1
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Hilwi M, Shulman K, Naroditsky I, Feld S, Gross-Cohen M, Boyango I, Soboh S, Vornicova O, Farhoud M, Singh P, Bar-Sela G, Goldberg H, Götte M, Sharrocks AD, Li Y, Sanderson RD, Ilan N, Vlodavsky I. Nuclear localization of heparanase 2 (Hpa2) attenuates breast carcinoma growth and metastasis. Cell Death Dis 2024; 15:232. [PMID: 38519456 PMCID: PMC10959965 DOI: 10.1038/s41419-024-06596-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024]
Abstract
Unlike the intense research effort devoted to exploring the significance of heparanase in cancer, very little attention was given to Hpa2, a close homolog of heparanase. Here, we explored the role of Hpa2 in breast cancer. Unexpectedly, we found that patients endowed with high levels of Hpa2 exhibited a higher incidence of tumor metastasis and survived less than patients with low levels of Hpa2. Immunohistochemical examination revealed that in normal breast tissue, Hpa2 localizes primarily in the cell nucleus. In striking contrast, in breast carcinoma, Hpa2 expression is not only decreased but also loses its nuclear localization and appears diffuse in the cell cytoplasm. Importantly, breast cancer patients in which nuclear localization of Hpa2 is retained exhibited reduced lymph-node metastasis, suggesting that nuclear localization of Hpa2 plays a protective role in breast cancer progression. To examine this possibility, we engineered a gene construct that directs Hpa2 to the cell nucleus (Hpa2-Nuc). Notably, overexpression of Hpa2 in breast carcinoma cells resulted in bigger tumors, whereas targeting Hpa2 to the cell nucleus attenuated tumor growth and tumor metastasis. RNAseq analysis was performed to reveal differentially expressed genes (DEG) in Hpa2-Nuc tumors vs. control. The analysis revealed, among others, decreased expression of genes associated with the hallmark of Kras, beta-catenin, and TNF-alpha (via NFkB) signaling. Our results imply that nuclear localization of Hpa2 prominently regulates gene transcription, resulting in attenuation of breast tumorigenesis. Thus, nuclear Hpa2 may be used as a predictive parameter in personalized medicine for breast cancer patients.
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Affiliation(s)
- Maram Hilwi
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | | | - Inna Naroditsky
- Departments of Pathology, Rambam Health Care Campus, Haifa, Israel
| | - Sari Feld
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Miriam Gross-Cohen
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Ilanit Boyango
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Soaad Soboh
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Olga Vornicova
- Department of Oncology, Ha'amek Medical Center, Afula, Israel
| | - Malik Farhoud
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Preeti Singh
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Gil Bar-Sela
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
- Department of Oncology, Ha'amek Medical Center, Afula, Israel
| | | | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Muenster, Germany
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Yaoyong Li
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ralph D Sanderson
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Neta Ilan
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Israel Vlodavsky
- Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, Israel.
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2
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Peters CJ, Ang Y, Ciccarelli FD, Coles H, Coleman HG, Contino G, Crosby T, Devonshire G, Eldridge M, Freeman A, Grehan N, McCord M, Nutzinger B, Zamani S, Parsons SL, Petty R, Sharrocks AD, Skipworth RJE, Smyth EC, Soomro I, Underwood TJ, Fitzgerald RC. A decade of the Oesophageal Cancer Clinical and Molecular Stratification Consortium. Nat Med 2024; 30:14-16. [PMID: 38114667 DOI: 10.1038/s41591-023-02676-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Affiliation(s)
- C J Peters
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Y Ang
- Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester, UK
| | - F D Ciccarelli
- Cancer Systems Biology, The Francis Crick Institute, London, UK
| | - H Coles
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - H G Coleman
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - G Contino
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - T Crosby
- Velindre University NHS Trust, Cardiff, UK
| | - G Devonshire
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - M Eldridge
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - A Freeman
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - N Grehan
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - M McCord
- Heartburn Cancer UK, Basingstoke, UK
| | - B Nutzinger
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - S Zamani
- Early Cancer Institute, University of Cambridge, Cambridge, UK
| | - S L Parsons
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - R Petty
- School of Medicine, University of Dundee, Dundee, UK
| | - A D Sharrocks
- Division of Molecular and Cellular Function, University of Manchester, Manchester, UK
| | | | - E C Smyth
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - I Soomro
- Nottingham University Hospital, Nottingham, UK
| | - T J Underwood
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - R C Fitzgerald
- Early Cancer Institute, University of Cambridge, Cambridge, UK.
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3
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Owen DJ, Aguilar-Martinez E, Ji Z, Li Y, Sharrocks AD. ZMYM2 controls human transposable element transcription through distinct co-regulatory complexes. eLife 2023; 12:RP86669. [PMID: 37934570 PMCID: PMC10629813 DOI: 10.7554/elife.86669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
ZMYM2 is a zinc finger transcriptional regulator that plays a key role in promoting and maintaining cell identity. It has been implicated in several diseases such as congenital anomalies of the kidney where its activity is diminished and cancer where it participates in oncogenic fusion protein events. ZMYM2 is thought to function through promoting transcriptional repression and here we provide more evidence to support this designation. Here we studied ZMYM2 function in human cells and demonstrate that ZMYM2 is part of distinct chromatin-bound complexes including the established LSD1-CoREST-HDAC1 corepressor complex. We also identify new functional and physical interactions with ADNP and TRIM28/KAP1. The ZMYM2-TRIM28 complex forms in a SUMO-dependent manner and is associated with repressive chromatin. ZMYM2 and TRIM28 show strong functional similarity and co-regulate a large number of genes. However, there are no strong links between ZMYM2-TRIM28 binding events and nearby individual gene regulation. Instead, ZMYM2-TRIM28 appears to regulate genes in a more regionally defined manner within TADs where it can directly regulate co-associated retrotransposon expression. We find that different types of ZMYM2 binding complex associate with and regulate distinct subclasses of retrotransposons, with ZMYM2-ADNP complexes at SINEs and ZMYM2-TRIM28 complexes at LTR elements. We propose a model whereby ZMYM2 acts directly through retrotransposon regulation, which may then potentially affect the local chromatin environment and associated coding gene expression.
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Affiliation(s)
- Danielle J Owen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford RoadManchesterUnited Kingdom
| | - Elisa Aguilar-Martinez
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford RoadManchesterUnited Kingdom
| | - Zongling Ji
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford RoadManchesterUnited Kingdom
| | - Yaoyong Li
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford RoadManchesterUnited Kingdom
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford RoadManchesterUnited Kingdom
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4
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Ogden S, Ahmed I, Yang SH, Fullwood P, Francavilla C, Sharrocks AD. Oncogenic ERRB2 signals through the AP-1 transcription factor to control mesenchymal-like properties of oesophageal adenocarcinoma. NAR Cancer 2023; 5:zcad001. [PMID: 36694726 PMCID: PMC9869078 DOI: 10.1093/narcan/zcad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/08/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Oesophageal adenocarcinoma (OAC) is a deadly disease with poor survival statistics and few targeted therapies available. One of the most common molecular aberrations in OAC is amplification or activation of the gene encoding the receptor tyrosine kinase ERBB2, and ERBB2 is targeted in the clinic for this subset of patients. However, the downstream consequences of these ERBB2 activating events are not well understood. Here we used a combination of phosphoproteomics, open chromatin profiling and transcriptome analysis on cell line models and patient-derived datasets to interrogate the molecular pathways operating downstream from ERBB2. Integrated analysis of these data sets converge on a model where dysregulated ERBB2 signalling is mediated at the transcriptional level by the transcription factor AP-1. AP-1 in turn controls cell behaviour by acting on cohorts of genes that regulate cell migration and adhesion, features often associated with EMT. Our study therefore provides a valuable resource for the cancer cell signalling community and reveals novel molecular determinants underlying the dysregulated behaviour of OAC cells.
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Affiliation(s)
- Samuel Ogden
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Ibrahim Ahmed
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Shen-Hsi Yang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Paul Fullwood
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | | | - Chiara Francavilla
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
- Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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5
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Ahmed I, Yang SH, Ogden S, Zhang W, Li Y, Sharrocks AD. eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways. eLife 2023; 12:80840. [PMID: 36803948 PMCID: PMC9998086 DOI: 10.7554/elife.80840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/20/2023] [Indexed: 02/22/2023] Open
Abstract
Cancer is driven by both genetic and epigenetic changes that impact on gene expression profiles and the resulting tumourigenic phenotype. Enhancers are transcriptional regulatory elements that are key to our understanding of how this rewiring of gene expression is achieved in cancer cells. Here, we have harnessed the power of RNA-seq data from hundreds of patients with oesophageal adenocarcinoma (OAC) or its precursor state Barrett's oesophagus coupled with open chromatin maps to identify potential enhancer RNAs and their associated enhancer regions in this cancer. We identify ~1000 OAC-specific enhancers and use these data to uncover new cellular pathways that are operational in OAC. Among these are enhancers for JUP, MYBL2, and CCNE1, and we show that their activity is required for cancer cell viability. We also demonstrate the clinical utility of our dataset for identifying disease stage and patient prognosis. Our data therefore identify an important set of regulatory elements that enhance our molecular understanding of OAC and point to potential new therapeutic directions.
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Affiliation(s)
- Ibrahim Ahmed
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Shen-Hsi Yang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Samuel Ogden
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Wei Zhang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Yaoyong Li
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | | | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
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6
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Ogden S, Carys K, Ahmed I, Bruce J, Sharrocks AD. Regulatory chromatin rewiring promotes metabolic switching during adaptation to oncogenic receptor tyrosine kinase inhibition. Oncogene 2022; 41:4808-4822. [PMID: 36153371 PMCID: PMC9586873 DOI: 10.1038/s41388-022-02465-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022]
Abstract
Oesophageal adenocarcinoma (OAC) patients show poor survival rates and there are few targeted molecular therapies available. However, components of the receptor tyrosine kinase (RTK) driven pathways are commonly mutated in OAC, typified by high frequency amplifications of the RTK ERBB2. ERBB2 can be therapeutically targeted, but this has limited clinical benefit due to the acquisition of drug resistance. Here we examined how OAC cells adapt to ERBB2 inhibition as they transition to a drug resistant state. ERBB2 inhibition triggers widespread remodelling of the accessible chromatin landscape and the underlying gene regulatory networks. The transcriptional regulators HNF4A and PPARGC1A play a key role in this network rewiring. Initially, inhibition of cell cycle associated gene expression programmes is observed, with compensatory increases in the programmes driving changes in metabolic activity. Both PPARGC1A and HNF4A are required for the acquisition of resistance to ERBB2 inhibition and PPARGC1A is instrumental in promoting a switch to dependency on oxidative phosphorylation. Our work therefore reveals the molecular pathways that support the acquisition of a resistant state and points to potential new therapeutic strategies to combat cellular adaptation and ensuing drug resistance.
