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Murphy C, Gornés Pons G, Keogh A, Ryan L, McCarra L, Jose CM, Kesar S, Nicholson S, Fitzmaurice GJ, Ryan R, Young V, Cuffe S, Finn SP, Gray SG. An Analysis of JADE2 in Non-Small Cell Lung Cancer (NSCLC). Biomedicines 2023; 11:2576. [PMID: 37761019 PMCID: PMC10526426 DOI: 10.3390/biomedicines11092576] [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: 04/12/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 09/29/2023] Open
Abstract
The JADE family comprises three members encoded by individual genes and roles for these proteins have been identified in chromatin remodeling, cell cycle progression, cell regeneration and the DNA damage response. JADE family members, and in particular JADE2 have not been studied in any great detail in cancer. Using a series of standard biological and bioinformatics approaches we investigated JADE2 expression in surgically resected non-small cell lung cancer (NSCLC) for both mRNA and protein to examine for correlations between JADE2 expression and overall survival. Additional correlations were identified using bioinformatic analyses on multiple online datasets. Our analysis demonstrates that JADE2 expression is significantly altered in NSCLC. High expression of JADE2 is associated with a better 5-year overall survival. Links between JADE2 mRNA expression and a number of mutated genes were identified, and associations between JADE2 expression and tumor mutational burden and immune cell infiltration were explored. Potential new drugs that can target JADE2 were identified. The results of this biomarker-driven study suggest that JADE2 may have potential clinical utility in the diagnosis, prognosis and stratification of patients into various therapeutically targetable options.
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Affiliation(s)
- Ciara Murphy
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
| | - Glòria Gornés Pons
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Faculty of Biology, University of Barcelona, 08025 Barcelona, Spain
| | - Anna Keogh
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Lisa Ryan
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Lorraine McCarra
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Chris Maria Jose
- School of Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Shagun Kesar
- School of Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Gerard J. Fitzmaurice
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Ronan Ryan
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Vincent Young
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Sinead Cuffe
- HOPE Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Stephen P. Finn
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Clinical Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
- School of Biological Sciences, Technological University Dublin, D07 XT95 Dublin, Ireland
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2
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Yu H, He J, Liu W, Feng S, Gao L, Xu Y, Zhang Y, Hou X, Zhou Y, Yang L, Wang X. The Transcriptional Coactivator, ALL1-Fused Gene From Chromosome 9, Simultaneously Sustains Hypoxia Tolerance and Metabolic Advantages in Liver Cancer. Hepatology 2021; 74:1952-1970. [PMID: 33928666 DOI: 10.1002/hep.31870] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/21/2021] [Accepted: 04/09/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND AND AIMS Proteins that recognize epigenetic modifications function as mediators to interpret epigenetic codes. Hypoxia response and metabolic rewiring are two major events during cancer progression. However, whether and how the epigenetic regulator integrates hypoxia response and metabolism together remain open for study. APPROACH AND RESULTS We data mined the clinical association of 33 histone lysine acetylation reader proteins with liver cancer and found that ALL1-fused gene from chromosome 9 (AF9) is up-regulated in cancer and correlates with tumor stage and poor prognosis. Conditional deletion of Af9 in mouse liver resulted in decreased tumor formation induced by c-MET proto-oncogene/β-catenin. Loss of AF9 heavily impaired cell proliferation and completely blocked solid tumor formation. We further discovered that AF9 formed a positive feedback circuit with hypoxia-inducible factor 1 alpha (HIF1α) and also stabilized MYC proto-oncogene (cMyc). Mechanically, AF9 interacted with HIF1α and targeted HIF1A promoter whereas AF9 recognized cMyc acetylation at K148, protected cMyc phosphorylation at S62, and then stabilized cMyc, which, in turn, up-regulates phosphofructokinase, platelet expression. Otherwise, knockout of Af9 in mouse hepatocytes increased the infiltration of CD8+ T cells, which is linked to the down-regulation of lactate dehydrogenase A. CONCLUSIONS AF9 is up-regulated to promote gene expression of hypoxia tolerance and glycolysis by simultaneously forming a complex with HIF1α and recognizing acetylated cMyc. Our results establish the oncogenic role of AF9 in human liver cancer, which could be a potential target for designing drugs against liver cancer.
