1
|
Brænne I, Onengut-Gumuscu S, Chen R, Manichaikul AW, Rich SS, Chen WM, Farber CR. Dynamic changes in immune gene co-expression networks predict development of type 1 diabetes. Sci Rep 2021; 11:22651. [PMID: 34811390 PMCID: PMC8609030 DOI: 10.1038/s41598-021-01840-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 11/01/2021] [Indexed: 01/13/2023] Open
Abstract
Significant progress has been made in elucidating genetic risk factors influencing Type 1 diabetes (T1D); however, features other than genetic variants that initiate and/or accelerate islet autoimmunity that lead to the development of clinical T1D remain largely unknown. We hypothesized that genetic and environmental risk factors can both contribute to T1D through dynamic alterations of molecular interactions in physiologic networks. To test this hypothesis, we utilized longitudinal blood transcriptomic profiles in The Environmental Determinants of Diabetes in the Young (TEDDY) study to generate gene co-expression networks. In network modules that contain immune response genes associated with T1D, we observed highly dynamic differences in module connectivity in the 600 days (~ 2 years) preceding clinical diagnosis of T1D. Our results suggest that gene co-expression is highly plastic and that connectivity differences in T1D-associated immune system genes influence the timing and development of clinical disease.
Collapse
Affiliation(s)
- Ingrid Brænne
- Center for Public Health Genomics, University of Virginia, P.O. Box 800717, Charlottesville, VA, 22908, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, P.O. Box 800717, Charlottesville, VA, 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ruoxi Chen
- Center for Public Health Genomics, University of Virginia, P.O. Box 800717, Charlottesville, VA, 22908, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, P.O. Box 800717, Charlottesville, VA, 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, P.O. Box 800717, Charlottesville, VA, 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, P.O. Box 800717, Charlottesville, VA, 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia, P.O. Box 800717, Charlottesville, VA, 22908, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.
| |
Collapse
|
2
|
Pellegrini M. Accurate prediction of breast cancer survival through coherent voting networks with gene expression profiling. Sci Rep 2021; 11:14645. [PMID: 34282236 PMCID: PMC8289832 DOI: 10.1038/s41598-021-94243-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
For a patient affected by breast cancer, after tumor removal, it is necessary to decide which adjuvant therapy is able to prevent tumor relapse and formation of metastases. A prediction of the outcome of adjuvant therapy tailored for the patient is hard, due to the heterogeneous nature of the disease. We devised a methodology for predicting 5-years survival based on the new machine learning paradigm of coherent voting networks, with improved accuracy over state-of-the-art prediction methods. The 'coherent voting communities' metaphor provides a certificate justifying the survival prediction for an individual patient, thus facilitating its acceptability in practice, in the vein of explainable Artificial Intelligence. The method we propose is quite flexible and applicable to other types of cancer.
Collapse
Affiliation(s)
- Marco Pellegrini
- Institute of Informatics and Telematics (IIT), CNR, 56124, Pisa, Italy.
| |
Collapse
|
3
|
Xhonneux LP, Knight O, Lernmark Å, Bonifacio E, Hagopian WA, Rewers MJ, She JX, Toppari J, Parikh H, Smith KGC, Ziegler AG, Akolkar B, Krischer JP, McKinney EF. Transcriptional networks in at-risk individuals identify signatures of type 1 diabetes progression. Sci Transl Med 2021; 13:eabd5666. [PMID: 33790023 PMCID: PMC8447843 DOI: 10.1126/scitranslmed.abd5666] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/24/2020] [Accepted: 03/12/2021] [Indexed: 12/11/2022]
Abstract
Type 1 diabetes (T1D) is a disease of insulin deficiency that results from autoimmune destruction of pancreatic islet β cells. The exact cause of T1D remains unknown, although asymptomatic islet autoimmunity lasting from weeks to years before diagnosis raises the possibility of intervention before the onset of clinical disease. The number, type, and titer of islet autoantibodies are associated with long-term disease risk but do not cause disease, and robust early predictors of individual progression to T1D onset remain elusive. The Environmental Determinants of Diabetes in the Young (TEDDY) consortium is a prospective cohort study aiming to determine genetic and environmental interactions causing T1D. Here, we analyzed longitudinal blood transcriptomes of 2013 samples from 400 individuals in the TEDDY study before both T1D and islet autoimmunity. We identified and interpreted age-associated gene expression changes in healthy infancy and age-independent changes tracking with progression to both T1D and islet autoimmunity, beginning before other evidence of islet autoimmunity was present. We combined multivariate longitudinal data in a Bayesian joint model to predict individual risk of T1D onset and validated the association of a natural killer cell signature with progression and the model's predictive performance on an additional 356 samples from 56 individuals in the independent Type 1 Diabetes Prediction and Prevention study. Together, our results indicate that T1D is characterized by early and longitudinal changes in gene expression, informing the immunopathology of disease progression and facilitating prediction of its course.
Collapse
Affiliation(s)
- Louis-Pascal Xhonneux
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Oliver Knight
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC Skåne University Hospital Malmo, Jan Waldenströms gata 35, Malmö, Sweden
| | - Ezio Bonifacio
- Center for Regenerative Therapies, Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - William A Hagopian
- Pacific Northwest Research Institute, 720 Broadway, Seattle, WA 98122, USA
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1462 Laney Walker Blvd., Augusta, GA 30912, USA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Kiinamyllynkatu 4-8, 20521 Turku, Finland
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turun Lyliopisto, Finland
| | - Hemang Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, and Klinikum rechts der Isar, Technische, Universität München, Forschergruppe Diabetes e.V., Arcisstraße 21, 80333 München, Germany
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, 9000 Rockville Pike Bethesda, MD 20892, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK.
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
- Cambridge Centre for Artificial Intelligence in Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
4
|
Behring M, Shrestha S, Manne U, Cui X, Gonzalez-Reymundez A, Grueneberg A, Vazquez AI. Integrated landscape of copy number variation and RNA expression associated with nodal metastasis in invasive ductal breast carcinoma. Oncotarget 2018; 9:36836-36848. [PMID: 30627325 PMCID: PMC6305147 DOI: 10.18632/oncotarget.26386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/31/2018] [Indexed: 01/01/2023] Open
Abstract
Background Lymph node metastasis (NM) in breast cancer is a clinical predictor of patient outcomes, but how its genetic underpinnings contribute to aggressive phenotypes is unclear. Our objective was to create the first landscape analysis of CNV-associated NM in ductal breast cancer. To assess the role of copy number variations (CNVs) in NM, we compared CNVs and/or associated mRNA expression in primary tumors of patients with NM to those without metastasis. Results We found CNV loss in chromosomes 1, 3, 9, 18, and 19 and gains in chromosomes 5, 8, 12, 14, 16-17, and 20 that were associated with NM and replicated in both databases. In primary tumors, per-gene CNVs associated with NM were ten times more frequent than mRNA expression; however, there were few CNV-driven changes in mRNA expression that differed by nodal status. Overlapping regions of CNV changes and mRNA expression were evident for the CTAGE5 gene. In 8q12, 11q13-14, 20q1, and 17q14-24 regions, there were gene-specific gains in CNV-driven mRNA expression associated with NM. Methods Data on CNV and mRNA expression from the TCGA and the METABRIC consortium of breast ductal carcinoma were utilized to identify CNV-based features associated with NM. Within each dataset, associations were compared across omic platforms to identify CNV-driven variations in gene expression. Only replications across both datasets were considered as determinants of NM. Conclusions Gains in CTAGE5, NDUFC2, EIF4EBP1, and PSCA genes and their expression may aid in early diagnosis of metastatic breast carcinoma and have potential as therapeutic targets.
Collapse
Affiliation(s)
- Michael Behring
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Upender Manne
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Department of Pathology and Surgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Xiangqin Cui
- Biostatistics Department, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Agustin Gonzalez-Reymundez
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Alexander Grueneberg
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Ana I Vazquez
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
5
|
Lung tumors with distinct p53 mutations respond similarly to p53 targeted therapy but exhibit genotype-specific statin sensitivity. Genes Dev 2017; 31:1339-1353. [PMID: 28790158 PMCID: PMC5580655 DOI: 10.1101/gad.298463.117] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/06/2017] [Indexed: 01/07/2023]
Abstract
In this study, Turrell et al. perform a comprehensive transcriptional and functional analysis of murine lung tumors with distinct p53 alterations (p53 loss, DNA contact [R270H], or conformational [R172H] mutations) and identified both common therapeutic vulnerabilities and mutation-specific liabilities in these tumors. Overall, their findings provide insight into new therapeutic approaches that may be clinically relevant for patients with mutant p53 lung tumors. Lung adenocarcinoma accounts for ∼40% of lung cancers, the leading cause of cancer-related death worldwide, and current therapies provide only limited survival benefit. Approximately half of lung adenocarcinomas harbor mutations in TP53 (p53), making these mutants appealing targets for lung cancer therapy. As mutant p53 remains untargetable, mutant p53-dependent phenotypes represent alternative targeting opportunities, but the prevalence and therapeutic relevance of such effects (gain of function and dominant-negative activity) in lung adenocarcinoma are unclear. Through transcriptional and functional analysis of murine KrasG12D-p53null, -p53R172H (conformational), and -p53R270H (contact) mutant lung tumors, we identified genotype-independent and genotype-dependent therapeutic sensitivities. Unexpectedly, we found that wild-type p53 exerts a dominant tumor-suppressive effect on mutant tumors, as all genotypes were similarly sensitive to its restoration in vivo. These data show that the potential of p53 targeted therapies is comparable across all p53-deficient genotypes and may explain the high incidence of p53 loss of heterozygosity in mutant tumors. In contrast, mutant p53 gain of function and their associated vulnerabilities can vary according to mutation type. Notably, we identified a p53R270H-specific sensitivity to simvastatin in lung tumors, and the transcriptional signature that underlies this sensitivity was also present in human lung tumors, indicating that this therapeutic approach may be clinically relevant.