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Affiliation(s)
- Samuel Ogden
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Kashmala Carys
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Ibrahim Ahmed
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Jason Bruce
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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7
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Carrera S, O'Donnell A, Li Y, Nowicki-Osuch K, Yang SH, Baker SM, Spiller D, Sharrocks AD. Complexities in the role of acetylation dynamics in modifying inducible gene activation parameters. Nucleic Acids Res 2021; 49:12744-12756. [PMID: 34850951 PMCID: PMC8682737 DOI: 10.1093/nar/gkab1176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/04/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 11/22/2022] Open
Abstract
High levels of histone acetylation are associated with the regulatory elements of active genes, suggesting a link between acetylation and gene activation. We revisited this model, in the context of EGF-inducible gene expression and found that rather than a simple unifying model, there are two broad classes of genes; one in which high lysine acetylation activity is required for efficient gene activation, and a second group where the opposite occurs and high acetylation activity is inhibitory. We examined the latter class in more detail using EGR2 as a model gene and found that lysine acetylation levels are critical for several activation parameters, including the timing of expression onset, and overall amplitudes of the transcriptional response. In contrast, DUSP1 responds in the canonical manner and its transcriptional activity is promoted by acetylation. Single cell approaches demonstrate heterogenous activation kinetics of a given gene in response to EGF stimulation. Acetylation levels modify these heterogenous patterns and influence both allele activation frequencies and overall expression profile parameters. Our data therefore point to a complex interplay between acetylation equilibria and target gene induction where acetylation level thresholds are an important determinant of transcriptional induction dynamics that are sensed in a gene-specific manner.
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Affiliation(s)
- Samantha Carrera
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Amanda O'Donnell
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Yaoyong Li
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Karol Nowicki-Osuch
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Shen-Hsi Yang
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Syed Murtuza Baker
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - David Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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8
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Abstract
Many biological studies of transcriptional control mechanisms produce lists of genes and non-coding genomic intervals from corresponding gene expression and epigenomic assays. In higher organisms, such as eukaryotes, genes may be regulated by distal elements, with these elements lying 10s–100s of kilobases away from a gene transcription start site. To gain insight into these distal regulatory mechanisms, it is important to determine comparative enrichment of genes of interest in relation to genomic regions of interest, and to be able to do so at a range of distances. Existing bioinformatics tools can annotate genomic regions to nearest known genes, or look for transcription factor binding sites in relation to gene transcription start sites. Here, we present PEGS (
Peak set
Enrichment in
Gene
Sets). This tool efficiently provides an exploratory analysis by calculating enrichment of multiple gene sets, associated with multiple non-coding elements (peak sets), at multiple genomic distances, and within topologically associated domains. We apply PEGS to gene sets derived from gene expression studies, and genomic intervals from corresponding ChIP-seq and ATAC-seq experiments to derive biologically meaningful results. We also demonstrate an extended application to tissue-specific gene sets and publicly available GWAS data, to find enrichment of sleep trait associated SNPs in relation to tissue-specific gene expression profiles.
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Affiliation(s)
- Peter Briggs
- Bioinformatics Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - A Louise Hunter
- Division of Diabetes, Endocrinology & Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Shen-Hsi Yang
- Division of Molecular & Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Andrew D Sharrocks
- Division of Molecular & Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Mudassar Iqbal
- Division of Informatics, Imaging & Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
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9
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Nowicki-Osuch K, Zhuang L, Jammula S, Bleaney CW, Mahbubani KT, Devonshire G, Katz-Summercorn A, Eling N, Wilbrey-Clark A, Madissoon E, Gamble J, Di Pietro M, O'Donovan M, Meyer KB, Saeb-Parsy K, Sharrocks AD, Teichmann SA, Marioni JC, Fitzgerald RC. Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition. Science 2021; 373:760-767. [PMID: 34385390 DOI: 10.1126/science.abd1449] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [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: 06/11/2020] [Revised: 01/26/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022]
Abstract
The origin of human metaplastic states and their propensity for cancer is poorly understood. Barrett's esophagus is a common metaplastic condition that increases the risk for esophageal adenocarcinoma, and its cellular origin is enigmatic. To address this, we harvested tissues spanning the gastroesophageal junction from healthy and diseased donors, including isolation of esophageal submucosal glands. A combination of single-cell transcriptomic profiling, in silico lineage tracing from methylation, open chromatin and somatic mutation analyses, and functional studies in organoid models showed that Barrett's esophagus originates from gastric cardia through c-MYC and HNF4A-driven transcriptional programs. Furthermore, our data indicate that esophageal adenocarcinoma likely arises from undifferentiated Barrett's esophagus cell types even in the absence of a pathologically identifiable metaplastic precursor, illuminating early detection strategies.
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Affiliation(s)
- Karol Nowicki-Osuch
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Lizhe Zhuang
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Sriganesh Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Christopher W Bleaney
- Faculty of Biology, Medicine and Health, Michael Smith Building, Oxford Road, University of Manchester, Manchester, UK
| | - Krishnaa T Mahbubani
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Annalise Katz-Summercorn
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Nils Eling
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Elo Madissoon
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John Gamble
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Massimiliano Di Pietro
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Maria O'Donovan
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kourosh Saeb-Parsy
- Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, Michael Smith Building, Oxford Road, University of Manchester, Manchester, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0X2, UK.
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10
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Ji Z, Li Y, Liu SX, Sharrocks AD. Correction to article "The forkhead transcription factor FOXK2 premarks lineage-specific genes in human embryonic stem cells for activation during differentiation''. Nucleic Acids Res 2021; 49:4198. [PMID: 33751103 PMCID: PMC8053109 DOI: 10.1093/nar/gkab221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Zongling Ji
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Yaoyong Li
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Sean X Liu
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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11
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Ji Z, Li Y, Liu SX, Sharrocks AD. The forkhead transcription factor FOXK2 premarks lineage-specific genes in human embryonic stem cells for activation during differentiation. Nucleic Acids Res 2021; 49:1345-1363. [PMID: 33434264 PMCID: PMC7897486 DOI: 10.1093/nar/gkaa1281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/06/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancers play important roles in controlling gene expression in a choreographed spatial and temporal manner during development. However, it is unclear how these regulatory regions are established during differentiation. Here we investigated the genome-wide binding profile of the forkhead transcription factor FOXK2 in human embryonic stem cells (ESCs) and downstream cell types. This transcription factor is bound to thousands of regulatory regions in human ESCs, and binding at many sites is maintained as cells differentiate to mesendodermal and neural precursor cell (NPC) types, alongside the emergence of new binding regions. FOXK2 binding is generally associated with active histone marks in any given cell type. Furthermore newly acquired, or retained FOXK2 binding regions show elevated levels of activating histone marks following differentiation to NPCs. In keeping with this association with activating marks, we demonstrate a role for FOXK transcription factors in gene activation during NPC differentiation. FOXK2 occupancy in ESCs is therefore an early mark for delineating the regulatory regions, which become activated in later lineages.
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Affiliation(s)
- Zongling Ji
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Yaoyong Li
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Sean X Liu
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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12
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Xu W, Ye Y, Sharrocks AD, Zhang W, Chen X. Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation. STAR Protoc 2020; 1:100187. [PMID: 33377081 PMCID: PMC7757419 DOI: 10.1016/j.xpro.2020.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Mapping the genomic locations of chromatin-associated proteins, such as transcription factors and histone modifications, is key to understanding the mechanisms of transcriptional regulation. ChIPmentation offers a simple and robust way of investigating the genomic binding sites of a protein using relatively low-input material. Here, we present a detailed protocol for the key steps that lead to a successful ChIPmentation experiment, as well as a quick analysis pipeline to examine the data. For complete details on the use and execution of this protocol, please refer to Schmidl et al. (2015). For example data produced by this protocol, please refer to Henriksson et al. (2019) and Zhang et al. (2019). Preparation of a transposase-assisted ChIP-seq library A simpler and cheaper approach than traditional ChIP-seq A sensitive and reliable method for transcription factors and histone modifications
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Affiliation(s)
- Wei Xu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Ying Ye
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Xi Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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13
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Connaughton DM, Dai R, Owen DJ, Marquez J, Mann N, Graham-Paquin AL, Nakayama M, Coyaud E, Laurent EMN, St-Germain JR, Blok LS, Vino A, Klämbt V, Deutsch K, Wu CHW, Kolvenbach CM, Kause F, Ottlewski I, Schneider R, Kitzler TM, Majmundar AJ, Buerger F, Onuchic-Whitford AC, Youying M, Kolb A, Salmanullah D, Chen E, van der Ven AT, Rao J, Ityel H, Seltzsam S, Rieke JM, Chen J, Vivante A, Hwang DY, Kohl S, Dworschak GC, Hermle T, Alders M, Bartolomaeus T, Bauer SB, Baum MA, Brilstra EH, Challman TD, Zyskind J, Costin CE, Dipple KM, Duijkers FA, Ferguson M, Fitzpatrick DR, Fick R, Glass IA, Hulick PJ, Kline AD, Krey I, Kumar S, Lu W, Marco EJ, Wentzensen IM, Mefford HC, Platzer K, Povolotskaya IS, Savatt JM, Shcherbakova NV, Senguttuvan P, Squire AE, Stein DR, Thiffault I, Voinova VY, Somers MJG, Ferguson MA, Traum AZ, Daouk GH, Daga A, Rodig NM, Terhal PA, van Binsbergen E, Eid LA, Tasic V, Rasouly HM, Lim TY, Ahram DF, Gharavi AG, Reutter HM, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Lifton RP, Xu H, Mane SM, Sanna-Cherchi S, Sharrocks AD, Raught B, Fisher SE, Bouchard M, Khokha MK, Shril S, Hildebrandt F. Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations. Am J Hum Genet 2020; 107:727-742. [PMID: 32891193 PMCID: PMC7536580 DOI: 10.1016/j.ajhg.2020.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 04/02/2020] [Accepted: 08/14/2020] [Indexed: 01/10/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) constitute one of the most frequent birth defects and represent the most common cause of chronic kidney disease in the first three decades of life. Despite the discovery of dozens of monogenic causes of CAKUT, most pathogenic pathways remain elusive. We performed whole-exome sequencing (WES) in 551 individuals with CAKUT and identified a heterozygous de novo stop-gain variant in ZMYM2 in two different families with CAKUT. Through collaboration, we identified in total 14 different heterozygous loss-of-function mutations in ZMYM2 in 15 unrelated families. Most mutations occurred de novo, indicating possible interference with reproductive function. Human disease features are replicated in X. tropicalis larvae with morpholino knockdowns, in which expression of truncated ZMYM2 proteins, based on individual mutations, failed to rescue renal and craniofacial defects. Moreover, heterozygous Zmym2-deficient mice recapitulated features of CAKUT with high penetrance. The ZMYM2 protein is a component of a transcriptional corepressor complex recently linked to the silencing of developmentally regulated endogenous retrovirus elements. Using protein-protein interaction assays, we show that ZMYM2 interacts with additional epigenetic silencing complexes, as well as confirming that it binds to FOXP1, a transcription factor that has also been linked to CAKUT. In summary, our findings establish that loss-of-function mutations of ZMYM2, and potentially that of other proteins in its interactome, as causes of human CAKUT, offering new routes for studying the pathogenesis of the disorder.
