1
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Kupp R, Ruff L, Terranova S, Nathan E, Ballereau S, Stark R, Sekhar Reddy Chilamakuri C, Hoffmann N, Wickham-Rahrmann K, Widdess M, Arabzade A, Zhao Y, Varadharajan S, Zheng T, Murugesan M, Pfister SM, Kawauchi D, Pajtler KW, Deneen B, Mack SC, Masih KE, Gryder BE, Khan J, Gilbertson RJ. ZFTA Translocations Constitute Ependymoma Chromatin Remodeling and Transcription Factors. Cancer Discov 2021; 11:2216-2229. [PMID: 33741711 PMCID: PMC8918067 DOI: 10.1158/2159-8290.cd-20-1052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 07/16/2020] [Revised: 01/06/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
ZFTA (C11orf95)-a gene of unknown function-partners with a variety of transcriptional coactivators in translocations that drive supratentorial ependymoma, a frequently lethal brain tumor. Understanding the function of ZFTA is key to developing therapies that inhibit these fusion proteins. Here, using a combination of transcriptomics, chromatin immunoprecipitation sequencing, and proteomics, we interrogated a series of deletion-mutant genes to identify a tripartite transformation mechanism of ZFTA-containing fusions, including: spontaneous nuclear translocation, extensive chromatin binding, and SWI/SNF, SAGA, and NuA4/Tip60 HAT chromatin modifier complex recruitment. Thereby, ZFTA tethers fusion proteins across the genome, modifying chromatin to an active state and enabling its partner transcriptional coactivators to promote promiscuous expression of a transforming transcriptome. Using mouse models, we validate further those elements of ZFTA-fusion proteins that are critical for transformation-including ZFTA zinc fingers and partner gene transactivation domains-thereby unmasking vulnerabilities for therapeutic targeting. SIGNIFICANCE: Ependymomas are hard-to-treat brain tumors driven by translocations between ZFTA and a variety of transcriptional coactivators. We dissect the transforming mechanism of these fusion proteins and identify protein domains indispensable for tumorigenesis, thereby providing insights into the molecular basis of ependymoma tumorigenesis and vulnerabilities for therapeutic targeting.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Robert Kupp
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Lisa Ruff
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Sabrina Terranova
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Erica Nathan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Stephane Ballereau
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Rory Stark
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | | | - Nadin Hoffmann
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | | | - Marcus Widdess
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Amir Arabzade
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Yanhua Zhao
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Srinidhi Varadharajan
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Tuyu Zheng
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mohankumar Murugesan
- Centre for Stem Cell Research, Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Kristian W Pajtler
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Deneen
- Cancer and Cell Biology Program, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
| | - Stephen C Mack
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Katherine E Masih
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Berkley E Gryder
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England.
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, England
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2
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Shu S, Wu HJ, Ge JY, Zeid R, Harris IS, Jovanović B, Murphy K, Wang B, Qiu X, Endress JE, Reyes J, Lim K, Font-Tello A, Syamala S, Xiao T, Reddy Chilamakuri CS, Papachristou EK, D'Santos C, Anand J, Hinohara K, Li W, McDonald TO, Luoma A, Modiste RJ, Nguyen QD, Michel B, Cejas P, Kadoch C, Jaffe JD, Wucherpfennig KW, Qi J, Liu XS, Long H, Brown M, Carroll JS, Brugge JS, Bradner J, Michor F, Polyak K. Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. Mol Cell 2020; 78:1096-1113.e8. [PMID: 32416067 PMCID: PMC7306005 DOI: 10.1016/j.molcel.2020.04.027] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [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: 11/25/2019] [Revised: 03/11/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022]
Abstract
BET bromodomain inhibitors (BBDIs) are candidate therapeutic agents for triple-negative breast cancer (TNBC) and other cancer types, but inherent and acquired resistance to BBDIs limits their potential clinical use. Using CRISPR and small-molecule inhibitor screens combined with comprehensive molecular profiling of BBDI response and resistance, we identified synthetic lethal interactions with BBDIs and genes that, when deleted, confer resistance. We observed synergy with regulators of cell cycle progression, YAP, AXL, and SRC signaling, and chemotherapeutic agents. We also uncovered functional similarities and differences among BRD2, BRD4, and BRD7. Although deletion of BRD2 enhances sensitivity to BBDIs, BRD7 loss leads to gain of TEAD-YAP chromatin binding and luminal features associated with BBDI resistance. Single-cell RNA-seq, ATAC-seq, and cellular barcoding analysis of BBDI responses in sensitive and resistant cell lines highlight significant heterogeneity among samples and demonstrate that BBDI resistance can be pre-existing or acquired.