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Affiliation(s)
- Hua Yu
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jun He
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Wei Liu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuya Feng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Li Gao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yingying Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yawei Zhang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Xuyang Hou
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yan Zhou
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Leping Yang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Xiongjun Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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3
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Chellamuthu A, Gray SG. The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer. Cells 2020; 9:cells9081758. [PMID: 32708015 PMCID: PMC7463552 DOI: 10.3390/cells9081758] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine is often associated as an epigenetic modifier in DNA. However, it is also found increasingly in a plethora of RNA species, predominantly transfer RNAs, but increasingly found in cytoplasmic and mitochondrial ribosomal RNAs, enhancer RNAs, and a number of long noncoding RNAs. Moreover, this modification can also be found in messenger RNAs and has led to an increasing appreciation that RNA methylation can functionally regulate gene expression and cellular activities. In mammalian cells, the addition of m5C to RNA cytosines is carried out by enzymes of the NOL1/NOP2/SUN domain (NSUN) family as well as the DNA methyltransferase homologue DNMT2. In this regard, NSUN2 is a critical RNA methyltransferase for adding m5C to mRNA. In this review, using non-small cell lung cancer and other cancers as primary examples, we discuss the recent developments in the known functions of this RNA methyltransferase and its potential critical role in cancer.
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Affiliation(s)
- Anitha Chellamuthu
- Department of Clinical Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland;
| | - Steven G. Gray
- Department of Clinical Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland;
- Thoracic Oncology Research Group, St. James’s Hospital, Dublin D08 RX0X, Ireland
- Correspondence:
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4
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Liu L, Damerell DR, Koukouflis L, Tong Y, Marsden BD, Schapira M. UbiHub: a data hub for the explorers of ubiquitination pathways. Bioinformatics 2020; 35:2882-2884. [PMID: 30601939 PMCID: PMC6691330 DOI: 10.1093/bioinformatics/bty1067] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/03/2018] [Accepted: 12/28/2018] [Indexed: 01/01/2023] Open
Abstract
Motivation Protein ubiquitination plays a central role in important cellular machineries such as protein degradation or chromatin-mediated signaling. With the recent discovery of the first potent ubiquitin-specific protease inhibitors, and the maturation of proteolysis targeting chimeras as promising chemical tools to exploit the ubiquitin-proteasome system, protein target classes associated with ubiquitination pathways are becoming the focus of intense drug-discovery efforts. Results We have developed UbiHub, an online resource that can be used to visualize a diverse array of biological, structural and chemical data on phylogenetic trees of human protein families involved in ubiquitination signaling, including E3 ligases and deubiquitinases. This interface can inform target prioritization and drug design, and serves as a navigation tool for medicinal chemists, structural and cell biologists exploring ubiquitination pathways. Availability and implementation https://ubihub.thesgc.org.