Collapse
|
6
|
van de Ven RA, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K, van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer MW, Sahai E, Derksen PW. p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. Nat Commun 2016; 7:13874. [PMID: 28004812 PMCID: PMC5192218 DOI: 10.1038/ncomms13874] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/07/2016] [Indexed: 02/07/2023] Open
Abstract
Spatiotemporal activation of RhoA and actomyosin contraction underpins cellular adhesion and division. Loss of cell-cell adhesion and chromosomal instability are cardinal events that drive tumour progression. Here, we show that p120-catenin (p120) not only controls cell-cell adhesion, but also acts as a critical regulator of cytokinesis. We find that p120 regulates actomyosin contractility through concomitant binding to RhoA and the centralspindlin component MKLP1, independent of cadherin association. In anaphase, p120 is enriched at the cleavage furrow where it binds MKLP1 to spatially control RhoA GTPase cycling. Binding of p120 to MKLP1 during cytokinesis depends on the N-terminal coiled-coil domain of p120 isoform 1A. Importantly, clinical data show that loss of p120 expression is a common event in breast cancer that strongly correlates with multinucleation and adverse patient survival. In summary, our study identifies p120 loss as a driver event of chromosomal instability in cancer.
Collapse
Affiliation(s)
- Robert A.H. van de Ven
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Jolien S. de Groot
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Danielle Park
- Tumour Cell Biology Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Robert van Domselaar
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Danielle de Jong
- Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Elsken van der Wall
- Department of Internal Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - H. Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Paul J. van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Martin W. Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Erik Sahai
- Tumour Cell Biology Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Patrick W.B. Derksen
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| |
Collapse
|
7
|
Thomas BC, Kay JD, Menon S, Vowler SL, Dawson SN, Bucklow LJ, Luxton HJ, Johnston T, Massie CE, Pugh M, Warren AY, Barker P, Burling K, Lynch AG, George A, Burge J, Corcoran M, Stearn S, Lamb AD, Sharma NL, Shaw GL, Neal DE, Whitaker HC. Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel. Endocr Relat Cancer 2016; 23:797-812. [PMID: 27578825 DOI: 10.1530/erc-16-0287] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 08/10/2016] [Indexed: 01/05/2023]
Abstract
Due to increased sensitivity, the expression of circulating nucleotides is rapidly gaining popularity in cancer diagnosis. Whole blood mRNA has been used in studies on a number of cancers, most notably two separate studies that used whole blood mRNA to define non-overlapping signatures of prostate cancer that has become castration independent. Prostate cancer is known to rely on androgens for initial growth, and there is increasing evidence on the importance of the androgen axis in advanced disease. Using whole blood mRNA samples from patients with prostate cancer, we have identified the four-gene panel of FAM129A, MME, KRT7 and SOD2 in circulating mRNA that are differentially expressed in a discovery cohort of metastatic samples. Validation of these genes at the mRNA and protein level was undertaken in additional cohorts defined by risk of relapse following surgery and hormone status. All the four genes were downregulated at the mRNA level in the circulation and in primary tissue, but this was not always reflected in tissue protein expression. MME demonstrated significant differences in the hormone cohorts, whereas FAM129A is downregulated at the mRNA level but is raised at the protein level in tumours. Using published ChIP-seq data, we have demonstrated that this may be due to AR binding at the FAM129A and MME loci in multiple cell lines. These data suggest that whole blood mRNA of androgen-regulated genes has the potential to be used for diagnosis and monitoring of prostate cancer.
Collapse
Affiliation(s)
- Benjamin C Thomas
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Jonathan D Kay
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular Diagnostics and Therapeutics GroupUniversity College London, London, UK
| | - Suraj Menon
- Bioinformatics and Statistics Core FacilityCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Astra Zeneca2 Riverside, Granta Park, Cambridge, UK
| | - Sarah L Vowler
- Bioinformatics and Statistics Core FacilityCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Astra Zeneca2 Riverside, Granta Park, Cambridge, UK
| | - Sarah N Dawson
- Bioinformatics and Statistics Core FacilityCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Laura J Bucklow
- Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Hayley J Luxton
- Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular Diagnostics and Therapeutics GroupUniversity College London, London, UK
| | - Thomas Johnston
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Charlie E Massie
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular and Computational Diagnostics GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Michelle Pugh
- Genomics Core FacilityCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Anne Y Warren
- Department of HistopathologyCambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Peter Barker
- National Institute for Health Research Cambridge Biomedical Research Centre Core Biochemistry Assay LaboratoryCambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Keith Burling
- National Institute for Health Research Cambridge Biomedical Research Centre Core Biochemistry Assay LaboratoryCambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Andy G Lynch
- Computational Biology GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Anne George
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Johanna Burge
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Marie Corcoran
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Sara Stearn
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Alastair D Lamb
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Naomi L Sharma
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Greg L Shaw
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK University College Hospital at Westmoreland StreetLondon, UK
| | - David E Neal
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Nuffield Department of Surgical SciencesJohn Radcliffe Hospital, Headington, Oxford, UK
| | - Hayley C Whitaker
- Uro-Oncology Research GroupCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Biomarker InitiativeCancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK Molecular Diagnostics and Therapeutics GroupUniversity College London, London, UK
| |
Collapse
|
8
|
Martín-Martín N, Piva M, Urosevic J, Aldaz P, Sutherland JD, Fernández-Ruiz S, Arreal L, Torrano V, Cortazar AR, Planet E, Guiu M, Radosevic-Robin N, Garcia S, Macías I, Salvador F, Domenici G, Rueda OM, Zabala-Letona A, Arruabarrena-Aristorena A, Zúñiga-García P, Caro-Maldonado A, Valcárcel-Jiménez L, Sánchez-Mosquera P, Varela-Rey M, Martínez-Chantar ML, Anguita J, Ibrahim YH, Scaltriti M, Lawrie CH, Aransay AM, Iovanna JL, Baselga J, Caldas C, Barrio R, Serra V, dM Vivanco M, Matheu A, Gomis RR, Carracedo A. Stratification and therapeutic potential of PML in metastatic breast cancer. Nat Commun 2016; 7:12595. [PMID: 27553708 PMCID: PMC4999521 DOI: 10.1038/ncomms12595] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 07/12/2016] [Indexed: 01/15/2023] Open
Abstract
Patient stratification has been instrumental for the success of targeted therapies in breast cancer. However, the molecular basis of metastatic breast cancer and its therapeutic vulnerabilities remain poorly understood. Here we show that PML is a novel target in aggressive breast cancer. The acquisition of aggressiveness and metastatic features in breast tumours is accompanied by the elevated PML expression and enhanced sensitivity to its inhibition. Interestingly, we find that STAT3 is responsible, at least in part, for the transcriptional upregulation of PML in breast cancer. Moreover, PML targeting hampers breast cancer initiation and metastatic seeding. Mechanistically, this biological activity relies on the regulation of the stem cell gene SOX9 through interaction of PML with its promoter region. Altogether, we identify a novel pathway sustaining breast cancer aggressiveness that can be therapeutically exploited in combination with PML-based stratification.