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Affiliation(s)
- Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Hua-Jun Wu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02215, USA
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Isaac S Harris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Binbin Wang
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jennifer E Endress
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Jaime Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sudeepa Syamala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tengfei Xiao
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Evangelia K Papachristou
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Clive D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Jayati Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Thomas O McDonald
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adrienne Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca J Modiste
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brittany Michel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - X Shirley Liu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - James Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA.
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3
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Nagarajan S, Rao SV, Sutton J, Cheeseman D, Dunn S, Papachristou EK, Prada JEG, Couturier DL, Kumar S, Kishore K, Chilamakuri CSR, Glont SE, Goode EA, Brodie C, Guppy N, Natrajan R, Bruna A, Caldas C, Russell A, Siersbæk R, Yusa K, Chernukhin I, Carroll JS. Author Correction: ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response. Nat Genet 2020; 52:354. [PMID: 32005967 DOI: 10.1038/s41588-020-0582-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
| | - Shalini V Rao
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Joseph Sutton
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Danya Cheeseman
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Sanjeev Kumar
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kamal Kishore
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | - Cara Brodie
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alejandra Bruna
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alasdair Russell
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rasmus Siersbæk
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, UK
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Igor Chernukhin
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
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4
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Nagarajan S, Rao SV, Sutton J, Cheeseman D, Dunn S, Papachristou EK, Prada JEG, Couturier DL, Kumar S, Kishore K, Chilamakuri CSR, Glont SE, Archer Goode E, Brodie C, Guppy N, Natrajan R, Bruna A, Caldas C, Russell A, Siersbæk R, Yusa K, Chernukhin I, Carroll JS. ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response. Nat Genet 2020; 52:187-197. [PMID: 31913353 PMCID: PMC7116647 DOI: 10.1038/s41588-019-0541-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022]
Abstract
Using genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screens to understand endocrine drug resistance, we discovered ARID1A and other SWI/SNF complex components as the factors most critically required for response to two classes of estrogen receptor-alpha (ER) antagonists. In this context, SWI/SNF-specific gene deletion resulted in drug resistance. Unexpectedly, ARID1A was also the top candidate in regard to response to the bromodomain and extraterminal domain inhibitor JQ1, but in the opposite direction, with loss of ARID1A sensitizing breast cancer cells to bromodomain and extraterminal domain inhibition. We show that ARID1A is a repressor that binds chromatin at ER cis-regulatory elements. However, ARID1A elicits repressive activity in an enhancer-specific, but forkhead box A1-dependent and active, ER-independent manner. Deletion of ARID1A resulted in loss of histone deacetylase 1 binding, increased histone 4 lysine acetylation and subsequent BRD4-driven transcription and growth. ARID1A mutations are more frequent in treatment-resistant disease, and our findings provide mechanistic insight into this process while revealing rational treatment strategies for these patients.