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Affiliation(s)
- Lihua Liu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - David R Damerell
- Structural Genomics Consortium, University of Oxford, Headington Oxford, Oxfordshire, UK
| | - Leonidas Koukouflis
- Structural Genomics Consortium, University of Oxford, Headington Oxford, Oxfordshire, UK
| | - Yufeng Tong
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Brian D Marsden
- Structural Genomics Consortium, University of Oxford, Headington Oxford, Oxfordshire, UK.,Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Headington, Oxford, Oxfordshire, UK
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
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5
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Simhadri C, Daze KD, Douglas SF, Milosevich N, Monjas L, Dev A, Brown TM, Hirsch AKH, Wulff JE, Hof F. Rational Adaptation of L3MBTL1 Inhibitors to Create Small‐Molecule Cbx7 Antagonists. ChemMedChem 2019; 14:1444-1456. [DOI: 10.1002/cmdc.201900021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/30/2019] [Indexed: 12/14/2022]
Affiliation(s)
| | - Kevin D. Daze
- Department of ChemistryUniversity of Victoria Victoria BC V8P 5C2 Canada
| | - Sarah F. Douglas
- Department of ChemistryUniversity of Victoria Victoria BC V8P 5C2 Canada
| | - Natalia Milosevich
- Department of ChemistryUniversity of Victoria Victoria BC V8P 5C2 Canada
| | - Leticia Monjas
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Amarjot Dev
- Department of ChemistryUniversity of Victoria Victoria BC V8P 5C2 Canada
| | - Tyler M. Brown
- Department of ChemistryUniversity of Victoria Victoria BC V8P 5C2 Canada
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
- Present affiliation: Department for Drug Design and Optimization and Department of Pharmacy, Helmholtz Institute for Pharmaceutical Research (HIPS)—Helmholtz Centre for Infection Research (HZI)Saarland University Campus Building E 8.1 66123 Saarbrücken Germany
| | - Jeremy E. Wulff
- Department of ChemistryUniversity of Victoria Victoria BC V8P 5C2 Canada
| | - Fraser Hof
- Department of ChemistryUniversity of Victoria Victoria BC V8P 5C2 Canada
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Abstract
Following the elucidation of the human genome, chemogenomics emerged in the beginning of the twenty-first century as an interdisciplinary research field with the aim to accelerate target and drug discovery by making best usage of the genomic data and the data linkable to it. What started as a systematization approach within protein target families now encompasses all types of chemical compounds and gene products. A key objective of chemogenomics is the establishment, extension, analysis, and prediction of a comprehensive SAR matrix which by application will enable further systematization in drug discovery. Herein we outline future perspectives of chemogenomics including the extension to new molecular modalities, or the potential extension beyond the pharma to the agro and nutrition sectors, and the importance for environmental protection. The focus is on computational sciences with potential applications for compound library design, virtual screening, hit assessment, analysis of phenotypic screens, lead finding and optimization, and systems biology-based prediction of toxicology and translational research.
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Affiliation(s)
- Edgar Jacoby
- Janssen Research & Development, Beerse, Belgium.
| | - J B Brown
- Life Science Informatics Research Unit, Laboratory of Molecular Biosciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
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7
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Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR. The ChEMBL database in 2017. Nucleic Acids Res 2016; 45:D945-D954. [PMID: 27899562 PMCID: PMC5210557 DOI: 10.1093/nar/gkw1074] [Citation(s) in RCA: 1386] [Impact Index Per Article: 173.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/21/2016] [Accepted: 10/30/2016] [Indexed: 11/14/2022] Open
Abstract
ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 and 2014 Nucleic Acids Research Database Issues. Since then, alongside the continued extraction of data from the medicinal chemistry literature, new sources of bioactivity data have also been added to the database. These include: deposited data sets from neglected disease screening; crop protection data; drug metabolism and disposition data and bioactivity data from patents. A number of improvements and new features have also been incorporated. These include the annotation of assays and targets using ontologies, the inclusion of targets and indications for clinical candidates, addition of metabolic pathways for drugs and calculation of structural alerts. The ChEMBL data can be accessed via a web-interface, RDF distribution, data downloads and RESTful web-services.