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Affiliation(s)
- Dervla M Connaughton
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Nephrology, Department of Medicine, University Hospital - London Health Sciences Centre, Schulich School of Medicine & Dentistry, Western University, 339 Windermere Road, London, ON N6A 5A5, Canada
| | - Rufeng Dai
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Danielle J Owen
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adda L Graham-Paquin
- Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Makiko Nakayama
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Jonathan R St-Germain
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Lot Snijders Blok
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands; Human Genetics Department, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Arianna Vino
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Verena Klämbt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantin Deutsch
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen-Han Wilfred Wu
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline M Kolvenbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Franziska Kause
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Ottlewski
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ronen Schneider
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas M Kitzler
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amar J Majmundar
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Florian Buerger
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ana C Onuchic-Whitford
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mao Youying
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Kolb
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daanya Salmanullah
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Evan Chen
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amelie T van der Ven
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Hadas Ityel
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Steve Seltzsam
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Johanna M Rieke
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Chen
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Asaf Vivante
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Tel Aviv University, Faculty of Medicine, Tel Aviv-Yafo 6997801, Israel
| | - Daw-Yang Hwang
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Kohl
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriel C Dworschak
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Hermle
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariëlle Alders
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Meibergdreef 9, 1105 Amsterdam, Netherlands
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle A Baum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Thomas D Challman
- Geisinger, Autism & Developmental Medicine Institute, 100 N Academy Avenue, Danville, PA 17822, USA
| | - Jacob Zyskind
- Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA
| | - Carrie E Costin
- Department of Clinical Genetics, Akron Children's Hospital, One Perkins Square, Akron, OH 44308, USA
| | - Katrina M Dipple
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Floor A Duijkers
- Department of Clinical Genetics, University of Amsterdam, 1012 WX Amsterdam, the Netherlands
| | - Marcia Ferguson
- Department of Clinical Genetics, Harvey Institute for Human Genetics, 6701 Charles St, Towson, MD 21204, USA
| | - David R Fitzpatrick
- MRC Institute of Genetics & Molecular Medicine, Royal Hospital for Sick Children, The University of Edinburgh, 2XU, Crewe Rd S, Edinburgh EH4 2XU, UK
| | - Roger Fick
- Mary Bridge Childrens Hospital, 316 Martin Luther King JR Way, Tacoma, WA 98405, USA
| | - Ian A Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, 1000 Central Street, Suite 610, Evanston, IL 60201, USA
| | - Antonie D Kline
- Department of Clinical Genetics, Harvey Institute for Human Genetics, 6701 Charles St, Towson, MD 21204, USA
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany; Swiss Epilepsy Center, Klinik Lengg, Bleulerstrasse 60, 8000 Zürich, Switzerland
| | - Selvin Kumar
- Department of Pediatric Nephrology, Institute of Child Health and Hospital for Children, Tamil Salai, Egmore, Chennai, Tamil Nadu 600008, India
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, 650 Albany Street, Boston, MA 02118, USA
| | - Elysa J Marco
- Cortica Healthcare, 4000 Civic Center Drive, Ste 100, San Rafael, CA 94939, USA
| | - Ingrid M Wentzensen
- Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Juliann M Savatt
- Geisinger, Autism & Developmental Medicine Institute, 100 N Academy Avenue, Danville, PA 17822, USA
| | - Natalia V Shcherbakova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta's Multi-Specialty Hospital, No.2, Mc Nichols Rd, Chetpet, Chennai, Tamil Nadu 600031, India
| | - Audrey E Squire
- Seattle Children's Hospital, Department of Genetic Medicine, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Deborah R Stein
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, 2401 Gillham Rd, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO 64108, USA; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, 5000 Holmes St, Kansas City, MO 64110, USA
| | - Victoria Y Voinova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Michael J G Somers
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Ferguson
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Avram Z Traum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ghaleb H Daouk
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ankana Daga
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nancy M Rodig
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje 1000, North Macedonia
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Tze Y Lim
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Dina F Ahram
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Heiko M Reutter
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany; Section of Neonatology and Pediatric Intensive Care, Clinic for Pediatrics, University Hospital Bonn, Adenauerallee 119, 53313 Bonn, Germany
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Kristen M Laricchia
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Richard P Lifton
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06510, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands
| | - Maxime Bouchard
- Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shirlee Shril
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Rogerson C, Ogden S, Britton E, Ang Y, Sharrocks AD. Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma. eLife 2020; 9:e57189. [PMID: 32880368 PMCID: PMC7544504 DOI: 10.7554/elife.57189] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 03/24/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
Oesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths. Barrett's oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the molecular events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin to directly regulate cell cycle genes specifically in OAC cells. This new KLF5 target gene programme has potential prognostic significance as high levels correlate with poorer patient survival. Thus, the repurposing of KLF5 for novel regulatory activity in OAC provides new insights into the mechanisms behind disease progression.
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Affiliation(s)
- Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Samuel Ogden
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | | | - Yeng Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
- GI Science Centre, Salford Royal NHS FT, University of ManchesterSalfordUnited Kingdom
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
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15
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Gerrard DT, Berry AA, Jennings RE, Birket MJ, Zarrineh P, Garstang MG, Withey SL, Short P, Jiménez-Gancedo S, Firbas PN, Donaldson I, Sharrocks AD, Hanley KP, Hurles ME, Gomez-Skarmeta JL, Bobola N, Hanley NA. Dynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disorders. Nat Commun 2020; 11:3920. [PMID: 32764605 PMCID: PMC7413392 DOI: 10.1038/s41467-020-17305-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 10/04/2019] [Accepted: 06/18/2020] [Indexed: 12/20/2022] Open
Abstract
How the genome activates or silences transcriptional programmes governs organ formation. Little is known in human embryos undermining our ability to benchmark the fidelity of stem cell differentiation or cell programming, or interpret the pathogenicity of noncoding variation. Here, we study histone modifications across thirteen tissues during human organogenesis. We integrate the data with transcription to build an overview of how the human genome differentially regulates alternative organ fates including by repression. Promoters from nearly 20,000 genes partition into discrete states. Key developmental gene sets are actively repressed outside of the appropriate organ without obvious bivalency. Candidate enhancers, functional in zebrafish, allow imputation of tissue-specific and shared patterns of transcription factor binding. Overlaying more than 700 noncoding mutations from patients with developmental disorders allows correlation to unanticipated target genes. Taken together, the data provide a comprehensive genomic framework for investigating normal and abnormal human development.
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Affiliation(s)
- Dave T Gerrard
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew A Berry
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Rachel E Jennings
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester, M13 9WU, UK
| | - Matthew J Birket
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Peyman Zarrineh
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Myles G Garstang
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Sarah L Withey
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Patrick Short
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sandra Jiménez-Gancedo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigacionnes Cientificas/Universidad Pablo de Olavide/Junta de Analucía, Sevilla, Spain
| | - Panos N Firbas
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigacionnes Cientificas/Universidad Pablo de Olavide/Junta de Analucía, Sevilla, Spain
| | - Ian Donaldson
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Karen Piper Hanley
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | | | - José Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigacionnes Cientificas/Universidad Pablo de Olavide/Junta de Analucía, Sevilla, Spain
| | - Nicoletta Bobola
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Neil A Hanley
- Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
- Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester, M13 9WU, UK.
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16
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Rowling EJ, Miskolczi Z, Nagaraju R, Wilcock DJ, Wang P, Telfer B, Li Y, Lasheras-Otero I, Redondo-Muñoz M, Sharrocks AD, Arozarena I, Wellbrock C. Cooperative behaviour and phenotype plasticity evolve during melanoma progression. Pigment Cell Melanoma Res 2020; 33:695-708. [PMID: 32145051 PMCID: PMC7496243 DOI: 10.1111/pcmr.12873] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/04/2020] [Accepted: 02/28/2020] [Indexed: 01/06/2023]
Abstract
A major challenge for managing melanoma is its tumour heterogeneity based on individual co-existing melanoma cell phenotypes. These phenotypes display variable responses to standard therapies, and they drive individual steps of melanoma progression; hence, understanding their behaviour is imperative. Melanoma phenotypes are defined by distinct transcriptional states, which relate to different melanocyte lineage development phases, ranging from a mesenchymal, neural crest-like to a proliferative, melanocytic phenotype. It is thought that adaptive phenotype plasticity based on transcriptional reprogramming drives melanoma progression, but at which stage individual phenotypes dominate and moreover, how they interact is poorly understood. We monitored melanocytic and mesenchymal phenotypes throughout melanoma progression and detected transcriptional reprogramming at different stages, with a gain in mesenchymal traits in circulating melanoma cells (CTCs) and proliferative features in metastatic tumours. Intriguingly, we found that distinct phenotype populations interact in a cooperative manner, which generates tumours of greater "fitness," supports CTCs and expands organotropic cues in metastases. Fibronectin, expressed in mesenchymal cells, acts as key player in cooperativity and promotes survival of melanocytic cells. Our data reveal an important role for inter-phenotype communications at various stages of disease progression, suggesting these communications could act as therapeutic target.
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Affiliation(s)
- Emily J Rowling
- Manchester Cancer Research Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Zsofia Miskolczi
- Manchester Cancer Research Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Raghavendar Nagaraju
- Manchester Cancer Research Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Daniel J Wilcock
- Manchester Cancer Research Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ping Wang
- Bioinformatics Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Brian Telfer
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Yaoyong Li
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Irene Lasheras-Otero
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Marta Redondo-Muñoz
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Andrew D Sharrocks
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Imanol Arozarena
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Claudia Wellbrock
- Manchester Cancer Research Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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17
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Baker SM, Rogerson C, Hayes A, Sharrocks AD, Rattray M. Classifying cells with Scasat, a single-cell ATAC-seq analysis tool. Nucleic Acids Res 2019; 47:e10. [PMID: 30335168 PMCID: PMC6344856 DOI: 10.1093/nar/gky950] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 04/04/2018] [Accepted: 10/04/2018] [Indexed: 01/22/2023] Open
Abstract
ATAC-seq is a recently developed method to identify the areas of open chromatin in a cell. These regions usually correspond to active regulatory elements and their location profile is unique to a given cell type. When done at single-cell resolution, ATAC-seq provides an insight into the cell-to-cell variability that emerges from otherwise identical DNA sequences by identifying the variability in the genomic location of open chromatin sites in each of the cells. This paper presents Scasat (single-cell ATAC-seq analysis tool), a complete pipeline to process scATAC-seq data with simple steps. Scasat treats the data as binary and applies statistical methods that are especially suitable for binary data. The pipeline is developed in a Jupyter notebook environment that holds the executable code along with the necessary description and results. It is robust, flexible, interactive and easy to extend. Within Scasat we developed a novel differential accessibility analysis method based on information gain to identify the peaks that are unique to a cell. The results from Scasat showed that open chromatin locations corresponding to potential regulatory elements can account for cellular heterogeneity and can identify regulatory regions that separates cells from a complex population.