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Affiliation(s)
| | - Shalini V Rao
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Joseph Sutton
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Danya Cheeseman
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Sanjeev Kumar
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kamal Kishore
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | - Cara Brodie
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alejandra Bruna
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alasdair Russell
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rasmus Siersbæk
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, UK
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Igor Chernukhin
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
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5
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Cidado J, Boiko S, Proia T, Ferguson D, Criscione SW, San Martin M, Pop-Damkov P, Su N, Roamio Franklin VN, Sekhar Reddy Chilamakuri C, D'Santos CS, Shao W, Saeh JC, Koch R, Weinstock DM, Zinda M, Fawell SE, Drew L. AZD4573 Is a Highly Selective CDK9 Inhibitor That Suppresses MCL-1 and Induces Apoptosis in Hematologic Cancer Cells. Clin Cancer Res 2019; 26:922-934. [DOI: 10.1158/1078-0432.ccr-19-1853] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/27/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022]
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6
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Peluffo G, Subedee A, Harper NW, Kingston N, Jovanović B, Flores F, Stevens LE, Beca F, Trinh A, Chilamakuri CSR, Papachristou EK, Murphy K, Su Y, Marusyk A, D'Santos CS, Rueda OM, Beck AH, Caldas C, Carroll JS, Polyak K. EN1 Is a Transcriptional Dependency in Triple-Negative Breast Cancer Associated with Brain Metastasis. Cancer Res 2019; 79:4173-4183. [PMID: 31239270 PMCID: PMC6698222 DOI: 10.1158/0008-5472.can-18-3264] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/28/2019] [Accepted: 06/14/2019] [Indexed: 11/16/2022]
Abstract
To define transcriptional dependencies of triple-negative breast cancer (TNBC), we identified transcription factors highly and specifically expressed in primary TNBCs and tested their requirement for cell growth in a panel of breast cancer cell lines. We found that EN1 (engrailed 1) is overexpressed in TNBCs and its downregulation preferentially and significantly reduced viability and tumorigenicity in TNBC cell lines. By integrating gene expression changes after EN1 downregulation with EN1 chromatin binding patterns, we identified genes involved in WNT and Hedgehog signaling, neurogenesis, and axonal guidance as direct EN1 transcriptional targets. Quantitative proteomic analyses of EN1-bound chromatin complexes revealed association with transcriptional repressors and coactivators including TLE3, TRIM24, TRIM28, and TRIM33. High expression of EN1 correlated with short overall survival and increased risk of developing brain metastases in patients with TNBC. Thus, EN1 is a prognostic marker and a potential therapeutic target in TNBC. SIGNIFICANCE: These findings show that the EN1 transcription factor regulates neurogenesis-related genes and is associated with brain metastasis in triple-negative breast cancer.
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Affiliation(s)
- Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Ashim Subedee
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
- BBS Program, Harvard Medical School, Boston, Massachusetts
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
| | - Natalie Kingston
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Felipe Flores
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Francisco Beca
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
| | - Ying Su
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Andriy Marusyk
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Clive S D'Santos
- Cambridge Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Oscar M Rueda
- Cambridge Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Andrew H Beck
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Carlos Caldas
- Cambridge Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jason S Carroll
- Cambridge Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- BBS Program, Harvard Medical School, Boston, Massachusetts
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7
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Pasala C, Chilamakuri CSR, Katari SK, Nalamolu RM, Bitla AR, Amineni U. Epitope-driven common subunit vaccine design against H. pylori strains. J Biomol Struct Dyn 2018; 37:3740-3750. [DOI: 10.1080/07391102.2018.1526714] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chiranjeevi Pasala
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, AP, India
| | | | - Sudheer Kumar Katari
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, AP, India
| | | | - Aparna R. Bitla
- Department of Biochemistry, SVIMS University, Tirupati, AP, India
| | - Umamaheswari Amineni
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, AP, India
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8
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Tomic G, Morrissey E, Kozar S, Ben-Moshe S, Hoyle A, Azzarelli R, Kemp R, Chilamakuri CSR, Itzkovitz S, Philpott A, Winton DJ. Phospho-regulation of ATOH1 Is Required for Plasticity of Secretory Progenitors and Tissue Regeneration. Cell Stem Cell 2018; 23:436-443.e7. [PMID: 30100168 PMCID: PMC6138952 DOI: 10.1016/j.stem.2018.07.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/25/2018] [Accepted: 07/06/2018] [Indexed: 01/07/2023]
Abstract
The intestinal epithelium is largely maintained by self-renewing stem cells but with apparently committed progenitors also contributing, particularly following tissue damage. However, the mechanism of, and requirement for, progenitor plasticity in mediating pathological response remain unknown. Here we show that phosphorylation of the transcription factor Atoh1 is required for both the contribution of secretory progenitors to the stem cell pool and for a robust regenerative response. As confirmed by lineage tracing, Atoh1+ cells (Atoh1(WT)CreERT2 mice) give rise to multilineage intestinal clones both in the steady state and after tissue damage. In a phosphomutant Atoh1(9S/T-A)CreERT2 line, preventing phosphorylation of ATOH1 protein acts to promote secretory differentiation and inhibit the contribution of progenitors to self-renewal. Following chemical colitis, Atoh1+ cells of Atoh1(9S/T-A)CreERT2 mice have reduced clonogenicity that affects overall regeneration. Progenitor plasticity maintains robust self-renewal in the intestinal epithelium, and the balance between stem and progenitor fate is directly coordinated by ATOH1 multisite phosphorylation.