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Affiliation(s)
- Anna Gaulton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Anne Hersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Michał Nowotka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - A Patrícia Bento
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jon Chambers
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - David Mendez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Prudence Mutowo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Francis Atkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Louisa J Bellis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Elena Cibrián-Uhalte
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Mark Davies
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Nathan Dedman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Anneli Karlsson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - María Paula Magariños
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - John P Overington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - George Papadatos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ines Smit
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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8
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Shah MA, Denton EL, Arrowsmith CH, Lupien M, Schapira M. A global assessment of cancer genomic alterations in epigenetic mechanisms. Epigenetics Chromatin 2014; 7:29. [PMID: 25484917 PMCID: PMC4258301 DOI: 10.1186/1756-8935-7-29] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/14/2014] [Indexed: 12/22/2022] Open
Abstract
Background The notion that epigenetic mechanisms may be central to cancer initiation and progression is supported by recent next-generation sequencing efforts revealing that genes involved in chromatin-mediated signaling are recurrently mutated in cancer patients. Results Here, we analyze mutational and transcriptional profiles from TCGA and the ICGC across a collection 441 chromatin factors and histones. Chromatin factors essential for rapid replication are frequently overexpressed, and those that maintain genome stability frequently mutated. We identify novel mutation hotspots such as K36M in histone H3.1, and uncover a general trend in which transcriptional profiles and somatic mutations in tumor samples favor increased transcriptionally repressive histone methylation, and defective chromatin remodeling. Conclusions This unbiased approach confirms previously published data, uncovers novel cancer-associated aberrations targeting epigenetic mechanisms, and justifies continued monitoring of chromatin-related alterations as a class, as more cancer types and distinct cancer stages are represented in cancer genomics data repositories. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-7-29) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad A Shah
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada
| | - Emily L Denton
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Courant Institute, New York University, 12th floor, 715 Broadway, New York, 10003 USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, M5G 2M9 ON Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, M5G 2M9 ON Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON Canada
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9
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Liu Y, Liu K, Qin S, Xu C, Min J. Epigenetic targets and drug discovery: part 1: histone methylation. Pharmacol Ther 2014; 143:275-94. [PMID: 24704322 DOI: 10.1016/j.pharmthera.2014.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/24/2014] [Indexed: 01/10/2023]
Abstract
Dynamic chromatin structure is modulated by post-translational modifications on histones, such as acetylation, phosphorylation and methylation. Research on histone methylation has become the most flourishing area of epigenetics in the past fourteen years, and a large amount of data has been accumulated regarding its biology and disease implications. Correspondingly, a lot of efforts have been made to develop small molecule compounds that can specifically modulate histone methyltransferases and methylation reader proteins, aiming for potential therapeutic drugs. Here, we summarize recent progress in chemical probe and drug discovery of histone methyltransferases and methylation reader proteins. For each target, we will review their biological/biochemical functions first, and then focus on their disease implications and drug discovery. We can also see that structure-based compound design and optimization plays a critical role in facilitating the development of highly potent and selective chemical probes and inhibitors for these targets.
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Affiliation(s)
- Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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10
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Sanchez R, Meslamani J, Zhou MM. The bromodomain: from epigenome reader to druggable target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:676-85. [PMID: 24686119 DOI: 10.1016/j.bbagrm.2014.03.011] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 03/15/2014] [Accepted: 03/23/2014] [Indexed: 10/25/2022]
Abstract
Lysine acetylation is a fundamental post-translational modification that plays an important role in the control of gene transcription in chromatin in an ordered fashion. The bromodomain, the conserved structural module present in transcription-associated proteins, functions exclusively to recognize acetyl-lysine on histones and non-histone proteins. The structural analyses of bromodomains' recognition of lysine-acetylated peptides derived from histones and cellular proteins provide detailed insights into the differences and unifying features of biological ligand binding selectivity by the bromodomains. Newly developed small-molecule inhibitors targeting bromodomain proteins further highlight the functional importance of bromodomain/acetyl-lysine binding as a key mechanism in orchestrating molecular interactions and regulation in chromatin biology and gene transcription. These new studies argue that modulating bromodomain/acetyl-lysine interactions with small-molecule chemicals offer new opportunities to control gene expression in a wide array of human diseases including cancer and inflammation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Roberto Sanchez
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jamel Meslamani
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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