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Affiliation(s)
- Syed Murtuza Baker
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
| | - Connor Rogerson
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
| | - Andrew Hayes
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK.,Manchester Academic Health Science Centre (MAHSC), Core Technology Facility, The University of Manchester, Manchester M13 9NT, UK
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
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18
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Li Y, Aguilar-Martinez E, Sharrocks AD. Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2018-0090/jib-2018-0090.xml. [PMID: 31301672 PMCID: PMC6798850 DOI: 10.1515/jib-2018-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/21/2019] [Indexed: 11/16/2022] Open
Abstract
The interconversion of sequences that constitute the genome and the proteome is becoming increasingly important due to the generation of large amounts of DNA sequence data. Following mapping of DNA segments to the genome, one fundamentally important task is to find the amino acid sequences which are coded within a list of genomic sections. Conversely, given a series of protein segments, an important task is to find the genomic loci which code for a list of protein regions. To perform these tasks on a region by region basis is extremely laborious when a large number of regions are being studied. We have therefore implemented an R package geno2proteo which performs the two mapping tasks and subsequent sequence retrieval in a batch fashion. In order to make the tool more accessible to users, we have created a web interface of the R package which allows the users to perform the mapping tasks by going to the web page http://sharrocksresources.manchester.ac.uk/tofigaps and using the web service.
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Affiliation(s)
- Yaoyong Li
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Elisa Aguilar-Martinez
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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19
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Abstract
Background: The ERK MAPK pathway plays a pivotal role in regulating numerous cellular processes during normal development and in the adult but is often deregulated in disease scenarios. One of its key nuclear targets is the transcription factor ELK1, which has been shown to play an important role in controlling gene expression in human embryonic stem cells (hESCs). ELK1 is known to act as a transcriptional activator in response to ERK pathway activation but repressive roles have also been uncovered, including a putative interaction with the PRC2 complex. Methods: Here we probe the activity of ELK1 in hESCs by using a combination of gene expression analysis in hESCs and during differentiation following ELK1 depletion and also analysis of chromatin occupancy of transcriptional regulators and histone mark deposition that accompany changes in gene expression. Results: We find that ELK1 can exert its canonical activating activity downstream from the ERK pathway but also possesses additional repressive activities. Despite its co-binding to PRC2 occupied regions, we could not detect any ELK1-mediated repression at these regions. Instead, we find that ELK1 has a repressive role at a subset of co-occupied SRF binding regions. Conclusions: ELK1 should therefore be viewed as a dichotomous transcriptional regulator that can act through SRF to generate both activating and repressing properties at different genomic loci.
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Affiliation(s)
- Ian Prise
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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20
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Rogerson C, Britton E, Withey S, Hanley N, Ang YS, Sharrocks AD. Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state. Genome Res 2019; 29:723-736. [PMID: 30962179 PMCID: PMC6499311 DOI: 10.1101/gr.243345.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 08/29/2018] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
Esophageal adenocarcinoma (EAC) is one of the most frequent causes of cancer death, and yet compared to other common cancers, we know relatively little about the molecular composition of this tumor type. To further our understanding of this cancer, we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in EAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centered on HNF4A and GATA6. These transcription factors work together to control the EAC transcriptome. We show that this network is activated in Barrett's esophagus, the putative precursor state to EAC, thereby providing novel molecular evidence in support of stepwise malignant transition. Furthermore, we show that HNF4A alone is sufficient to drive chromatin opening and activation of a Barrett's-like chromatin signature when expressed in normal human epithelial cells. Collectively, these data provide a new way to categorize EAC at a genome scale and implicate HNF4A activation as a potential pivotal event in its malignant transition from healthy cells.
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Affiliation(s)
- Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Sarah Withey
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Neil Hanley
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom.,Endocrinology Department, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WU, United Kingdom
| | - Yeng S Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom.,GI Science Centre, Salford Royal NHS FT, University of Manchester, Salford M6 8HD, United Kingdom
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
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21
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Prise I, Sharrocks AD. ELK1 has a dual activating and repressive role in human embryonic stem cells. Wellcome Open Res 2019; 4:41. [DOI: 10.12688/wellcomeopenres.15091.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2019] [Indexed: 11/20/2022] Open
Abstract
Background: The ERK MAPK pathway plays a pivotal role in regulating numerous cellular processes during normal development and in the adult but is often deregulated in disease scenarios. One of its key nuclear targets is the transcription factor ELK1, which has been shown to play an important role in controlling gene expression in human embryonic stem cells (hESCs). ELK1 is known to act as a transcriptional activator in response to ERK pathway activation but repressive roles have also been uncovered, including a putative interaction with the PRC2 complex. Methods: Here we probe the activity of ELK1 in hESCs by using a combination of gene expression analysis in hESCs and during differentiation following ELK1 depletion and also analysis of chromatin occupancy of transcriptional regulators and histone mark deposition that accompany changes in gene expression. Results: We find that ELK1 can exert its canonical activating activity downstream from the ERK pathway but also possesses additional repressive activities. Despite its co-binding to PRC2 occupied regions, we could not detect any ELK1-mediated repression at these regions. Instead, we find that ELK1 has a repressive role at a subset of co-occupied SRF binding regions. This latter repressive role appears not to be exerted through competition with MRTF family co-activators. Conclusions: ELK1 should therefore be viewed as a dichotomous transcriptional regulator that can act through SRF to generate both activating and repressing properties at different genomic loci.
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22
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Garcia E, Hayden A, Birts C, Britton E, Rogerson C, Bleaney CW, Cowie A, Pickard K, Mellone M, Choh C, Derouet M, Duriez P, Noble F, White MJ, Primrose JN, Strefford JC, Rose-Zerilli M, Thomas GJ, Ang Y, Sharrocks AD, Fitzgerald RC, Underwood TJ. Author Correction: Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1. Sci Rep 2019; 9:318. [PMID: 30670740 PMCID: PMC6342942 DOI: 10.1038/s41598-018-37591-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A correction has been published and is appended to both the HTML and PDF versions of this paper. The error has not been fixed in the paper.
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Affiliation(s)
- Edwin Garcia
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Annette Hayden
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Charles Birts
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Edward Britton
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Connor Rogerson
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Christopher W Bleaney
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Andrew Cowie
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Karen Pickard
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Massimiliano Mellone
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Clarisa Choh
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Mathieu Derouet
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Patrick Duriez
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Fergus Noble
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Michael J White
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - John N Primrose
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Jonathan C Strefford
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Matthew Rose-Zerilli
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Gareth J Thomas
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Yeng Ang
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Timothy J Underwood
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom.
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23
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Nestal de Moraes G, Ji Z, Fan LYN, Yao S, Zona S, Sharrocks AD, Lam EWF. SUMOylation modulates FOXK2-mediated paclitaxel sensitivity in breast cancer cells. Oncogenesis 2018; 7:29. [PMID: 29540677 PMCID: PMC5852961 DOI: 10.1038/s41389-018-0038-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/31/2018] [Accepted: 02/08/2018] [Indexed: 01/13/2023] Open
Abstract
The forkhead transcription factor FOXK2 plays a critical role in suppressing tumorigenesis and mediating cytotoxic drug action in breast cancer. However, the mechanism by which the biological function of FOXK2 is regulated remains poorly understood. Here, we investigated the role of SUMOylation in modulating FOXK2-mediated drug sensitivity. We identified SUMOylation consensus motifs within the FOXK2 sequence and constructed two SUMOylation-defective double mutants by converting lysine 527 and 633 to arginines and glutamic acid 529 and 635 to alanines, respectively. We found that both the FOXK2 SUMOylation-deficient (K527/633 R) and (E529/635 A) mutants were ineffective in mediating the cytotoxic function of paclitaxel when compared to the wild-type (WT) FOXK2. When overexpressed, unlike the wild-type (WT) FOXK2, the K527/633 R mutant had little effect on the sensitivity of MCF-7 and MDA-MB-231 cells to paclitaxel, as examined by cell viability and clonogenic assays. Our results also showed that MCF-7 cells overexpressing the K527/633 R mutant form of FOXK2 or the empty expression vector have lower protein and mRNA levels of its tumour suppressive transcriptional target FOXO3 compared to the wild-type FOXK2. Consistently, ChIP assays revealed that unlike wild-type FOXK2, the SUMOylation-defective (K527/633 R) mutant is unable to bind to the FOXO3 promoter, despite expressing comparable levels of protein and having the same subcellular localization as the wild-type FOXK2 in MCF-7 cells. Interestingly, expression of neither the wild-type nor the K527/633 R mutant FOXK2 had any effect on the proliferation and paclitaxel sensitivity of the MCF-7 TaxR paclitaxel-resistant cells. In agreement, both the wild-type and the (K527/633 R) mutant FOXK2 failed to bind to the endogenous FOXO3 promoter in these cells. Collectively, our results suggest that SUMOylation positively regulates FOXK2 transcriptional activity and has a role in mediating the cytotoxic response to paclitaxel through the tumour suppressor FOXO3.
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Affiliation(s)
- Gabriela Nestal de Moraes
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), Du Cane Road, London, W12 0NN, UK
- Laboratório de Hemato-Oncologia Celular e Molecular, Programa de Hemato-Oncologia Molecular, Instituto Nacional de Câncer (INCA), Praça da Cruz Vermelha, 23/6° andar, Centro, 20230-130, Rio de Janeiro, Brazil
| | - Zongling Ji
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Lavender Y-N Fan
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), Du Cane Road, London, W12 0NN, UK
| | - Shang Yao
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), Du Cane Road, London, W12 0NN, UK
| | - Stefania Zona
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), Du Cane Road, London, W12 0NN, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Eric W-F Lam
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), Du Cane Road, London, W12 0NN, UK.
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24
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Britton E, Rogerson C, Mehta S, Li Y, Li X, Fitzgerald RC, Ang YS, Sharrocks AD. Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma. PLoS Genet 2017; 13:e1006879. [PMID: 28859074 PMCID: PMC5578490 DOI: 10.1371/journal.pgen.1006879] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 12/06/2016] [Accepted: 06/20/2017] [Indexed: 01/04/2023] Open
Abstract
Oesophageal adenocarcinoma (OAC) is one of the ten most prevalent forms of cancer and is showing a rapid increase in incidence and yet exhibits poor survival rates. Compared to many other common cancers, the molecular changes that occur in this disease are relatively poorly understood. However, genes encoding chromatin remodeling enzymes are frequently mutated in OAC. This is consistent with the emerging concept that cancer cells exhibit reprogramming of their chromatin environment which leads to subsequent changes in their transcriptional profile. Here, we have used ATAC-seq to interrogate the chromatin changes that occur in OAC using both cell lines and patient-derived material. We demonstrate that there are substantial changes in the regulatory chromatin environment in the cancer cells and using this data we have uncovered an important role for ETS and AP1 transcription factors in driving the changes in gene expression found in OAC cells.
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Affiliation(s)
- Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Shaveta Mehta
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Christie Hospital, Manchester, United Kingdom
| | - Yaoyong Li
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Xiaodun Li
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | | | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Yeng S. Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- GI Science Centre, Salford Royal NHS FT, University of Manchester, Stott Lane, Salford, United Kingdom
| | - Andrew D. Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- GI Science Centre, Salford Royal NHS FT, University of Manchester, Stott Lane, Salford, United Kingdom
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25
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Abstract
Protein SUMOylation represents an important regulatory event that changes the activities of numerous proteins. Recent evidence demonstrates that polySUMO chains can act as a trigger to direct the ubiquitin ligase RNF4 to substrates to cause their turnover through the ubiquitin pathway. RNF4 uses multiple SUMO interaction motifs (SIMs) to bind to these chains. However, in addition to polySUMO chains, a multimeric binding surface created by the simultaneous SUMOylation of multiple residues on a protein or complex could also provide a platform for the recruitment of multi-SIM proteins like RNF4. Here we demonstrate that multiSUMOylated ETV4 can bind to RNF4 and that a unique combination of SIMs is required for RNF4 to interact with this multiSUMOylated platform. Thus RNF4 can bind to proteins that are either polySUMOylated through a single site or multiSUMOylated on several sites and raises the possibility that such multiSIM-multiSUMO interactions might be more widespread.