Collapse
Affiliation(s)
| | - Marco Piva
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Jelena Urosevic
- Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
| | - Paula Aldaz
- Oncology Area, Biodonostia Institute, 20014 San Sebastian, Spain
| | | | | | - Leire Arreal
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Verónica Torrano
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Ana R. Cortazar
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Evarist Planet
- Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marc Guiu
- Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
| | - Nina Radosevic-Robin
- ERTICa Research Group, University of Auvergne EA4677, Clermont-Ferrand, France
- Biodiagnostics Laboratory OncoGenAuvergne, Pathology Unit, Jean Perrin Comprehensive Cancer Center, 63000 Clermont-Ferrand, France
| | - Stephane Garcia
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR 1068, CNRS UMR 7258, Aix-Marseille University and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
| | - Iratxe Macías
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Fernando Salvador
- Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
| | - Giacomo Domenici
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | | | | | | | | | | | | | - Marta Varela-Rey
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Maria Luz Martínez-Chantar
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Juan Anguita
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- IKERBASQUE, Basque foundation for science, 48013 Bilbao, Spain
| | - Yasir H. Ibrahim
- Experimental Therapeutics Group, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
- Weill Cornell Medicine, New York 10021, USA
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Department of Pathology, Memorial Sloan-Kettering Cancer Center, 10065 New York, USA
| | - Charles H. Lawrie
- Oncology Area, Biodonostia Institute, 20014 San Sebastian, Spain
- IKERBASQUE, Basque foundation for science, 48013 Bilbao, Spain
| | - Ana M. Aransay
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR 1068, CNRS UMR 7258, Aix-Marseille University and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
| | - Jose Baselga
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan-Kettering Cancer Center, 10065 New York, USA
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Rosa Barrio
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Maria dM Vivanco
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Ander Matheu
- Oncology Area, Biodonostia Institute, 20014 San Sebastian, Spain
- IKERBASQUE, Basque foundation for science, 48013 Bilbao, Spain
| | - Roger R. Gomis
- Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Arkaitz Carracedo
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- IKERBASQUE, Basque foundation for science, 48013 Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), 48949 Leioa, Spain
| |
Collapse
|
9
|
Iddawela M, Rueda OM, Klarqvist M, Graf S, Earl HM, Caldas C. Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay. BMC Med Genomics 2016; 9:54. [PMID: 27542606 PMCID: PMC4992321 DOI: 10.1186/s12920-016-0215-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, selection, extension, and ligation (DASL) assay is a platform for gene expression profiling from FFPE tissue and hence could allow analysis of large collections of tissue with associated clinical data from existing archives, therefore facilitating the development of novel biomarkers. METHOD RNA isolated from matched fresh frozen (FF) and FFPE cancer specimens was profiled using both the DASL whole-genome (WG) platform, and Illumina BeadArray's, and results were compared. Samples utilized were obtained from the breast cancer tumour bank held at the Cambridge University Hospitals NHS Foundation Trust. RESULTS The number of reliably detected probes was comparable between the DASL and BeadArray platforms, indicating that the source of RNA did not result in a significant difference in the detection rates (Mean probes- 17114 in FFPE & 17400 in FF). There was a significant degree of correlation between replicates within the FF and FFPE sample sets (r (2) = 0.96-0.98) as well as between the two platforms (DASL vs. BeadArray r (2) = range 0.83-0.89). Hierarchical clustering using the most informative probes showed that replicate and matched samples were grouped into the same sub-cluster, regardless of whether RNA was derived from FF or FFPE tissue. CONCLUSION Both FF and FFPE material generated reproducible gene expression profiles, although there was more noise in profiles from FFPE specimens. We have shown that the DASL WG platform is suitable for profiling formalin-fixed paraffin-embedded samples, but robust bioinformatics analysis is required.
Collapse
Affiliation(s)
- Mahesh Iddawela
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800 Australia
- School of Clinical Sciences, Monash University, Clayton, Victoria Australia
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Marcus Klarqvist
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Stefan Graf
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Helena M. Earl
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
| |
Collapse
|
10
|
Identification of host transcriptional networks showing concentration-dependent regulation by HPV16 E6 and E7 proteins in basal cervical squamous epithelial cells. Sci Rep 2016; 6:29832. [PMID: 27457222 PMCID: PMC4960560 DOI: 10.1038/srep29832] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/22/2016] [Indexed: 12/19/2022] Open
Abstract
Development of cervical squamous cell carcinoma requires increased expression of the major high-risk human-papillomavirus (HPV) oncogenes E6 and E7 in basal cervical epithelial cells. We used a systems biology approach to identify host transcriptional networks in such cells and study the concentration-dependent changes produced by HPV16-E6 and -E7 oncoproteins. We investigated sample sets derived from the W12 model of cervical neoplastic progression, for which high quality phenotype/genotype data were available. We defined a gene co-expression matrix containing a small number of highly-connected hub nodes that controlled large numbers of downstream genes (regulons), indicating the scale-free nature of host gene co-expression in W12. We identified a small number of ‘master regulators’ for which downstream effector genes were significantly associated with protein levels of HPV16 E6 (n = 7) or HPV16 E7 (n = 5). We validated our data by depleting E6/E7 in relevant cells and by functional analysis of selected genes in vitro. We conclude that the network of transcriptional interactions in HPV16-infected basal-type cervical epithelium is regulated in a concentration-dependent manner by E6/E7, via a limited number of central master-regulators. These effects are likely to be significant in cervical carcinogenesis, where there is competitive selection of cells with elevated expression of virus oncoproteins.
Collapse
|
11
|
Laé M, La Rosa P, Mandel J, Reyal F, Hupé P, Terrier P, Couturier J. Whole-genome profiling helps to classify phyllodes tumours of the breast. J Clin Pathol 2016; 69:1081-1087. [DOI: 10.1136/jclinpath-2016-203684] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/21/2016] [Accepted: 04/28/2016] [Indexed: 11/03/2022]
|
12
|
Stojic L, Niemczyk M, Orjalo A, Ito Y, Ruijter AEM, Uribe-Lewis S, Joseph N, Weston S, Menon S, Odom DT, Rinn J, Gergely F, Murrell A. Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions. Nat Commun 2016; 7:10406. [PMID: 26832224 PMCID: PMC4740813 DOI: 10.1038/ncomms10406] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate gene expression via their RNA product or through transcriptional interference, yet a strategy to differentiate these two processes is lacking. To address this, we used multiple small interfering RNAs (siRNAs) to silence GNG12-AS1, a nuclear lncRNA transcribed in an antisense orientation to the tumour-suppressor DIRAS3. Here we show that while most siRNAs silence GNG12-AS1 post-transcriptionally, siRNA complementary to exon 1 of GNG12-AS1 suppresses its transcription by recruiting Argonaute 2 and inhibiting RNA polymerase II binding. Transcriptional, but not post-transcriptional, silencing of GNG12-AS1 causes concomitant upregulation of DIRAS3, indicating a function in transcriptional interference. This change in DIRAS3 expression is sufficient to impair cell cycle progression. In addition, the reduction in GNG12-AS1 transcripts alters MET signalling and cell migration, but these are independent of DIRAS3. Thus, differential siRNA targeting of a lncRNA allows dissection of the functions related to the process and products of its transcription.
Collapse
Affiliation(s)
- Lovorka Stojic
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Malwina Niemczyk
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Arturo Orjalo
- Biosearch Technologies Inc., 2199S. McDowell Boulevard, Petaluma, California 94954, USA
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Anna Elisabeth Maria Ruijter
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Nimesh Joseph
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen Weston
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Duncan T. Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - John Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Adele Murrell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| |
Collapse
|
13
|
Madhu B, Narita M, Jauhiainen A, Menon S, Stubbs M, Tavaré S, Narita M, Griffiths JR. Metabolomic changes during cellular transformation monitored by metabolite-metabolite correlation analysis and correlated with gene expression. Metabolomics 2015; 11:1848-1863. [PMID: 26491426 PMCID: PMC4605990 DOI: 10.1007/s11306-015-0838-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/27/2015] [Indexed: 12/13/2022]
Abstract
To investigate metabolic changes during cellular transformation, we used a 1H NMR based metabolite-metabolite correlation analysis (MMCA) method, which permits analysis of homeostatic mechanisms in cells at the steady state, in an inducible cell transformation model. Transcriptomic data were used to further explain the results. Transformed cells showed many more metabolite-metabolite correlations than control cells. Some had intuitively plausible explanations: a shift from glycolysis to amino acid oxidation after transformation was accompanied by a strongly positive correlation between glucose and glutamine and a strongly negative one between lactate and glutamate; there were also many correlations between the branched chain amino acids and the aromatic amino acids. Others remain puzzling: after transformation strong positive correlations developed between choline and a group of five amino acids, whereas the same amino acids showed negative correlations with phosphocholine, a membrane phospholipid precursor. MMCA in conjunction with transcriptome analysis has opened a new window into the metabolome.
Collapse
Affiliation(s)
- Basetti Madhu
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Masako Narita
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Alexandra Jauhiainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Early Clinical Biometrics, AstraZeneca AB R&D, Mölndal, Sweden
| | - Suraj Menon
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Marion Stubbs
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Simon Tavaré
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Masashi Narita
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - John R. Griffiths
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| |
Collapse
|
14
|
Mohammed H, Russell IA, Stark R, Rueda OM, Hickey TE, Tarulli GA, Serandour AAA, Birrell SN, Bruna A, Saadi A, Menon S, Hadfield J, Pugh M, Raj GV, Brown GD, D’Santos C, Robinson JLL, Silva G, Launchbury R, Perou CM, Stingl J, Caldas C, Tilley WD, Carroll JS. Progesterone receptor modulates ERα action in breast cancer. Nature 2015; 523:313-7. [PMID: 26153859 PMCID: PMC4650274 DOI: 10.1038/nature14583] [Citation(s) in RCA: 482] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/22/2015] [Indexed: 01/27/2023]
Abstract
Progesterone receptor (PR) expression is used as a biomarker of oestrogen receptor-α (ERα) function and breast cancer prognosis. Here we show that PR is not merely an ERα-induced gene target, but is also an ERα-associated protein that modulates its behaviour. In the presence of agonist ligands, PR associates with ERα to direct ERα chromatin binding events within breast cancer cells, resulting in a unique gene expression programme that is associated with good clinical outcome. Progesterone inhibited oestrogen-mediated growth of ERα(+) cell line xenografts and primary ERα(+) breast tumour explants, and had increased anti-proliferative effects when coupled with an ERα antagonist. Copy number loss of PGR, the gene coding for PR, is a common feature in ERα(+) breast cancers, explaining lower PR levels in a subset of cases. Our findings indicate that PR functions as a molecular rheostat to control ERα chromatin binding and transcriptional activity, which has important implications for prognosis and therapeutic interventions.