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Affiliation(s)
- Goran Tomic
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Edward Morrissey
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sarah Kozar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alice Hoyle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Roberta Azzarelli
- Department of Oncology, Hutchison/Medical Research Council (MRC) Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Richard Kemp
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Philpott
- Department of Oncology, Hutchison/Medical Research Council (MRC) Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.
| | - Douglas J Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
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9
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Pasala C, Chilamakuri CSR, Katari SK, Nalamolu RM, Bitla AR, Umamaheswari A. An in silico study: Novel targets for potential drug and vaccine design against drug resistant H. pylori. Microb Pathog 2018; 122:156-161. [DOI: 10.1016/j.micpath.2018.05.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 05/19/2018] [Accepted: 05/22/2018] [Indexed: 02/08/2023]
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10
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Papachristou EK, Kishore K, Holding AN, Harvey K, Roumeliotis TI, Chilamakuri CSR, Omarjee S, Chia KM, Swarbrick A, Lim E, Markowetz F, Eldridge M, Siersbaek R, D'Santos CS, Carroll JS. A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes. Nat Commun 2018; 9:2311. [PMID: 29899353 PMCID: PMC5998130 DOI: 10.1038/s41467-018-04619-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/03/2018] [Indexed: 11/10/2022] Open
Abstract
Understanding the dynamics of endogenous protein-protein interactions in complex networks is pivotal in deciphering disease mechanisms. To enable the in-depth analysis of protein interactions in chromatin-associated protein complexes, we have previously developed a method termed RIME (Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins). Here, we present a quantitative multiplexed method (qPLEX-RIME), which integrates RIME with isobaric labelling and tribrid mass spectrometry for the study of protein interactome dynamics in a quantitative fashion with increased sensitivity. Using the qPLEX-RIME method, we delineate the temporal changes of the Estrogen Receptor alpha (ERα) interactome in breast cancer cells treated with 4-hydroxytamoxifen. Furthermore, we identify endogenous ERα-associated proteins in human Patient-Derived Xenograft tumours and in primary human breast cancer clinical tissue. Our results demonstrate that the combination of RIME with isobaric labelling offers a powerful tool for the in-depth and quantitative characterisation of protein interactome dynamics, which is applicable to clinical samples.
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Affiliation(s)
- Evangelia K Papachristou
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Andrew N Holding
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Kate Harvey
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | | | | | - Soleilmane Omarjee
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Kee Ming Chia
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Alex Swarbrick
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, UNSW, Sydney, NSW 2052, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, UNSW, Sydney, NSW 2052, Australia
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Matthew Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Rasmus Siersbaek
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Clive S D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK. Clive.D'
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
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11
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de Santiago I, Liu W, Yuan K, O'Reilly M, Chilamakuri CSR, Ponder BAJ, Meyer KB, Markowetz F. BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes. Genome Biol 2017; 18:39. [PMID: 28235418 PMCID: PMC5326502 DOI: 10.1186/s13059-017-1165-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/01/2017] [Indexed: 02/07/2023] Open
Abstract
Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods of detecting an allelic imbalance assume diploid genomes. This assumption severely limits their applicability to cancer samples with frequent DNA copy-number changes. Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of background allele frequency on the observed ChIP-seq read counts. BaalChIP allows the joint analysis of multiple ChIP-seq samples across a single variant and outperforms competing approaches in simulations. Using 548 ENCODE ChIP-seq and six targeted FAIRE-seq samples, we show that BaalChIP effectively corrects allele-specific analysis for copy-number variation and increases the power to detect putative cis-acting regulatory variants in cancer genomes.
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Affiliation(s)
- Ines de Santiago
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
- Present Address: Seven Bridges Genomics LTD, UK. 101 Euston Road NW1 2RA, London, UK
| | - Wei Liu
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
- Present Address: Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ke Yuan
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
- Present Address: School of Computing Science, University of Glasgow, Glasgow, UK
| | - Martin O'Reilly
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | | | - Bruce A J Ponder
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - Kerstin B Meyer
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK.