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Affiliation(s)
- Elisa Aguilar-Martinez
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Baoqiang Guo
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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26
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Abstract
Protein SUMOylation represents an important regulatory event that changes the activities of numerous proteins. Recent evidence demonstrates that polySUMO chains can act as a trigger to direct the ubiquitin ligase RNF4 to substrates to cause their turnover through the ubiquitin pathway. RNF4 uses multiple SUMO interaction motifs (SIMs) to bind to these chains. However, in addition to polySUMO chains, a multimeric binding surface created by the simultaneous SUMOylation of multiple residues on a protein or complex could also provide a platform for the recruitment of multi-SIM proteins like RNF4. Here we demonstrate that multiSUMOylated ETV4 can bind to RNF4 and that a unique combination of SIMs is required for RNF4 to interact with this multiSUMOylated platform. Thus RNF4 can bind to proteins that are either polySUMOylated through a single site or multiSUMOylated on several sites and raises the possibility that such multiSIM-multiSUMO interactions might be more widespread.
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27
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Garcia E, Hayden A, Birts C, Britton E, Cowie A, Pickard K, Mellone M, Choh C, Derouet M, Duriez P, Noble F, White MJ, Primrose JN, Strefford JC, Rose-Zerilli M, Thomas GJ, Ang Y, Sharrocks AD, Fitzgerald RC, Underwood TJ. Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1. Sci Rep 2016; 6:32417. [PMID: 27600491 PMCID: PMC5013399 DOI: 10.1038/srep32417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 04/14/2016] [Accepted: 08/04/2016] [Indexed: 12/16/2022] Open
Abstract
New biological tools are required to understand the functional significance of genetic events revealed by whole genome sequencing (WGS) studies in oesophageal adenocarcinoma (OAC). The MFD-1 cell line was isolated from a 55-year-old male with OAC without recombinant-DNA transformation. Somatic genetic variations from MFD-1, tumour, normal oesophagus, and leucocytes were analysed with SNP6. WGS was performed in tumour and leucocytes. RNAseq was performed in MFD-1, and two classic OAC cell lines FLO1 and OE33. Transposase-accessible chromatin sequencing (ATAC-seq) was performed in MFD-1, OE33, and non-neoplastic HET1A cells. Functional studies were performed. MFD-1 had a high SNP genotype concordance with matched germline/tumour. Parental tumour and MFD-1 carried four somatically acquired mutations in three recurrent mutated genes in OAC: TP53, ABCB1 and SEMA5A, not present in FLO-1 or OE33. MFD-1 displayed high expression of epithelial and glandular markers and a unique fingerprint of open chromatin. MFD-1 was tumorigenic in SCID mouse and proliferative and invasive in 3D cultures. The clinical utility of whole genome sequencing projects will be delivered using accurate model systems to develop molecular-phenotype therapeutics. We have described the first such system to arise from the oesophageal International Cancer Genome Consortium project.
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Affiliation(s)
- Edwin Garcia
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Annette Hayden
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Charles Birts
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Edward Britton
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Andrew Cowie
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Karen Pickard
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Massimiliano Mellone
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Clarisa Choh
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Mathieu Derouet
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Patrick Duriez
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Fergus Noble
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Michael J. White
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - John N. Primrose
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Jonathan C. Strefford
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Matthew Rose-Zerilli
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Gareth J. Thomas
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Yeng Ang
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Andrew D. Sharrocks
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Rebecca C. Fitzgerald
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ United Kingdom
| | - Timothy J. Underwood
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
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28
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Wiseman EF, Chen X, Han N, Webber A, Ji Z, Sharrocks AD, Ang YS. Erratum to: 'Deregulation of the FOXM1 target gene network and its coregulatory partners in oesophageal adenocarcinoma'. Mol Cancer 2016; 15:21. [PMID: 26936268 PMCID: PMC4774172 DOI: 10.1186/s12943-016-0506-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 12/01/2022] Open
Affiliation(s)
- Elizabeth F Wiseman
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.,Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK
| | - Xi Chen
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.,Present address: The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Namshik Han
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.,Present address: Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Aaron Webber
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Zongling Ji
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Yeng S Ang
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK
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29
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Veluscek G, Li Y, Yang SH, Sharrocks AD. Jun-Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency. Stem Cells 2016; 34:1213-24. [PMID: 26850660 PMCID: PMC4864893 DOI: 10.1002/stem.2294] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/02/2015] [Indexed: 01/02/2023]
Abstract
Embryonic stem cells (ESC) are able to give rise to any somatic cell type. A lot is known about how ESC pluripotency is maintained, but comparatively less is known about how differentiation is promoted. Cell fate decisions are regulated by interactions between signaling and transcriptional networks. Recent studies have shown that the overexpression or downregulation of the transcription factor Jun can affect the ESC fate. Here we have focussed on the role of the Jun in the exit of mouse ESCs from ground state pluripotency and the onset of early differentiation. Transcriptomic analysis of differentiating ESCs reveals that Jun is required to upregulate a programme of genes associated with cell adhesion as ESCs exit the pluripotent ground state. Several of these Jun-regulated genes are shown to be required for efficient adhesion. Importantly this adhesion is required for the timely regulated exit of ESCs from ground state pluripotency and the onset of early differentiation events. Stem Cells 2016;34:1213-1224.
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Affiliation(s)
- Giulia Veluscek
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Yaoyong Li
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Shen-Hsi Yang
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew D Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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30
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Ramkumar P, Lee CM, Moradian A, Sweredoski MJ, Hess S, Sharrocks AD, Haines DS, Reddy EP. JNK-associated Leucine Zipper Protein Functions as a Docking Platform for Polo-like Kinase 1 and Regulation of the Associating Transcription Factor Forkhead Box Protein K1. J Biol Chem 2015; 290:29617-28. [PMID: 26468278 PMCID: PMC4705960 DOI: 10.1074/jbc.m115.664649] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 05/18/2015] [Revised: 10/04/2015] [Indexed: 11/06/2022] Open
Abstract
JLP (JNK-associated leucine zipper protein) is a scaffolding protein that interacts with various signaling proteins associated with coordinated regulation of cellular process such as endocytosis, motility, neurite outgrowth, cell proliferation, and apoptosis. Here we identified PLK1 (Polo-like kinase 1) as a novel interaction partner of JLP through mass spectrometric approaches. Our results indicate that JLP is phospho-primed by PLK1 on Thr-351, which is recognized by the Polo box domain of PLK1 leading to phosphorylation of JLP at additional sites. Stable isotope labeling by amino acids in cell culture and quantitative LC-MS/MS analysis was performed to identify PLK1-dependent JLP-interacting proteins. Treatment of cells with the PLK1 kinase inhibitor BI2536 suppressed binding of the Forkhead box protein K1 (FOXK1) transcriptional repressor to JLP. JLP was found to interact with PLK1 and FOXK1 during mitosis. Moreover, knockdown of PLK1 affected the interaction between JLP and FOXK1. FOXK1 is a known transcriptional repressor of the CDK inhibitor p21/WAF1, and knockdown of JLP resulted in increased FOXK1 protein levels and a reduction of p21 transcript levels. Our results suggest a novel mechanism by which FOXK1 protein levels and activity are regulated by associating with JLP and PLK1.
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Affiliation(s)
- Poornima Ramkumar
- From the Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Clement M Lee
- From the Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Annie Moradian
- the Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and
| | - Michael J Sweredoski
- the Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and
| | - Sonja Hess
- the Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and
| | - Andrew D Sharrocks
- the Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Dale S Haines
- the Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania 19122
| | - E Premkumar Reddy
- From the Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029,
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31
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Chen X, Ji Z, Webber A, Sharrocks AD. Genome-wide binding studies reveal DNA binding specificity mechanisms and functional interplay amongst Forkhead transcription factors. Nucleic Acids Res 2015; 44:1566-78. [PMID: 26578569 PMCID: PMC4770209 DOI: 10.1093/nar/gkv1120] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 07/22/2015] [Accepted: 10/14/2015] [Indexed: 01/19/2023] Open
Abstract
Transcription factors belonging to the same transcription factor families contain very similar DNA binding domains and hence have the potential to bind to related DNA sequences. However, subtle differences in binding specificities can be detected in vitro with the potential to direct specific responses in vivo. Here, we have examined the binding properties of three Forkhead (FOX) transcription factors, FOXK2, FOXO3 and FOXJ3 in vivo. Extensive overlap in chromatin binding is observed, although underlying differential DNA binding specificity can dictate the recruitment of FOXK2 and FOXJ3 to chromatin. However, functionally, FOXO3-dependent gene regulation is generally mediated not through uniquely bound regions but through regions occupied by both FOXK2 and FOXO3 where both factors play a regulatory role. Our data point to a model whereby FOX transcription factors control gene expression through dynamically binding and generating partial occupancy of the same site rather than mutually exclusive binding derived by stable binding of individual FOX proteins.
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Affiliation(s)
- Xi Chen
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Zongling Ji
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Aaron Webber
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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32
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Dibb M, Han N, Choudhury J, Hayes S, Valentine H, West C, Sharrocks AD, Ang YS. FOXM1 and polo-like kinase 1 are co-ordinately overexpressed in patients with gastric adenocarcinomas. BMC Res Notes 2015; 8:676. [PMID: 26576650 PMCID: PMC4650505 DOI: 10.1186/s13104-015-1658-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/02/2015] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Gastric cancers present late in life with advanced disease and carry a poor prognosis. Polo-like Kinase 1 (PLK1) is a mitotic kinase with regulatory functions during G2/M and mitosis in the cell cycle. In mammalian cells, there is an intricate co-regulatory relationship between PLK1 and the forkhead transcription factor FOXM1. It has been demonstrated that individually either PLK1 or FOXM1 expression predicts poorer survival. However, the co-expression of both of these markers in gastric adenocarcinomas has not been reported previously. METHODS We aimed to assess the expression of PLK1 and FOXM1 in Gastric adenocarcinomas in a Western Population, to examine whether there is a relationship of PLK1 to FOXM1 in cancer samples. We assess both the protein and mRNA expression in this patient population by Tissue Microarray immunohistochemistry and RT-PCR. RESULTS Immunohistochemistry was performed on biopsy samples from 79 patients with gastric cancer. Paired normal controls were available in 47 patients. FOXM1 expression was significantly associated with gastric adenocarcinoma (p = 0.001). PLK1 and FOXM1 co-expression was demonstrated in 6/8 (75 %) tumours when analysed by RT-PCR. FOXM1 is overexpressed in a large proportion of gastric carcinomas at the protein level and FOXM1 and PLK1 are concomitantly overexpressed at the mRNA level in this cancer type. CONCLUSIONS This study has demonstrated that FOXM1 and its target gene PLK1 are coordinately overexpressed in a proportion of gastric adenocarcinomas. This suggests that chemotherapeutic treatments that target this pathway may be of clinical utility.
