International American University College of Medicine, Vieux Fort, St. Lucia, WI
| | - Allan V. Kalueff
- Zebrafish Neuroscience Research Consortium (ZNRC) and ZENEREI Institute, 309
Palmer Court, Slidell, Louisiana 70458, United States
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