Collapse
Affiliation(s)
- Hisham Mohammed
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - I. Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Rory Stark
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Theresa E. Hickey
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, SA 5005, Australia
| | - Gerard A. Tarulli
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, SA 5005, Australia
| | - Aurelien A. A. Serandour
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Stephen N. Birrell
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Amel Saadi
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - James Hadfield
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Michelle Pugh
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ganesh V. Raj
- Department of Urology, University of Texas, Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Gordon D. Brown
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Clive D’Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jessica L. L. Robinson
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Grace Silva
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB7295, Chapel Hill, NC, 27599, USA
| | - Rosalind Launchbury
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB7295, Chapel Hill, NC, 27599, USA
| | - John Stingl
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge, CB2 0RE
| | - Wayne D. Tilley
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jason S. Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| |
Collapse
|
15
|
Redmond AM, Byrne C, Bane FT, Brown GD, Tibbitts P, O'Brien K, Hill ADK, Carroll JS, Young LS. Genomic interaction between ER and HMGB2 identifies DDX18 as a novel driver of endocrine resistance in breast cancer cells. Oncogene 2015; 34:3871-80. [PMID: 25284587 DOI: 10.1038/onc.2014.323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 08/04/2014] [Accepted: 08/24/2014] [Indexed: 01/01/2023]
Abstract
Breast cancer resistance to endocrine therapies such as tamoxifen and aromatase inhibitors is a significant clinical problem. Steroid receptor coactivator-1 (SRC-1), a coregulatory protein of the oestrogen receptor (ER), has previously been shown to have a significant role in the progression of breast cancer. The chromatin protein high mobility group box 2 (HMGB2) was identified as an SRC-1 interacting protein in the endocrine-resistant setting. We investigated the expression of HMGB2 in a cohort of 1068 breast cancer patients and found an association with increased disease-free survival time in patients treated with endocrine therapy. However, it was also verified that HMGB2 expression could be switched on in endocrine-resistant tumours from breast cancer patients. To explore the function of this poorly characterized protein, we performed HMGB2 ChIPseq and found distinct binding patterns between the two contexts. In the resistant setting, the HMGB2, SRC-1 and ER complex are enriched at promoter regions of target genes, with bioinformatic analysis indicating a switch in binding partners between the sensitive and resistant phenotypes. Integration of binding and gene expression data reveals a concise set of target genes of this complex including the RNA helicase DDX18. Modulation of DDX18 directly affects growth of tamoxifen-resistant cells, suggesting that it may be a critical downstream effector of the HMGB2:ER complex. This study defines HMGB2 interactions with the ER complex at specific target genes in the tamoxifen-resistant setting.
Collapse
MESH Headings
- Animals
- Antineoplastic Agents, Hormonal/pharmacology
- Antineoplastic Agents, Hormonal/therapeutic use
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Cell Line, Tumor
- Cell Proliferation/genetics
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- HMGB2 Protein/genetics
- HMGB2 Protein/metabolism
- Humans
- Kaplan-Meier Estimate
- MCF-7 Cells
- Mice, Inbred BALB C
- Mice, SCID
- Nuclear Receptor Coactivator 1/genetics
- Nuclear Receptor Coactivator 1/metabolism
- Oligonucleotide Array Sequence Analysis
- Promoter Regions, Genetic/genetics
- Protein Binding
- RNA Interference
- Receptors, Estrogen/genetics
- Receptors, Estrogen/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Tamoxifen/pharmacology
- Tamoxifen/therapeutic use
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- A M Redmond
- 1] Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland [2] Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - C Byrne
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - F T Bane
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - G D Brown
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - P Tibbitts
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - K O'Brien
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - A D K Hill
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - J S Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - L S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
16
|
Lussier AA, Stepien KA, Weinberg J, Kobor MS. Prenatal alcohol exposure alters gene expression in the rat brain: Experimental design and bioinformatic analysis of microarray data. Data Brief 2015. [PMID: 26217797 PMCID: PMC4510447 DOI: 10.1016/j.dib.2015.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We previously identified gene expression changes in the prefrontal cortex and hippocampus of rats prenatally exposed to alcohol under both steady-state and challenge conditions (Lussier et al., 2015, Alcohol.: Clin. Exp. Res., 39, 251–261). In this study, adult female rats from three prenatal treatment groups (ad libitum-fed control, pair-fed, and ethanol-fed) were injected with physiological saline solution or complete Freund׳s adjuvant (CFA) to induce arthritis (adjuvant-induced arthritis, AA). The prefrontal cortex and hippocampus were collected 16 days (peak of arthritis) or 39 days (during recovery) following injection, and whole genome gene expression was assayed using Illumina׳s RatRef-12 expression microarray. Here, we provide additional metadata, detailed explanations of data pre-processing steps and quality control, as well as a basic framework for the bioinformatic analyses performed. The datasets from this study are publicly available on the GEO repository (accession number GSE63561).
Collapse
Affiliation(s)
- Alexandre A. Lussier
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katarzyna A. Stepien
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joanne Weinberg
- Department of Cellular and Physiological Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
- Corresponding author. Tel.: +1 604 822 6214; fax: +1 604 822 2316.
| | - Michael S. Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Human Early Learning Partnership, University of British Columbia, Room 2024, 950 West 28th Avenue, Vancouver, British Columbia, Canada V5Z 4H4
- Corresponding author. Tel.: +1 604 875 3803; fax: +1 604 875 3840.
| |
Collapse
|
17
|
Jurmeister S, Ramos-Montoya A, Neal DE, Fryer LGD. Transcriptomic analysis reveals inhibition of androgen receptor activity by AMPK in prostate cancer cells. Oncotarget 2015; 5:3785-99. [PMID: 25003216 PMCID: PMC4116520 DOI: 10.18632/oncotarget.1997] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Metabolic alterations contribute to prostate cancer development and progression; however, the role of the central metabolic regulator AMP-activated protein kinase (AMPK) remains controversial. The androgen receptor (AR), a key driver of prostate cancer, regulates prostate cancer cell metabolism by driving the expression of a network of metabolic genes and activates AMPK through increasing the expression of one of its upstream kinases. To more clearly define the role of AMPK in prostate cancer, we performed expression profiling following pharmacologic activation of this kinase. We found that genes down-regulated upon AMPK activation were over-expressed in prostate cancer, consistent with a tumour suppressive function of AMPK. Strikingly, we identified the AR as one of the most significantly enriched transcription factors mediating gene expression changes downstream of AMPK signalling in prostate cancer cells. Activation of AMPK inhibited AR transcriptional activity and reduced androgen-dependent expression of known AR target genes. Conversely, knock-down of AMPK increased AR activity. Modulation of AR expression could not explain these effects. Instead, we observed that activation of AMPK reduced nuclear localisation of the AR. We thus propose the presence of a negative feedback loop in prostate cancer cells whereby AR activates AMPK and AMPK feeds back to limit AR-driven transcription.
Collapse
Affiliation(s)
- Sarah Jurmeister
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, UK
| | | | | | - Lee G D Fryer
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, UK
| |
Collapse
|
18
|
Forster L, McCooke J, Bellgard M, Joske D, Finlayson J, Ghassemifar R. Differential gene expression analysis in early and late erythroid progenitor cells in β-thalassaemia. Br J Haematol 2015; 170:257-67. [DOI: 10.1111/bjh.13432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/19/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Luke Forster
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
| | - John McCooke
- Centre for Comparative Genomics; Murdoch University; Murdoch WA Australia
| | - Matthew Bellgard
- Centre for Comparative Genomics; Murdoch University; Murdoch WA Australia
| | - David Joske
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
| | - Jill Finlayson
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
| | - Reza Ghassemifar
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
| |
Collapse
|
19
|
Massie CE, Spiteri I, Ross-Adams H, Luxton H, Kay J, Whitaker HC, Dunning MJ, Lamb AD, Ramos-Montoya A, Brewer DS, Cooper CS, Eeles R, Warren AY, Tavaré S, Neal DE, Lynch AG. HES5 silencing is an early and recurrent change in prostate tumourigenesis. Endocr Relat Cancer 2015; 22:131-44. [PMID: 25560400 PMCID: PMC4335379 DOI: 10.1530/erc-14-0454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 12/18/2014] [Accepted: 01/05/2015] [Indexed: 02/06/2023]
Abstract
Prostate cancer is the most common cancer in men, resulting in over 10 000 deaths/year in the UK. Sequencing and copy number analysis of primary tumours has revealed heterogeneity within tumours and an absence of recurrent founder mutations, consistent with non-genetic disease initiating events. Using methylation profiling in a series of multi-focal prostate tumours, we identify promoter methylation of the transcription factor HES5 as an early event in prostate tumourigenesis. We confirm that this epigenetic alteration occurs in 86-97% of cases in two independent prostate cancer cohorts (n=49 and n=39 tumour-normal pairs). Treatment of prostate cancer cells with the demethylating agent 5-aza-2'-deoxycytidine increased HES5 expression and downregulated its transcriptional target HES6, consistent with functional silencing of the HES5 gene in prostate cancer. Finally, we identify and test a transcriptional module involving the AR, ERG, HES1 and HES6 and propose a model for the impact of HES5 silencing on tumourigenesis as a starting point for future functional studies.