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Affiliation(s)
- M Dibb
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK.
| | - N Han
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | - J Choudhury
- Department of Histopathology, Salford Royal Foundation Trust, Stott Lane, Salford, M6 8HD, UK.
| | - S Hayes
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK.
- Department of Histopathology, Salford Royal Foundation Trust, Stott Lane, Salford, M6 8HD, UK.
| | - H Valentine
- School of Cancer and Enabling Sciences, Christie Hospital, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - C West
- School of Cancer and Enabling Sciences, Christie Hospital, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - A D Sharrocks
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Yeng S Ang
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK.
- GI Science Centre, Salford Royal NHS FT, University of Manchester, Stott Lane, Salford, M6 8HD, UK.
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33
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Darieva Z, Webber A, Warwood S, Sharrocks AD. Protein kinase C coordinates histone H3 phosphorylation and acetylation. eLife 2015; 4:e09886. [PMID: 26468616 PMCID: PMC4714974 DOI: 10.7554/elife.09886] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 10/14/2015] [Indexed: 12/11/2022] Open
Abstract
The re-assembly of chromatin following DNA replication is a critical event in the maintenance of genome integrity. Histone H3 acetylation at K56 and phosphorylation at T45 are two important chromatin modifications that accompany chromatin assembly. Here we have identified the protein kinase Pkc1 as a key regulator that coordinates the deposition of these modifications in S. cerevisiae under conditions of replicative stress. Pkc1 phosphorylates the histone acetyl transferase Rtt109 and promotes its ability to acetylate H3K56. Our data also reveal novel cross-talk between two different histone modifications as Pkc1 also enhances H3T45 phosphorylation and this modification is required for H3K56 acetylation. Our data therefore uncover an important role for Pkc1 in coordinating the deposition of two different histone modifications that are important for chromatin assembly. DOI:http://dx.doi.org/10.7554/eLife.09886.001 Prior to cell division, DNA must be copied so that each new cell gets a complete copy of the cell’s genetic instructions. But DNA is so long that it is stored in a heavily compacted form in the nucleus of the cell, with the strands of DNA coiled around several proteins called histones. Before the DNA is copied, it must be unfurled. Then each new copy of DNA must be repackaged to fit compactly inside the nucleus of each new cell. If errors occur in the process of copying DNA, it can lead to genetic mutations that may cause diseases like cancer. To prevent this, cells have mechanisms to identify errors and correct them before the DNA is repackaged. This requires a pause to allow the repairs to occur before the DNA recoils. However, it is not completely clear how this process is controlled. Now, Darieva et al. show that an enzyme called protein kinase C (or Pkc1 for short) is essential to repackaging DNA after the errors are corrected. Several experiments showed that Pkc1 plays an important role when cells were exposed to stressful conditions that potentially cause errors in DNA copying. Specifically, Pkc1 helps prepare the third histone protein (histone H3) so that DNA can recoil around it. Pkc1 waits until the stressful conditions have passed and the DNA has been repaired to make the necessary changes. Once the stress has passed, Pkc1 adds a phosphate to another enzyme called Rtt109 that prepares the histone. The Pkc1 simultaneously contributes to another necessary change to histone H3. These new details about DNA repackaging may help researchers understand how cells protect against DNA copying errors, and how this process goes wrong in cancer. DOI:http://dx.doi.org/10.7554/eLife.09886.002
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Affiliation(s)
- Zoulfia Darieva
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Aaron Webber
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Stacey Warwood
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew D Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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34
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Nestal de Moraes G, Khongkow P, Gong C, Yao S, Gomes AR, Ji Z, Kandola N, Delbue D, Man EPS, Khoo US, Sharrocks AD, Lam EWF. Forkhead box K2 modulates epirubicin and paclitaxel sensitivity through FOXO3a in breast cancer. Oncogenesis 2015; 4:e167. [PMID: 26344694 PMCID: PMC4767938 DOI: 10.1038/oncsis.2015.26] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 06/15/2015] [Revised: 07/22/2015] [Accepted: 08/04/2015] [Indexed: 12/15/2022] Open
Abstract
The forkhead transcription factor FOXK2 has recently been implicated in cancer cell proliferation and survival, but a role in cancer chemotherapeutic drug resistance has hitherto not been explored. Here we demonstrate that FOXK2 has a central role in mediating the cytotoxic drug response in breast cancer. Clonogenic and cell viability assays showed that enhanced FOXK2 expression sensitizes MCF-7 breast cancer cells to paclitaxel or epirubicin treatment, whereas FOXK2 depletion by small interfering RNAs (siRNAs) confers drug resistance. Our data also showed that the activation of the tumour suppressor FOXO3a by paclitaxel and epirubicin is mediated through the induction of FOXK2, as depletion of FOXK2 by siRNA limits the induction of FOXO3a by these drugs in MCF-7 cells. Chromatin immunoprecipitation (ChIP) analysis showed that in response to drug treatment, FOXK2 accumulates and binds to the proximal FOXO3a promoter region in MCF-7 cells. Furthermore, we also uncovered that FOXK2 is deregulated and, therefore, can express at high levels in the nucleus of both the paclitaxel and epirubicin drug-resistant MCF-7 cells. Our results showed that ectopically overexpressed FOXK2 accumulates in the nuclei of drug-resistant MCF-7 cells but failed to be recruited to target genes, including FOXO3a. Crucially, we found that FOXO3a is required for the anti-proliferative and epirubicin-induced cytotoxic function of FOXK2 in MCF-7 cells by sulphorhodamine and clonogenic assays. The physiological importance of the regulation of FOXO3a by FOXK2 is further confirmed by the significant correlations between FOXO3a and FOXK2 expression in breast carcinoma patient samples. Further survival analysis also reveals that high nuclear FOXK2 expression significantly associates with poorer clinical outcome, particularly in patients who have received conventional chemotherapy, consistent with our finding that FOXK2 is deregulated in drug-resistant cells. In summary, our results suggest that paclitaxel and epirubicin target the FOXK2 to modulate their cytotoxicity and deregulated FOXK2 confers drug resistance.
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Affiliation(s)
- G Nestal de Moraes
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, UK.,Laboratório de Hemato-Oncologia Celular e Molecular, Programa de Hemato-Oncologia Molecular, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - P Khongkow
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, UK
| | - C Gong
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, UK.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - S Yao
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, UK
| | - A R Gomes
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, UK
| | - Z Ji
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - N Kandola
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, UK
| | - D Delbue
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, UK.,Laboratório de Hemato-Oncologia Celular e Molecular, Programa de Hemato-Oncologia Molecular, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - E P S Man
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - U S Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - A D Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - E W-F Lam
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, UK
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35
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Aguilar-Martinez E, Morrisroe C, Sharrocks AD. The ubiquitin ligase UBE3A dampens ERK pathway signalling in HPV E6 transformed HeLa cells. PLoS One 2015; 10:e0119366. [PMID: 25815718 PMCID: PMC4376912 DOI: 10.1371/journal.pone.0119366] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 09/26/2014] [Accepted: 01/13/2015] [Indexed: 11/23/2022] Open
Abstract
Signalling through the ERK MAP kinase pathway plays an important role in many biological processes and it is often deregulated in disease states such as cancer. One major effect of MAP kinase signalling is to promote gene expression through the phosphorylation and activation of transcription factors like ELK1. ELK1 in turn controls the activity of immediate-early genes such as FOS. Here we have used ELK1 activation in HeLa cells as a read out to conduct a genome-wide siRNA screen to identify negative regulators of ERK-mediated immediate-early gene activation. One of the candidates that we identified was the E3 ubiquitin ligase UBE3A/E6-AP. Reductions in UBE3A levels cause increased basal levels of ERK activity, a loss of growth factor-mediated ERK activation and concomitant defects in immediate-early gene expression. Thus, UBE3A acts to dampen down basal level ERK activation and to prime the pathway for growth factor-mediated activation. Mechanistically, we demonstrate that UBE3A functions in HeLa cells through its binding partner, HPV18 E6 protein and the E6 target protein p53. Loss of either E6 or p53 blocks the effect of UBE3A depletion on ERK pathway signalling, indicating that in the context of oncogenic viral protein expression, UBE3A plays an important role in negating the consequences of p53 activation on ERK pathway signalling.
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Affiliation(s)
- Elisa Aguilar-Martinez
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Claire Morrisroe
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Andrew D. Sharrocks
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, United Kingdom
- * E-mail:
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36
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Wiseman EF, Chen X, Han N, Webber A, Ji Z, Sharrocks AD, Ang YS. Deregulation of the FOXM1 target gene network and its coregulatory partners in oesophageal adenocarcinoma. Mol Cancer 2015; 14:69. [PMID: 25889361 PMCID: PMC4392876 DOI: 10.1186/s12943-015-0339-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/11/2015] [Indexed: 12/19/2022] Open
Abstract
Background Survival rates for oesophageal adenocarcinoma (OAC) remain disappointingly poor and current conventional treatment modalities have minimal impact on long-term survival. This is partly due to a lack of understanding of the molecular changes that occur in this disease. Previous studies have indicated that the transcription factor FOXM1 is commonly upregulated in this cancer type but the impact of this overexpression on gene expression in the context of OAC is largely unknown. FOXM1 does not function alone but works alongside the antagonistically-functioning co-regulatory MMB and DREAM complexes. Methods To establish how FOXM1 affects gene expression in OAC we have identified the FOXM1 target gene network in OAC-derived cells using ChIP-seq and determined the expression of both its coregulatory partners and members of this target gene network in OAC by digital transcript counting using the Nanostring gene expression assay. Results We find co-upregulation of FOXM1 with its target gene network in OAC. Furthermore, we find changes in the expression of its coregulatory partners, including co-upregulation of LIN9 and, surprisingly, reduced expression of LIN54. Mechanistically, we identify LIN9 as the direct binding partner for FOXM1 in the MMB complex. In the context of OAC, both coregulator (eg LIN54) and target gene (eg UHRF1) expression levels are predictive of disease stage. Conclusions Together our data demonstrate that there are global changes to the FOXM1 regulatory network in OAC and the expression of components of this network help predict cancer prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0339-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth F Wiseman
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK. .,Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK.
| | - Xi Chen
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK. .,Present address: The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Namshik Han
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK. .,Present address: Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK.
| | - Aaron Webber
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Zongling Ji
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Andrew D Sharrocks
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Yeng S Ang
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK.
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37
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Abstract
The current knowledge on how protein–protein interactions regulate the function of transcription factors (TFs) has remained limited due to an incomplete knowledge of their interaction partners. In their recent work, Chen and colleagues (Li et al, 2015) analyse the interactome of 56 TFs and reveal distinct chromatin-associated and soluble TF complexes.