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK.
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Chilamakuri CSR, Lorenz S, Madoui MA, Vodák D, Sun J, Hovig E, Myklebost O, Meza-Zepeda LA. Performance comparison of four exome capture systems for deep sequencing. BMC Genomics 2014; 15:449. [PMID: 24912484 PMCID: PMC4092227 DOI: 10.1186/1471-2164-15-449] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent developments in deep (next-generation) sequencing technologies are significantly impacting medical research. The global analysis of protein coding regions in genomes of interest by whole exome sequencing is a widely used application. Many technologies for exome capture are commercially available; here we compare the performance of four of them: NimbleGen's SeqCap EZ v3.0, Agilent's SureSelect v4.0, Illumina's TruSeq Exome, and Illumina's Nextera Exome, all applied to the same human tumor DNA sample. RESULTS Each capture technology was evaluated for its coverage of different exome databases, target coverage efficiency, GC bias, sensitivity in single nucleotide variant detection, sensitivity in small indel detection, and technical reproducibility. In general, all technologies performed well; however, our data demonstrated small, but consistent differences between the four capture technologies. Illumina technologies cover more bases in coding and untranslated regions. Furthermore, whereas most of the technologies provide reduced coverage in regions with low or high GC content, the Nextera technology tends to bias towards target regions with high GC content. CONCLUSIONS We show key differences in performance between the four technologies. Our data should help researchers who are planning exome sequencing to select appropriate exome capture technology for their particular application.
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Metsu S, Rooms L, Rainger J, Taylor MS, Bengani H, Wilson DI, Chilamakuri CSR, Morrison H, Vandeweyer G, Reyniers E, Douglas E, Thompson G, Haan E, Gecz J, FitzPatrick DR, Kooy RF. FRA2A is a CGG repeat expansion associated with silencing of AFF3. PLoS Genet 2014; 10:e1004242. [PMID: 24763282 PMCID: PMC3998887 DOI: 10.1371/journal.pgen.1004242] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 02/02/2014] [Indexed: 11/19/2022] Open
Abstract
Folate-sensitive fragile sites (FSFS) are a rare cytogenetically visible subset of dynamic mutations. Of the eight molecularly characterized FSFS, four are associated with intellectual disability (ID). Cytogenetic expression results from CGG tri-nucleotide-repeat expansion mutation associated with local CpG hypermethylation and transcriptional silencing. The best studied is the FRAXA site in the FMR1 gene, where large expansions cause fragile X syndrome, the most common inherited ID syndrome. Here we studied three families with FRA2A expression at 2q11 associated with a wide spectrum of neurodevelopmental phenotypes. We identified a polymorphic CGG repeat in a conserved, brain-active alternative promoter of the AFF3 gene, an autosomal homolog of the X-linked AFF2/FMR2 gene: Expansion of the AFF2 CGG repeat causes FRAXE ID. We found that FRA2A-expressing individuals have mosaic expansions of the AFF3 CGG repeat in the range of several hundred repeat units. Moreover, bisulfite sequencing and pyrosequencing both suggest AFF3 promoter hypermethylation. cSNP-analysis demonstrates monoallelic expression of the AFF3 gene in FRA2A carriers thus predicting that FRA2A expression results in functional haploinsufficiency for AFF3 at least in a subset of tissues. By whole-mount in situ hybridization the mouse AFF3 ortholog shows strong regional expression in the developing brain, somites and limb buds in 9.5–12.5dpc mouse embryos. Our data suggest that there may be an association between FRA2A and a delay in the acquisition of motor and language skills in the families studied here. However, additional cases are required to firmly establish a causal relationship. Some human genetic diseases are caused by dynamic mutations, or expansions of a short repeated sequence in the genome that can be unstably passed on from generation to generation. A subset of these dynamic mutations known as fragile sites can be seen as a break or gap on the chromosome when cells are cultured under specific conditions. To date eight folate-sensitive fragile sites (FSFS) have been characterized, and all are due to CGG-repeat expansions within the 5′ UTR or promoter region of the respective gene. When the repeat expands in size, it becomes hypermethylated and the adjacent gene or genes are transcriptionally silenced. For at least four of the eight known fragile sites this silencing of the associated gene(s) lead to intellectual disability syndromes such as fragile X. In this work we describe molecular characterization of an autosomal FSFS called FRA2A on chromosome 2. As the molecular cause of FRA2A, we identify an expansion of a CGG repeat which subsequently results in silencing of the neighbouring gene AFF3. This gene is one of the four autosomal paralogss of the AFF2/FMR2 gene which, when mutated, is the cause of the FRAXE syndrome. We find that FRA2A expression is associated with highly variable developmental anomalies in the three FRA2A families studied.