Collapse
Affiliation(s)
- Charles E Massie
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Inmaculada Spiteri
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Helen Ross-Adams
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Hayley Luxton
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Jonathan Kay
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Hayley C Whitaker
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Mark J Dunning
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Antonio Ramos-Montoya
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Daniel S Brewer
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Colin S Cooper
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Rosalind Eeles
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Anne Y Warren
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Simon Tavaré
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - David E Neal
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| |
Collapse
|
20
|
Hoeksema MA, Scicluna BP, Boshuizen MCS, van der Velden S, Neele AE, Van den Bossche J, Matlung HL, van den Berg TK, Goossens P, de Winther MPJ. IFN-γ priming of macrophages represses a part of the inflammatory program and attenuates neutrophil recruitment. THE JOURNAL OF IMMUNOLOGY 2015; 194:3909-16. [PMID: 25750432 DOI: 10.4049/jimmunol.1402077] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 02/02/2015] [Indexed: 01/22/2023]
Abstract
Macrophages form a heterogeneous population of immune cells, which is critical for both the initiation and resolution of inflammation. They can be skewed to a proinflammatory subtype by the Th1 cytokine IFN-γ and further activated with TLR triggers, such as LPS. In this work, we investigated the effects of IFN-γ priming on LPS-induced gene expression in primary mouse macrophages. Surprisingly, we found that IFN-γ priming represses a subset of LPS-induced genes, particularly genes involved in cellular movement and leukocyte recruitment. We found STAT1-binding motifs enriched in the promoters of these repressed genes. Furthermore, in the absence of STAT1, affected genes are derepressed. We also observed epigenetic remodeling by IFN-γ priming on enhancer or promoter sites of repressed genes, which resulted in less NF-κB p65 recruitment to these sites without effects on global NF-κB activation. Finally, the epigenetic and transcriptional changes induced by IFN-γ priming reduce neutrophil recruitment in vitro and in vivo. Our data show that IFN-γ priming changes the inflammatory repertoire of macrophages, leading to a change in neutrophil recruitment to inflammatory sites.
Collapse
Affiliation(s)
- Marten A Hoeksema
- Experimental Vascular Biology Laboratory, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Brendon P Scicluna
- Center for Experimental Molecular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Center for Infection and Immunity, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Marieke C S Boshuizen
- Experimental Vascular Biology Laboratory, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Saskia van der Velden
- Experimental Vascular Biology Laboratory, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Annette E Neele
- Experimental Vascular Biology Laboratory, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jan Van den Bossche
- Experimental Vascular Biology Laboratory, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Hanke L Matlung
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; and
| | - Timo K van den Berg
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; and
| | - Pieter Goossens
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, UM2, 13288 Marseille, France
| | - Menno P J de Winther
- Experimental Vascular Biology Laboratory, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands;
| |
Collapse
|
21
|
Kirschner K, Samarajiwa SA, Cairns JM, Menon S, Pérez-Mancera PA, Tomimatsu K, Bermejo-Rodriguez C, Ito Y, Chandra T, Narita M, Lyons SK, Lynch AG, Kimura H, Ohbayashi T, Tavaré S, Narita M. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genet 2015; 11:e1005053. [PMID: 25790137 PMCID: PMC4366240 DOI: 10.1371/journal.pgen.1005053] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/02/2015] [Indexed: 01/15/2023] Open
Abstract
The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage) and chronically activated (in senescent or pro-apoptotic conditions) p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.
Collapse
Affiliation(s)
- Kristina Kirschner
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Shamith A. Samarajiwa
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Jonathan M. Cairns
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Pedro A. Pérez-Mancera
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Camino Bermejo-Rodriguez
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Tamir Chandra
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Masako Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Scott K. Lyons
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Andy G. Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Ohbayashi
- Research Center for Bioscience and Technology, Tottori University, Yonago, Japan
| | - Simon Tavaré
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| |
Collapse
|
22
|
Modelska A, Turro E, Russell R, Beaton J, Sbarrato T, Spriggs K, Miller J, Gräf S, Provenzano E, Blows F, Pharoah P, Caldas C, Le Quesne J. The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape. Cell Death Dis 2015; 6:e1603. [PMID: 25611378 PMCID: PMC4669741 DOI: 10.1038/cddis.2014.542] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 01/09/2023]
Abstract
Human mRNA DeXD/H-box helicases are ubiquitous molecular motors that are required for the majority of cellular processes that involve RNA metabolism. One of the most abundant is eIF4A, which is required during the initiation phase of protein synthesis to unwind regions of highly structured mRNA that would otherwise impede the scanning ribosome. Dysregulation of protein synthesis is associated with tumorigenesis, but little is known about the detailed relationships between RNA helicase function and the malignant phenotype in solid malignancies. Therefore, immunohistochemical analysis was performed on over 3000 breast tumors to investigate the relationship among expression of eIF4A1, the helicase-modulating proteins eIF4B, eIF4E and PDCD4, and clinical outcome. We found eIF4A1, eIF4B and eIF4E to be independent predictors of poor outcome in ER-negative disease, while in contrast, the eIF4A1 inhibitor PDCD4 was related to improved outcome in ER-positive breast cancer. Consistent with these data, modulation of eIF4A1, eIF4B and PCDC4 expression in cultured MCF7 cells all restricted breast cancer cell growth and cycling. The eIF4A1-dependent translatome of MCF7 cells was defined by polysome profiling, and was shown to be highly enriched for several classes of oncogenic genes, including G-protein constituents, cyclins and protein kinases, and for mRNAs with G/C-rich 5'UTRs with potential to form G-quadruplexes and with 3'UTRs containing microRNA target sites. Overall, our data show that dysregulation of mRNA unwinding contributes to the malignant phenotype in breast cancer via preferential translation of a class of genes involved in pro-oncogenic signaling at numerous levels. Furthermore, immunohistochemical tests are promising biomarkers for tumors sensitive to anti-helicase therapies.
Collapse
Affiliation(s)
- A Modelska
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - E Turro
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Haematology, University of Cambridge, NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK
| | - R Russell
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - J Beaton
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - T Sbarrato
- Medical Research Council Toxicology Unit, Lancaster Road, Leicester LE1 9HN, UK
| | - K Spriggs
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - J Miller
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - S Gräf
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Haematology, University of Cambridge, NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - E Provenzano
- Cambridge Experimental Cancer Medicine Centre (ECMR) and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Cambridge Breast Unit and Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - F Blows
- Strangeways Research Institute, 2 Worts' Causeway, Cambridge CB1 8RN, UK
| | - P Pharoah
- Cambridge Experimental Cancer Medicine Centre (ECMR) and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Strangeways Research Institute, 2 Worts' Causeway, Cambridge CB1 8RN, UK
| | - C Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cambridge Experimental Cancer Medicine Centre (ECMR) and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - J Le Quesne
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Medical Research Council Toxicology Unit, Lancaster Road, Leicester LE1 9HN, UK
| |
Collapse
|
23
|
Khaled WT, Choon Lee S, Stingl J, Chen X, Raza Ali H, Rueda OM, Hadi F, Wang J, Yu Y, Chin SF, Stratton M, Futreal A, Jenkins NA, Aparicio S, Copeland NG, Watson CJ, Caldas C, Liu P. BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells. Nat Commun 2015; 6:5987. [PMID: 25574598 PMCID: PMC4338552 DOI: 10.1038/ncomms6987] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/28/2014] [Indexed: 01/03/2023] Open
Abstract
Triple-negative breast cancer (TNBC) has poor prognostic outcome compared with other types of breast cancer. The molecular and cellular mechanisms underlying TNBC pathology are not fully understood. Here, we report that the transcription factor BCL11A is overexpressed in TNBC including basal-like breast cancer (BLBC) and that its genomic locus is amplified in up to 38% of BLBC tumours. Exogenous BCL11A overexpression promotes tumour formation, whereas its knockdown in TNBC cell lines suppresses their tumourigenic potential in xenograft models. In the DMBA-induced tumour model, Bcl11a deletion substantially decreases tumour formation, even in p53-null cells and inactivation of Bcl11a in established tumours causes their regression. At the cellular level, Bcl11a deletion causes a reduction in the number of mammary epithelial stem and progenitor cells. Thus, BCL11A has an important role in TNBC and normal mammary epithelial cells. This study highlights the importance of further investigation of BCL11A in TNBC-targeted therapies.