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Affiliation(s)
- Zongling Ji
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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Ji Z, Mohammed H, Webber A, Ridsdale J, Han N, Carroll JS, Sharrocks AD. The forkhead transcription factor FOXK2 acts as a chromatin targeting factor for the BAP1-containing histone deubiquitinase complex. Nucleic Acids Res 2014; 42:6232-42. [PMID: 24748658 PMCID: PMC4041447 DOI: 10.1093/nar/gku274] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [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: 01/15/2014] [Revised: 03/07/2014] [Accepted: 03/24/2014] [Indexed: 12/17/2022] Open
Abstract
There are numerous forkhead transcription factors in mammalian cells but we know little about the molecular functions of the majority of these. FOXK2 is a ubiquitously expressed family member suggesting an important function across multiple cell types. Here, we show that FOXK2 binds to the SIN3A and PR-DUB complexes. The PR-DUB complex contains the important tumour suppressor protein, the deubiquitinase BAP1. FOXK2 recruits BAP1 to DNA, promotes local histone deubiquitination and causes changes in target gene activity. Our results therefore provide an important link between BAP1 and the transcription factor FOXK2 and demonstrate how BAP1 can be recruited to specific regulatory loci.
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Affiliation(s)
- Zongling Ji
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Hisham Mohammed
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Aaron Webber
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Jenna Ridsdale
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Namshik Han
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Jason S Carroll
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Andrew D Sharrocks
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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O'Donnell A, Yang SH, Sharrocks AD. PARP1 orchestrates variant histone exchange in signal-mediated transcriptional activation. EMBO Rep 2013; 14:1084-91. [PMID: 24145797 PMCID: PMC3981078 DOI: 10.1038/embor.2013.164] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 08/02/2013] [Accepted: 09/16/2013] [Indexed: 12/02/2022] Open
Abstract
This study reveals an essential role for PARP1 in the exchange of the histone variant H2A.Z by H2A at the -1 nucleosome of the FOS promoter, which promotes signal-induced transcriptional activation. Transcriptional activation is accompanied by multiple molecular events that remodel the local chromatin environment in promoter regions. These molecular events are often orchestrated in response to the activation of signalling pathways, as exemplified by the response of immediate early genes such as FOS to ERK MAP kinase signalling. Here, we demonstrate that inducible NFI recruitment permits PARP1 binding to the FOS promoter by a mutually reinforcing loop. PARP1 and its poly(ADP-ribosyl)ation activity are required for maintaining FOS activation kinetics. We also show that the histone variant H2A.Z associates with the FOS promoter and acts in a transcription-suppressive manner. However, in response to ERK pathway signalling, H2A.Z is replaced by H2A; PARP1 activity is required to promote this exchange. Thus, our work has revealed an additional facet of PARP1 function in promoting dynamic remodelling of promoter-associated nucleosomes to allow transcriptional activation in response to cellular signalling.
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Affiliation(s)
- Amanda O'Donnell
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
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Affiliation(s)
- Shen-Hsi Yang
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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41
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Odrowaz Z, Sharrocks AD. The ETS transcription factors ELK1 and GABPA regulate different gene networks to control MCF10A breast epithelial cell migration. PLoS One 2012; 7:e49892. [PMID: 23284628 PMCID: PMC3527487 DOI: 10.1371/journal.pone.0049892] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [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: 09/26/2012] [Accepted: 10/17/2012] [Indexed: 12/29/2022] Open
Abstract
Members of the ETS transcription factor family often target the same binding regions and hence have the potential to regulate the same genes and downstream biological processes. However, individual family members also preferentially bind to other genomic regions, thus providing the potential for controlling distinct transcriptional programmes and generating specific biological effects. The ETS transcription factor ELK1 controls cell migration in breast epithelial cells through targeting a cohort of genes, independently from another family member GABPA, and therefore achieves biological specificity. Here, we demonstrate that GABPA also controls cell migration in breast epithelial cells. However, GABPA controls the expression of a different network of target genes to ELK1. Both direct and indirect target genes for GABPA are identified and amongst the direct targets we confirm the importance of RAC1 and KIF20A for cell migration. Therefore, although ELK1 and GABPA ultimately control the same biological process, they do so by regulating different cohorts of target genes associated with cytoskeletal functions and cell migration control.
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Affiliation(s)
- Zaneta Odrowaz
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew D. Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Yang SH, Kalkan T, Morrisroe C, Smith A, Sharrocks AD. A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation. PLoS Genet 2012; 8:e1003112. [PMID: 23271975 PMCID: PMC3521700 DOI: 10.1371/journal.pgen.1003112] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [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: 04/19/2012] [Accepted: 10/08/2012] [Indexed: 01/13/2023] Open
Abstract
Embryonic stem cells and induced pluripotent stem cells represent potentially important therapeutic agents in regenerative medicine. Complex interlinked transcriptional and signaling networks control the fate of these cells towards maintenance of pluripotency or differentiation. In this study we have focused on how mouse embryonic stem cells begin to differentiate and lose pluripotency and, in particular, the role that the ERK MAP kinase and GSK3 signaling pathways play in this process. Through a genome-wide siRNA screen we have identified more than 400 genes involved in loss of pluripotency and promoting the onset of differentiation. These genes were functionally associated with the ERK and/or GSK3 pathways, providing an important resource for studying the roles of these pathways in controlling escape from the pluripotent ground state. More detailed analysis identified MAP kinase phosphatases as a focal point of regulation and demonstrated an important role for these enzymes in controlling ERK activation kinetics and subsequently determining early embryonic stem cell fate decisions.
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Affiliation(s)
- Shen-Hsi Yang
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Tuzer Kalkan
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Claire Morrisroe
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Austin Smith
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Andrew D. Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Dibb M, Han N, Choudhury J, Hayes S, Valentine H, West C, Ang YS, Sharrocks AD. The FOXM1-PLK1 axis is commonly upregulated in oesophageal adenocarcinoma. Br J Cancer 2012; 107:1766-75. [PMID: 23037713 PMCID: PMC3493860 DOI: 10.1038/bjc.2012.424] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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: 06/15/2012] [Revised: 08/29/2012] [Accepted: 08/29/2012] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The transcription factor FOXM1 is an important regulator of the cell cycle through controlling periodic gene expression during the G2 and M phases. One key target for FOXM1 is the gene encoding the protein kinase PLK1 and PLK1 itself acts in a positive feedback loop to phosphorylate and activate FOXM1. Both FOXM1 and PLK1 have been shown to be overexpressed in a variety of different tumour types. METHODS We have used a combination of RT-PCR, western blotting, tissue microarrays and metadata analysis of microarray data to study whether the FOXM1-PLK1 regulatory axis is upregulated and operational in oesophageal adenocarcinoma. RESULTS FOXM1 and PLK1 are expressed in oesophageal adenocarcinoma-derived cell lines and demonstrate cross-regulatory interactions. Importantly, we also demonstrate the concomitant overexpression of FOXM1 and PLK1 in a large proportion of oesophageal adenocarcinoma samples. This co-association was extended to the additional FOXM1 target genes CCNB1, AURKB and CKS1. In a cohort of patients who subsequently underwent surgery, the expression of several FOXM1 target genes was prognostic for overall survival. CONCLUSIONS FOXM1 and its target gene PLK1 are commonly overexpressed in oesophageal adenocarcinomas and this association can be extended to other FOXM1 target genes, providing potentially important biomarkers for predicting post-surgery disease survival.
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Affiliation(s)
- M Dibb
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK
| | - N Han
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - J Choudhury
- Department of Histopathology, Salford Royal Foundation Trust, Stott Lane, Salford M6 8HD, UK
| | - S Hayes
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK
- Department of Histopathology, Salford Royal Foundation Trust, Stott Lane, Salford M6 8HD, UK
| | - H Valentine
- School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital, Manchester, UK
| | - C West
- School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital, Manchester, UK
| | - Y S Ang
- Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, UK
| | - A D Sharrocks
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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Yang SH, Sharrocks AD, Whitmarsh AJ. MAP kinase signalling cascades and transcriptional regulation. Gene 2012; 513:1-13. [PMID: 23123731 DOI: 10.1016/j.gene.2012.10.033] [Citation(s) in RCA: 307] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 10/08/2012] [Accepted: 10/18/2012] [Indexed: 02/06/2023]
Abstract
The MAP kinase (MAPK) signalling pathways play fundamental roles in a wide range of cellular processes and are often deregulated in disease states. One major mode of action for these pathways is in controlling gene expression, in particular through regulating transcription. In this review, we discuss recent significant advances in this area. In particular we focus on the mechanisms by which MAPKs are targeted to the nucleus and chromatin, and once there, how they impact on chromatin structure and subsequent gene regulation. We also discuss how systems biology approaches have contributed to our understanding of MAPK signaling networks, and also how the MAPK pathways intersect with other regulatory pathways in the nucleus. Finally, we summarise progress in studying the physiological functions of key MAPK transcriptional targets.
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Affiliation(s)
- Shen-Hsi Yang
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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Pritchett J, Harvey E, Athwal V, Berry A, Rowe C, Oakley F, Moles A, Mann DA, Bobola N, Sharrocks AD, Thomson BJ, Zaitoun AM, Irving WL, Guha IN, Hanley NA, Hanley KP. Osteopontin is a novel downstream target of SOX9 with diagnostic implications for progression of liver fibrosis in humans. Hepatology 2012; 56:1108-16. [PMID: 22488688 PMCID: PMC3638324 DOI: 10.1002/hep.25758] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
UNLABELLED Osteopontin (OPN) is an important component of the extracellular matrix (ECM), which promotes liver fibrosis and has been described as a biomarker for its severity. Previously, we have demonstrated that Sex-determining region Y-box 9 (SOX9) is ectopically expressed during activation of hepatic stellate cells (HSC) when it is responsible for the production of type 1 collagen, which causes scar formation in liver fibrosis. Here, we demonstrate that SOX9 regulates OPN. During normal development and in the mature liver, SOX9 and OPN are coexpressed in the biliary duct. In rodent and human models of fibrosis, both proteins were increased and colocalized to fibrotic regions in vivo and in culture-activated HSCs. SOX9 bound a conserved upstream region of the OPN gene, and abrogation of Sox9 in HSCs significantly decreased OPN production. Hedgehog (Hh) signaling has previously been shown to regulate OPN expression directly by glioblastoma (GLI) 1. Our data indicate that in models of liver fibrosis, Hh signaling more likely acts through SOX9 to modulate OPN. In contrast to Gli2 and Gli3, Gli1 is sparse in HSCs and is not increased upon activation. Furthermore, reduction of GLI2, but not GLI3, decreased the expression of both SOX9 and OPN, whereas overexpressing SOX9 or constitutively active GLI2 could rescue the antagonistic effects of cyclopamine on OPN expression. CONCLUSION These data reinforce SOX9, downstream of Hh signaling, as a core factor mediating the expression of ECM components involved in liver fibrosis. Understanding the role and regulation of SOX9 during liver fibrosis will provide insight into its potential modulation as an antifibrotic therapy or as a means of identifying potential ECM targets, similar to OPN, as biomarkers of fibrosis.