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Affiliation(s)
- Sofie Metsu
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Liesbeth Rooms
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jacqueline Rainger
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin S. Taylor
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Hemant Bengani
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - David I. Wilson
- University of Southampton, Centre for Human Development, Stem Cells and Regeneration, Human Genetics, Southampton, United Kingdom
| | | | - Harris Morrison
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Edwin Reyniers
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Geoffrey Thompson
- Department of Paediatrics, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Paediatrics and Child Health, Flinders University, Adelaide, South Australia, Australia
| | - Eric Haan
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- South Australian Clinical Genetic Service, SA Pathology (at Women's and Children's Hospital), Adelaide, South Australia, Australia
| | - Jozef Gecz
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Department of Paediatrics, The University of Adelaide, Adelaide, South Australia, Australia
| | - David R. FitzPatrick
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (DRF); (RFK)
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
- * E-mail: (DRF); (RFK)
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Sharma Y, Chilamakuri CSR, Bakke M, Lenhard B. Computational characterization of modes of transcriptional regulation of nuclear receptor genes. PLoS One 2014; 9:e88880. [PMID: 24551185 PMCID: PMC3923872 DOI: 10.1371/journal.pone.0088880] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/15/2014] [Indexed: 11/18/2022] Open
Abstract
Background Nuclear receptors are a large structural class of transcription factors that act with their co-regulators and repressors to maintain a variety of biological and physiological processes such as metabolism, development and reproduction. They are activated through the binding of small ligands, which can be replaced by drug molecules, making nuclear receptors promising drug targets. Transcriptional regulation of the genes that encode them is central to gaining a deeper understanding of the diversity of their biochemical and biophysical roles and their role in disease and therapy. Even though they share evolutionary history, nuclear receptor genes have fundamentally different expression patterns, ranging from ubiquitously expressed to tissue-specific and spatiotemporally complex. However, current understanding of regulation in nuclear receptor gene family is still nascent. Methodology/Principal Findings In this study, we investigate the relationship between long-range regulation of nuclear receptor family and their known functionality. Towards this goal, we identify the nuclear receptor genes that are potential targets based on counts of highly conserved non-coding elements. We validate our results using publicly available expression (RNA-seq) and histone modification (ChIP-seq) data from the ENCODE project. We find that nuclear receptor genes involved in developmental roles show strong evidence of long-range mechanism of transcription regulation with distinct cis-regulatory content they feature clusters of highly conserved non-coding elements distributed in regions spanning several Megabases, long and multiple CpG islands, bivalent promoter marks and statistically significant higher enrichment of enhancer mark around their gene loci. On the other hand nuclear receptor genes that are involved in tissue-specific roles lack these features, having simple transcriptional controls and a greater variety of mechanisms for producing paralogs. We further examine the combinatorial patterns of histone maps associated with dynamic functional elements in order to explore the regulatory landscape of the gene family. The results show that our proposed classification capturing long-range regulation is strongly indicative of the functional roles of the nuclear receptors compared to existing classifications. Conclusions/Significanc We present a new classification for nuclear receptor gene family capturing whether a nuclear receptor is a possible target of long-range regulation or not. We compare our classification to existing structural (mechanism of action) and homology-based classifications. Our results show that understanding long-range regulation of nuclear receptors can provide key insight into their functional roles as well as evolutionary history; and this strongly merits further study.
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Affiliation(s)
- Yogita Sharma
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Marit Bakke
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, and MRC Clinical Sciences Centre, London, United Kingdom
- Department of Informatics, University of Bergen, Bergen, Norway
- * E-mail:
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