Collapse
Affiliation(s)
- Walid T. Khaled
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
- These authors contributed equally to this work
| | - Song Choon Lee
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
- These authors contributed equally to this work
| | - John Stingl
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Xiongfeng Chen
- SAIC-Frederic, National Cancer Institute-Frederick, Frederick, Maryland 21701, USA
| | - H. Raza Ali
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Fazal Hadi
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Juexuan Wang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Yong Yu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mike Stratton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Andy Futreal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Nancy A. Jenkins
- The Methodist Hospital Research Institute, 6670 Bertner Street, Houston, Texas 77030, USA
| | - Sam Aparicio
- Molecular Oncology Department, BC Cancer Agency Research Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Neal G. Copeland
- The Methodist Hospital Research Institute, 6670 Bertner Street, Houston, Texas 77030, USA
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute, and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK
- Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| |
Collapse
|
24
|
Whitaker HC, Shiong LL, Kay JD, Grönberg H, Warren AY, Seipel A, Wiklund F, Thomas B, Wiklund P, Miller JL, Menon S, Ramos-Montoya A, Vowler SL, Massie C, Egevad L, Neal DE. N-acetyl-L-aspartyl-L-glutamate peptidase-like 2 is overexpressed in cancer and promotes a pro-migratory and pro-metastatic phenotype. Oncogene 2014; 33:5274-87. [PMID: 24240687 DOI: 10.1038/onc.2013.464] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 08/27/2013] [Accepted: 09/16/2013] [Indexed: 02/02/2023]
Abstract
N-acetyl-L-aspartyl-L-glutamate peptidase-like 2 (NAALADL2) is a member of the glutamate carboxypeptidase II family, best characterized by prostate-specific membrane antigen (PSMA/NAALAD1). Using immunohistochemistry (IHC), we have shown overexpression of NAALADL2 in colon and prostate tumours when compared with benign tissue. In prostate cancer, NAALADL2 expression was associated with stage and Grade, as well as circulating mRNA levels of the NAALADL2 gene. Overexpression of NAALADL2 was shown to predict poor survival following radical prostatectomy. In contrast to PSMA/NAALAD1, NAALADL2 was localized at the basal cell surface where it promotes adhesion to extracellular matrix proteins. Using stable knockdown and overexpression cell lines, we have demonstrated NAALADL2-dependent changes in cell migration, invasion and colony-forming potential. Expression arrays of the knockdown and overexpression cell lines have identified nine genes that co-expressed with NAALADL2, which included membrane proteins and genes known to be androgen regulated, including the prostate cancer biomarkers AGR2 and SPON2. Androgen regulation was confirmed in a number of these genes, although NAALADL2 itself was not found to be androgen regulated. NAALADL2 was also found to regulate levels of Ser133 phosphorylated C-AMP-binding protein (CREB), a master regulator of a number of cellular processes involved in cancer development and progression. In combination, these data suggest that changes in expression of NAALADL2 can impact upon a number of pro-oncogenic pathways and processes, making it a useful biomarker for both diagnosis and prognosis.
Collapse
Affiliation(s)
- H C Whitaker
- 1] Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Cancer Research UK Biomarker Initiative, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - L L Shiong
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - J D Kay
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - H Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - A Y Warren
- 1] Department of Histopathology and ISH Core Facility, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - A Seipel
- Department of Pathology, Karolinska Institute, Stockholm, Sweden
| | - F Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - B Thomas
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - P Wiklund
- Department of Pathology, Karolinska Institute, Stockholm, Sweden
| | - J L Miller
- 1] Department of Histopathology and ISH Core Facility, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - S Menon
- Bioinformatics Core Facility, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - A Ramos-Montoya
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - S L Vowler
- Bioinformatics Core Facility, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - C Massie
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - L Egevad
- Department of Pathology, Karolinska Institute, Stockholm, Sweden
| | - D E Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| |
Collapse
|
25
|
Prater MD, Petit V, Alasdair Russell I, Giraddi RR, Shehata M, Menon S, Schulte R, Kalajzic I, Rath N, Olson MF, Metzger D, Faraldo MM, Deugnier MA, Glukhova MA, Stingl J. Mammary stem cells have myoepithelial cell properties. Nat Cell Biol 2014; 16:942-50, 1-7. [PMID: 25173976 PMCID: PMC4183554 DOI: 10.1038/ncb3025] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 07/10/2014] [Indexed: 01/17/2023]
Abstract
Contractile myoepithelial cells dominate the basal layer of the mammary epithelium and are considered to be differentiated cells. However, we observe that up to 54% of single basal cells can form colonies when seeded into adherent culture in the presence of agents that disrupt actin-myosin interactions, and on average, 65% of the single-cell-derived basal colonies can repopulate a mammary gland when transplanted in vivo. This indicates that a high proportion of basal myoepithelial cells can give rise to a mammary repopulating unit (MRU). We demonstrate that myoepithelial cells, flow-sorted using two independent myoepithelial-specific reporter strategies, have MRU capacity. Using an inducible lineage-tracing approach we follow the progeny of myoepithelial cells that express α-smooth muscle actin and show that they function as long-lived lineage-restricted stem cells in the virgin state and during pregnancy.
Collapse
MESH Headings
- Actins/metabolism
- Animals
- Benzamides/pharmacology
- Cell Proliferation/drug effects
- Cells, Cultured
- Dioxoles/pharmacology
- Epithelial Cells/cytology
- Epithelial Cells/metabolism
- Female
- Flow Cytometry
- Gene Expression Profiling
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Interleukin Receptor Common gamma Subunit/deficiency
- Interleukin Receptor Common gamma Subunit/genetics
- Mammary Glands, Animal/cytology
- Mammary Glands, Animal/metabolism
- Mice, Inbred C57BL
- Mice, Inbred CBA
- Mice, Inbred NOD
- Mice, SCID
- Mice, Transgenic
- Microscopy, Fluorescence
- Myocytes, Smooth Muscle/cytology
- Myocytes, Smooth Muscle/metabolism
- Oligonucleotide Array Sequence Analysis
- Receptors, Transforming Growth Factor beta/antagonists & inhibitors
- Receptors, Transforming Growth Factor beta/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Stem Cells/cytology
- Stem Cells/metabolism
Collapse
Affiliation(s)
- Michael D Prater
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Valérie Petit
- 1] Institut Curie, Centre de Recherche, Paris, F-75248, France [2] CNRS, UMR144, Paris, F-75248, France
| | - I Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Rajshekhar R Giraddi
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mona Shehata
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Reiner Schulte
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Ivo Kalajzic
- Reconstructive Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3705, USA
| | - Nicola Rath
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Michael F Olson
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Daniel Metzger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, (CNRS/INSERM/Université de Strasbourg/Collège de France), Illkirch Cedex 67404, France
| | - Marisa M Faraldo
- 1] Institut Curie, Centre de Recherche, Paris, F-75248, France [2] CNRS, UMR144, Paris, F-75248, France
| | - Marie-Ange Deugnier
- 1] Institut Curie, Centre de Recherche, Paris, F-75248, France [2] CNRS, UMR144, Paris, F-75248, France
| | - Marina A Glukhova
- 1] Institut Curie, Centre de Recherche, Paris, F-75248, France [2] CNRS, UMR144, Paris, F-75248, France
| | - John Stingl
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| |
Collapse
|
26
|
Schiller BJ, Chodankar R, Watson LC, Stallcup MR, Yamamoto KR. Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes. Genome Biol 2014; 15:418. [PMID: 25085117 PMCID: PMC4149261 DOI: 10.1186/s13059-014-0418-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/17/2014] [Indexed: 11/10/2022] Open
Abstract
Background Glucocorticoid receptor (GR) is a hormone-activated, DNA-binding transcriptional regulatory factor that controls inflammation, metabolism, stress responses, and other physiological processes. In vitro, GR binds as an inverted dimer to a motif consisting of two imperfectly palindromic 6 bp half sites separated by 3 bp spacers. In vivo, GR employs different patterns of functional surfaces of GR to regulate different target genes. The relationships between GR genomic binding and functional surface utilization have not been defined. Results We find that A477T, a GR mutant that disrupts the dimerization interface, differs from wild-type GRα in binding and regulation of target genes. Genomic regions strongly occupied by A477T are enriched for a novel half site motif. In vitro, GRα binds half sites as a monomer. Through the overlap between GRα- and A477T-bound regions, we identify GRα-bound regions containing only half sites. We further identify GR target genes linked with half sites and not with the full motif. Conclusions Genomic regions bound by GR differ in underlying DNA sequence motifs and in the GR functional surfaces employed for regulation. Identification of GR binding regions that selectively utilize particular GR surfaces may discriminate sub-motifs, including the half site motif, that favor those surfaces. This approach may contribute to predictive models for GR activity and therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0418-y) contains supplementary material, which is available to authorized users.