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Affiliation(s)
- James Pritchett
- Endocrinology and Diabetes Group, School of Biomedicine, University of ManchesterManchester, United Kingdom
| | - Emma Harvey
- Endocrinology and Diabetes Group, School of Biomedicine, University of ManchesterManchester, United Kingdom
| | - Varinder Athwal
- Endocrinology and Diabetes Group, School of Biomedicine, University of ManchesterManchester, United Kingdom
| | - Andrew Berry
- Endocrinology and Diabetes Group, School of Biomedicine, University of ManchesterManchester, United Kingdom
| | - Cliff Rowe
- Endocrinology and Diabetes Group, School of Biomedicine, University of ManchesterManchester, United Kingdom
| | - Fiona Oakley
- Liver Research Group, Institute of Cellular Medicine, University of NewcastleNewcastle-upon-Tyne, United Kingdom
| | - Anna Moles
- Liver Research Group, Institute of Cellular Medicine, University of NewcastleNewcastle-upon-Tyne, United Kingdom
| | - Derek A Mann
- Liver Research Group, Institute of Cellular Medicine, University of NewcastleNewcastle-upon-Tyne, United Kingdom
| | - Nicoletta Bobola
- School of Dentistry, University of ManchesterManchester, United Kingdom
| | - Andrew D Sharrocks
- Faculty of Life Sciences, University of ManchesterManchester, United Kingdom
| | - Brian J Thomson
- School of Molecular Medical Sciences, Nottingham Digestive Diseases Center, Biomedical Research Unit in Gastroenterology and Liver Disease, University of Nottingham and Nottingham University Hospitals, Queens Medical Center CampusNottingham United Kingdom
| | - Abed M Zaitoun
- Department of Cellular Pathology, Nottingham Digestive Diseases Center, Biomedical Research Unit in Gastroenterology and Liver Disease, University of Nottingham and Nottingham University Hospitals, Queens Medical Center CampusNottingham United Kingdom
| | - William L Irving
- School of Molecular Medical Sciences, Nottingham Digestive Diseases Center, Biomedical Research Unit in Gastroenterology and Liver Disease, University of Nottingham and Nottingham University Hospitals, Queens Medical Center CampusNottingham United Kingdom
| | - Indra N Guha
- Liver Unit, National Institute of Health Research, Nottingham Digestive Diseases Center, Biomedical Research Unit in Gastroenterology and Liver Disease, University of Nottingham and Nottingham University Hospitals, Queens Medical Center CampusNottingham United Kingdom
| | - Neil A Hanley
- Endocrinology and Diabetes Group, School of Biomedicine, University of ManchesterManchester, United Kingdom
| | - Karen Piper Hanley
- Endocrinology and Diabetes Group, School of Biomedicine, University of ManchesterManchester, United Kingdom
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46
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Odrowaz Z, Sharrocks AD. ELK1 uses different DNA binding modes to regulate functionally distinct classes of target genes. PLoS Genet 2012; 8:e1002694. [PMID: 22589737 PMCID: PMC3349735 DOI: 10.1371/journal.pgen.1002694] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [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: 01/04/2012] [Accepted: 03/22/2012] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic transcription factors are grouped into families and, due to their similar DNA binding domains, often have the potential to bind to the same genomic regions. This can lead to redundancy at the level of DNA binding, and mechanisms are required to generate specific functional outcomes that enable distinct gene expression programmes to be controlled by a particular transcription factor. Here we used ChIP–seq to uncover two distinct binding modes for the ETS transcription factor ELK1. In one mode, other ETS transcription factors can bind regulatory regions in a redundant fashion; in the second, ELK1 binds in a unique fashion to another set of genomic targets. Each binding mode is associated with different binding site features and also distinct regulatory outcomes. Furthermore, the type of binding mode also determines the control of functionally distinct subclasses of genes and hence the phenotypic response elicited. This is demonstrated for the unique binding mode where a novel role for ELK1 in controlling cell migration is revealed. We have therefore uncovered an unexpected link between the type of binding mode employed by a transcription factor, the subsequent gene regulatory mechanisms used, and the functional categories of target genes controlled. One of the major outstanding questions in eukaryotic gene regulation is how transcription factors with seemingly very similar DNA binding specificities elicit specific biological responses. The ETS transcription factor family provides a paradigm for investigating this phenomenon. Here, we have focused on the ETS transcription factor ELK1, and by combining genome-wide binding analysis coupled with gene expression analysis we have dissected two distinct gene regulatory activities for this transcription factor. In each of these regulatory modes, ELK1 exhibits distinct DNA binding characteristics which correlate with either positive or negative transcriptional activities and give rise to functionally distinct gene expression programmes. We demonstrate a novel function for ELK1 in controlling cell migration through one of these regulatory modes. Thus, we have demonstrated a clear link between the types of regulatory region bound by a transcription factor and its ability to control gene expression (i.e. in a positive or negative manner) and the functional downstream consequences of its target gene cohort. This work has implications for understanding how members of other multi-protein transcription factor families might function to generate different downstream functional consequences through engaging with different types of regulatory regions.
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Affiliation(s)
| | - Andrew D. Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Keld R, Guo B, Downey P, Cummins R, Gulmann C, Ang YS, Sharrocks AD. PEA3/ETV4-related transcription factors coupled with active ERK signalling are associated with poor prognosis in gastric adenocarcinoma. Br J Cancer 2011; 105:124-30. [PMID: 21673681 PMCID: PMC3137405 DOI: 10.1038/bjc.2011.187] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [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] [Indexed: 12/30/2022] Open
Abstract
Background: Transcription factors often play important roles in tumourigenesis. Members of the PEA3 subfamily of ETS-domain transcription factors fulfil such a role and have been associated with tumour metastasis in several different cancers. Moreover, the activity of the PEA3 subfamily transcription factors is potentiated by Ras-ERK pathway signalling, which is itself often deregulated in tumour cells. Methods: Immunohistochemical patterns of PEA3 expression and active ERK signalling were analysed and mRNA expression levels of PEA3, ER81, MMP-1 and MMP-7 were determined in gastric adenocarcinoma samples. Results: Here, we have studied the expression of the PEA3 subfamily members PEA3/ETV4 and ER81/ETV1 in gastric adenocarcinomas. PEA3 is upregulated at the protein level in gastric adenocarcinomas and both PEA3/ETV4 and ER81/ETV1 are upregulated at the mRNA level in gastric adenocarcinoma tissues. This increased expression correlates with the expression of a target gene associated with metastasis, MMP-1. Enhanced ERK signalling is also more prevalent in late-stage gastric adenocarcinomas, and the co-association of ERK signalling and PEA3 expression also occurs in late-stage gastric adenocarcinomas. Furthermore, the co-association of ERK signalling and PEA3 expression correlates with decreased survival rates. Conclusions: This study shows that members of the PEA3 subfamily of transcription factors are upregulated in gastric adenocarcinomas and that the simultaneous upregulation of PEA3 expression and ERK pathway signalling is indicative of late-stage disease and a poor survival prognosis.
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Affiliation(s)
- R Keld
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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Guo B, Panagiotaki N, Warwood S, Sharrocks AD. Dynamic modification of the ETS transcription factor PEA3 by sumoylation and p300-mediated acetylation. Nucleic Acids Res 2011; 39:6403-13. [PMID: 21543453 PMCID: PMC3159455 DOI: 10.1093/nar/gkr267] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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] [Indexed: 11/15/2022] Open
Abstract
Transcription factor activity is often controlled through the dynamic use of post-translational modifications. Two such modifications are acetylation and sumoylation, which both occur on lysine residues, providing the opportunity for cross-talk at the molecular level. Here, we focussed on the ETS-domain transcription factor PEA3 and studied the potential interplay between these two modifications. We demonstrate that PEA3 is acetylated in a p300-dependent manner. ERK MAPK pathway signalling potentiates acetylation of PEA3, and enhances its trans-activation capacity. However, the major acetylation and sumoylation events take place on the same sites in PEA3 making simultaneous modification impossible. Indeed, manipulation of either the sumoylation or acetylation pathways causes reciprocal changes in PEA3 acetylation and sumoylation respectively. However, despite the mutually exclusive nature of these modifications, both contribute to the trans-activation capacity of PEA3, implying that a dynamic series of modification events occurs during the activation process.
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Affiliation(s)
- Baoqiang Guo
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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49
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Demir O, Aysit N, Onder Z, Turkel N, Ozturk G, Sharrocks AD, Kurnaz IA. ETS-domain transcription factor Elk-1 mediates neuronal survival: SMN as a potential target. Biochim Biophys Acta Mol Basis Dis 2011; 1812:652-62. [PMID: 21362474 DOI: 10.1016/j.bbadis.2011.02.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 02/11/2011] [Accepted: 02/23/2011] [Indexed: 11/16/2022]
Abstract
Elk-1 belongs to the ternary complex factors (TCFs) subfamily of the ETS domain proteins, and plays a critical role in the expression of immediate-early genes (IEGs) upon mitogen stimulation and activation of the mitogen-activated protein kinase (MAPK) cascade. The association of TCFs with serum response elements (SREs) on IEG promoters has been widely studied and a role for Elk-1 in promoting cell cycle entry has been determined. However, the presence of the ETS domain transcription factor Elk-1 in axons and dendrites of post-mitotic adult brain neurons has implications for an alternative function for Elk-1 in neurons other than controlling proliferation. In this study, possible alternative roles for Elk-1 in neurons were investigated, and it was demonstrated that blocking TCF-mediated transactivation in neuronal cells leads to apoptosis through a caspase-dependent mechanism. Indeed RNAi-mediated depletion of endogenous Elk-1 results in increased caspase activity. Conversely, overexpression of either Elk-1 or Elk-VP16 fusion proteins was shown to rescue PC12 cells from chemically-induced apoptosis, and that higher levels of endogenous Elk-1 correlated with longer survival of DRGs in culture. It was shown that Elk-1 regulated the Mcl-1 gene expression required for survival, and that RNAi-mediated degradation of endogenous Elk-1 resulted in elimination of the mcl-1 message. We have further identified the survival-of-motor neuron-1 (SMN1) gene as a novel target of Elk-1, and show that the ets motifs in the SMN1 promoter are involved in this regulation.
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Affiliation(s)
- Ozlem Demir
- Yeditepe University, Department of Genetics and Bioengineering, 26 Agustos Yerlesimi, 34755, Kayisdagi, Istanbul, Turkey
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50
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Purtill FS, Whitehall SK, Williams ES, McInerny CJ, Sharrocks AD, Morgan BA. A homeodomain transcription factor regulates the DNA replication checkpoint in yeast. Cell Cycle 2011; 10:664-70. [PMID: 21304269 DOI: 10.4161/cc.10.4.14824] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Checkpoints monitor the successful completion of cell cycle processes, such as DNA replication, and also regulate the expression of cell cycle-dependent genes that are required for responses. In the model yeast Schizosaccharomyces pombe G 1/S phase-specific gene expression is regulated by the MBF (also known as DSC1) transcription factor complex and is also activated by the mammalian ATM/ATR-related Rad3 DNA replication checkpoint. Here, we show that the Yox1 homeodomain transcription factor acts to co-ordinate the expression of MBF-regulated genes during the cell division cycle. Moreover, our data suggests that Yox1 is inactivated by the Rad3 DNA replication checkpoint via phosphorylation by the conserved Cds1 checkpoint kinase. Collectively, our data has implications for understanding the mechanisms underlying the coordination of cell cycle processes in eukaryotes.
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Affiliation(s)
- Frances S Purtill
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon tyne, UK
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