Collapse
|
27
|
Sharma NL, Massie CE, Butter F, Mann M, Bon H, Ramos-Montoya A, Menon S, Stark R, Lamb AD, Scott HE, Warren AY, Neal DE, Mills IG. The ETS family member GABPα modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer. Nucleic Acids Res 2014; 42:6256-69. [PMID: 24753418 PMCID: PMC4041454 DOI: 10.1093/nar/gku281] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 12/31/2022] Open
Abstract
In prostate cancer (PC), the androgen receptor (AR) is a key transcription factor at all disease stages, including the advanced stage of castrate-resistant prostate cancer (CRPC). In the present study, we show that GABPα, an ETS factor that is up-regulated in PC, is an AR-interacting transcription factor. Expression of GABPα enables PC cell lines to acquire some of the molecular and cellular characteristics of CRPC tissues as well as more aggressive growth phenotypes. GABPα has a transcriptional role that dissects the overlapping cistromes of the two most common ETS gene fusions in PC: overlapping significantly with ETV1 but not with ERG target genes. GABPα bound predominantly to gene promoters, regulated the expression of one-third of AR target genes and modulated sensitivity to AR antagonists in hormone responsive and castrate resistant PC models. This study supports a critical role for GABPα in CRPC and reveals potential targets for therapeutic intervention.
Collapse
Affiliation(s)
- Naomi L Sharma
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK Department of Urology, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Charlie E Massie
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Falk Butter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Helene Bon
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Antonio Ramos-Montoya
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Suraj Menon
- Department of Bioinformatics, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Rory Stark
- Department of Bioinformatics, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Alastair D Lamb
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Helen E Scott
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - David E Neal
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK Department of Urology, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Ian G Mills
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK Prostate Cancer Research Group, Centre for Molecular Medicine (Norway), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Gaustadalleen 21, Oslo N-0349, Norway Department of Cancer Prevention and Department of Urology, Oslo University Hospital, Oslo N-0349, Norway
| |
Collapse
|
28
|
Eftang LL, Esbensen Y, Tannæs TM, Blom GP, Bukholm IRK, Bukholm G. Up-regulation of CLDN1 in gastric cancer is correlated with reduced survival. BMC Cancer 2013; 13:586. [PMID: 24321518 PMCID: PMC4029627 DOI: 10.1186/1471-2407-13-586] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 11/21/2013] [Indexed: 12/13/2022] Open
Abstract
Background The genetic changes in gastric adenocarcinoma are extremely complex and reliable tumor markers have not yet been identified. There are also remarkable geographical differences in the distribution of this disease. Our aim was to identify the most differentially regulated genes in 20 gastric adenocarcinomas from a Norwegian selection, compared to matched normal mucosa, and we have related our findings to prognosis, survival and chronic Helicobacter pylori infection. Methods Biopsies from gastric adenocarcinomas and adjacent normal gastric mucosa were obtained from 20 patients immediately following surgical resection of the tumor. Whole genome, cDNA microarray analysis was performed on the RNA isolated from the sample pairs to compare the gene expression profiles between the tumor against matched mucosa. The samples were microscopically examined to classify gastritis. The presence of H. pylori was examined using microscopy and immunohistochemistry. Results 130 genes showed differential regulation above a predefined cut-off level. Interleukin-8 (IL-8) and Claudin-1 (CLDN1) were the most consistently up-regulated genes in the tumors. Very high CLDN1 expression in the tumor was identified as an independent and significant predictor gene of reduced post-operative survival. There were distinctly different expression profiles between the tumor group and the control mucosa group, and the histological subsets of mixed type, diffuse type and intestinal type cancer demonstrated further sub-clustering. Up-regulated genes were mapped to cell-adhesion, collagen-related processes and angiogenesis, whereas normal intestinal functions such as digestion and excretion were associated with down-regulated genes. We relate the current findings to our previous study on the gene response of gastric epithelial cells to H. pylori infection. Conclusions CLDN1 was highly up-regulated in gastric cancer, and CLDN1 expression was independently associated with a poor post-operative prognosis, and may have important prognostic value. IL-8 and CLDN1 may represent central links between the gene response seen in acute H. pylori infection of gastric epithelial cells, and ultimately gastric cancer.
Collapse
Affiliation(s)
- Lars L Eftang
- Department of Clinical Molecular Biology and Laboratory Sciences (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, N-1478 Nordbyhagen, Oslo, Norway.
| | | | | | | | | | | |
Collapse
|
29
|
Robinson JLL, Hickey TE, Warren AY, Vowler SL, Carroll T, Lamb AD, Papoutsoglou N, Neal DE, Tilley WD, Carroll JS. Elevated levels of FOXA1 facilitate androgen receptor chromatin binding resulting in a CRPC-like phenotype. Oncogene 2013; 33:5666-74. [PMID: 24292680 PMCID: PMC4051595 DOI: 10.1038/onc.2013.508] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/18/2013] [Accepted: 10/23/2013] [Indexed: 12/18/2022]
Abstract
Castration-resistant prostate cancer (CRPC) continues to pose a significant clinical challenge with new generation second line hormonal therapies affording limited improvement in disease outcome. As the androgen receptor (AR) remains a critical driver in CRPC, understanding the determinants of its transcriptional activity is important for developing new AR targeted therapies. FOXA1 is a key component of the AR transcriptional complex yet its role in prostate cancer progression and the relationship between AR and FOXA1 are not completely resolved. It is well established that FOXA1 levels are elevated in advanced prostate cancer and metastases. We mimicked these conditions by over-expressing FOXA1 in the androgen-responsive LNCaP prostate cancer cell line and observed a significant increase in AR genomic binding at novel regions that possess increased chromatin accessibility. High levels of FOXA1 resulted in increased proliferation at both sub-optimal and high 5α-dihydrotestosterone (DHT) concentrations. Immunohistochemical staining for FOXA1 in a clinical prostate cancer cohort revealed that high FOXA1 expression is associated with shorter time to biochemical recurrence after radical prostatectomy (HR 5.0, 95% CI 1.2-21.1, p=0.028), positive surgical margins and higher stage disease at diagnosis. The gene expression program that results from FOXA1 over-expression is enriched for PTEN, Wnt and other pathways typically represented in CRPC gene signatures. Together these results suggest that in an androgen-depleted state, elevated levels of FOXA1 enhance AR binding at genomic regions not normally occupied by AR, which in turn facilitates prostate cancer cell growth.
Collapse
Affiliation(s)
- J L L Robinson
- 1] Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Department of Oncology, University of Cambridge, Cambridge, UK
| | - T E Hickey
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - A Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundations Trust, Cambridge, UK
| | - S L Vowler
- 1] Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Department of Oncology, University of Cambridge, Cambridge, UK
| | - T Carroll
- 1] Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Department of Oncology, University of Cambridge, Cambridge, UK
| | - A D Lamb
- 1] Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Department of Oncology, University of Cambridge, Cambridge, UK [3] Department of Urology, Cambridge University Hospitals NHS Foundations Trust, Cambridge, UK
| | - N Papoutsoglou
- Department of Urology, Cambridge University Hospitals NHS Foundations Trust, Cambridge, UK
| | - D E Neal
- 1] Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Department of Oncology, University of Cambridge, Cambridge, UK [3] Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - W D Tilley
- Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - J S Carroll
- 1] Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK [2] Department of Oncology, University of Cambridge, Cambridge, UK
| |
Collapse
|
30
|
Lawrenson K, Notaridou M, Lee N, Benjamin E, Jacobs IJ, Jones C, Gayther SA. In vitro three-dimensional modeling of fallopian tube secretory epithelial cells. BMC Cell Biol 2013; 14:43. [PMID: 24070420 PMCID: PMC3849984 DOI: 10.1186/1471-2121-14-43] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 09/23/2013] [Indexed: 11/29/2022] Open
Abstract
Background Fallopian tube secretory epithelial cells (FTSECs) have been implicated as a cell-of-origin for high-grade serous epithelial ovarian cancer. However, there are relatively few in vitro models of this tissue type available for use in studies of FTSEC biology and malignant transformation. In vitro three-dimensional (3D) cell culture models aim to recreate the architecture and geometry of tissues in vivo and restore the complex network of cell-cell/cell-matrix interactions that occur throughout the surface of the cell membrane. Results We have established and characterized 3D spheroid culture models of primary FTSECs. FTSEC spheroids contain central cores of hyaline matrix surrounded by mono- or multi-layer epithelial sheets. We found that 3D culturing alters the molecular characteristics of FTSECs compared to 2D cultures of the same cells. Gene expression profiling identified more than a thousand differentially expressed genes between 3D and 2D cultures of the same FTSEC lines. Pathways significantly under-represented in 3D FTSEC cultures were associated with cell cycle progression and DNA replication. This was also reflected in the reduced proliferative indices observed in 3D spheroids stained for the proliferation marker MIB1. Comparisons with gene expression profiles of fresh fallopian tube tissues revealed that 2D FTSEC cultures clustered with follicular phase tubal epithelium, whereas 3D FTSEC cultures clustered with luteal phase samples. Conclusions This 3D model of fallopian tube secretory epithelial cells will advance our ability to study the underlying biology and etiology of fallopian tube tissues and the pathogenesis of high-grade serous epithelial ovarian cancer.
Collapse
Affiliation(s)
- Kate Lawrenson
- Department of Preventive Medicine, University of Southern California/Keck School of Medicine, 1450 Biggy Street, Los Angeles, California.
| | | | | | | | | | | | | |
Collapse
|
31
|
Byers DE, Alexander-Brett J, Patel AC, Agapov E, Dang-Vu G, Jin X, Wu K, You Y, Alevy Y, Girard JP, Stappenbeck TS, Patterson GA, Pierce RA, Brody SL, Holtzman MJ. Long-term IL-33-producing epithelial progenitor cells in chronic obstructive lung disease. J Clin Invest 2013; 123:3967-82. [PMID: 23945235 DOI: 10.1172/jci65570] [Citation(s) in RCA: 271] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 06/13/2013] [Indexed: 01/03/2023] Open
Abstract
Chronic obstructive lung disease is characterized by persistent abnormalities in epithelial and immune cell function that are driven, at least in part, by infection. Analysis of parainfluenza virus infection in mice revealed an unexpected role for innate immune cells in IL-13-dependent chronic lung disease, but the upstream driver for the immune axis in this model and in humans with similar disease was undefined. We demonstrate here that lung levels of IL-33 are selectively increased in postviral mice with chronic obstructive lung disease and in humans with very severe chronic obstructive pulmonary disease (COPD). In the mouse model, IL-33/IL-33 receptor signaling was required for Il13 and mucin gene expression, and Il33 gene expression was localized to a virus-induced subset of airway serous cells and a constitutive subset of alveolar type 2 cells that are both linked conventionally to progenitor function. In humans with COPD, IL33 gene expression was also associated with IL13 and mucin gene expression, and IL33 induction was traceable to a subset of airway basal cells with increased capacities for pluripotency and ATP-regulated release of IL-33. Together, these findings provide a paradigm for the role of the innate immune system in chronic disease based on the influence of long-term epithelial progenitor cells programmed for excess IL-33 production.
Collapse
Affiliation(s)
- Derek E Byers
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress. Br J Cancer 2013; 109:983-93. [PMID: 23880827 PMCID: PMC3749568 DOI: 10.1038/bjc.2013.396] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 12/31/2022] Open
Abstract
Objective: We have previously identified peroxiredoxin-3 (PRDX-3) as a cell-surface protein that is androgen regulated in the LNCaP prostate cancer (PCa) cell line. PRDX-3 is a member of the peroxiredoxin family that are responsible for neutralising reactive oxygen species. Experimental design: PRDX-3 expression was examined in tissue from 32 patients using immunohistochemistry. Subcellular distribution was determined using confocal microscopy. PRDX-3 expression was determined in antiandrogen-resistant cell lines by western blotting and quantitative RT–PCR. The pathways of PRDX-3 overexpression and knockdown on apoptosis and response to oxidative stress were investigated using protein arrays. Results: PRDX-3 is upregulated in a number of endocrine-regulated tumours; in particular in PCa and prostatic intraepithelial neoplasia. Although the majority of PRDX-3 is localised to the mitochondria, we have confirmed that PRDX-3 at the cell membrane is androgen regulated. In antiandrogen-resistant LNCaP cell lines, PRDX-3 is upregulated at the protein but not RNA level. Resistant cells also possess an upregulation of the tricarboxylic acid (TCA) pathway and resistance to H2O2-induced apoptosis through a failure to activate pro-apoptotic pathways. Knockdown of PRDX-3 restored H2O2 sensitivity. Conclusion: Our results suggest that PRDX-3 has an essential role in regulating oxidation-induced apoptosis in antiandrogen-resistant cells. PRDX-3 may have potential as a therapeutic target in castrate-independent PCa.
Collapse
|
33
|
Hussain S, Tuorto F, Menon S, Blanco S, Cox C, Flores JV, Watt S, Kudo NR, Lyko F, Frye M. The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation. Mol Cell Biol 2013; 33:1561-70. [PMID: 23401851 PMCID: PMC3624257 DOI: 10.1128/mcb.01523-12] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/30/2013] [Indexed: 11/20/2022] Open
Abstract
Posttranscriptional regulatory mechanisms are crucial for protein synthesis during spermatogenesis and are often organized by the chromatoid body. Here, we identify the RNA methyltransferase NSun2 as a novel component of the chromatoid body and, further, show that NSun2 is essential for germ cell differentiation in the mouse testis. In NSun2-depleted testes, genes encoding Ddx4, Miwi, and Tudor domain-containing (Tdr) proteins are repressed, indicating that RNA-processing and posttranscriptional pathways are impaired. Loss of NSun2 specifically blocked meiotic progression of germ cells into the pachytene stage, as spermatogonial and Sertoli cells were unaffected in knockout mice. We observed the same phenotype when we simultaneously deleted NSun2 and Dnmt2, the only other cytosine-5 RNA methyltransferase characterized to date, indicating that Dnmt2 was not functionally redundant with NSun2 in spermatogonial stem cells or Sertoli cells. Specific NSun2- and Dnmt2-methylated tRNAs decreased in abundance when both methyltransferases were deleted, suggesting that RNA methylation pathways play an essential role in male germ cell differentiation.
Collapse
Affiliation(s)
- Shobbir Hussain
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Francesca Tuorto
- Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
| | - Suraj Menon
- CR-UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Sandra Blanco
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Claire Cox
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Joana V. Flores
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Stephen Watt
- CR-UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Nobuaki R. Kudo
- IRDB, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Frank Lyko
- Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
| | - Michaela Frye
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
34
|
Schwalbe EC, Williamson D, Lindsey JC, Hamilton D, Ryan SL, Megahed H, Garami M, Hauser P, Dembowska-Baginska B, Perek D, Northcott PA, Taylor MD, Taylor RE, Ellison DW, Bailey S, Clifford SC. DNA methylation profiling of medulloblastoma allows robust subclassification and improved outcome prediction using formalin-fixed biopsies. Acta Neuropathol 2013; 125:359-71. [PMID: 23291781 DOI: 10.1007/s00401-012-1077-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 12/21/2012] [Accepted: 12/21/2012] [Indexed: 12/12/2022]
Abstract
Molecular subclassification is rapidly informing the clinical management of medulloblastoma. However, the disease remains associated with poor outcomes and therapy-associated late effects, and the majority of patients are not characterized by a validated prognostic biomarker. Here, we investigated the potential of epigenetic DNA methylation for disease subclassification, particularly in formalin-fixed biopsies, and to identify biomarkers for improved therapeutic individualization. Tumor DNA methylation profiles were assessed, alongside molecular and clinical disease features, in 230 patients primarily from the SIOP-UKCCSG PNET3 clinical trial. We demonstrate by cross-validation in frozen training and formalin-fixed test sets that medulloblastoma comprises four robust DNA methylation subgroups (termed WNT, SHH, G3 and G4), highly related to their transcriptomic counterparts, and which display distinct molecular, clinical and pathological disease characteristics. WNT patients displayed an expected favorable prognosis, while outcomes for SHH, G3 and G4 were equivalent in our cohort. MXI1 and IL8 methylation were identified as novel independent high-risk biomarkers in cross-validated survival models of non-WNT patients, and were validated using non-array methods. Incorporation of MXI1 and IL8 into current survival models significantly improved the assignment of disease risk; 46 % of patients could be classified as 'favorable risk' (>90 % survival) compared to 13 % using current models, while the high-risk group was reduced from 30 to 16 %. DNA methylation profiling enables the robust subclassification of four disease subgroups in frozen and routinely collected/archival formalin-fixed biopsy material, and the incorporation of DNA methylation biomarkers can significantly improve disease-risk stratification. These findings have important implications for future risk-adapted clinical disease management.
Collapse
Affiliation(s)
- Edward C Schwalbe
- Northern Institute for Cancer Research, Newcastle University, Sir James Spence Institute Level 5, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Mohammed H, D’Santos C, Serandour AA, Raza Ali H, Brown GD, Atkins A, Rueda OM, Holmes KA, Theodorou V, Robinson JLL, Zwart W, Saadi A, Ross-Innes CS, Chin SF, Menon S, Stingl J, Palmieri C, Caldas C, Carroll JS. Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor. Cell Rep 2013; 3:342-9. [PMID: 23403292 PMCID: PMC7116645 DOI: 10.1016/j.celrep.2013.01.010] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/21/2012] [Accepted: 01/14/2013] [Indexed: 12/17/2022] Open
Abstract
Estrogen receptor-α (ER) is the driving transcription factor in most breast cancers, and its associated proteins can influence drug response, but direct methods for identifying interacting proteins have been limited. We purified endogenous ER using an approach termed RIME (rapid immunoprecipitation mass spectrometry of endogenous proteins) and discovered the interactome under agonist- and antagonist-liganded conditions in breast cancer cells, revealing transcriptional networks in breast cancer. The most estrogen-enriched ER interactor is GREB1, a potential clinical biomarker with no known function. GREB1 is shown to be a chromatin-bound ER coactivator and is essential for ER-mediated transcription, because it stabilizes interactions between ER and additional cofactors. We show a GREB1-ER interaction in three xenograft tumors, and using a directed protein-protein approach, we find GREB1-ER interactions in half of ER(+) primary breast cancers. This finding is supported by histological expression of GREB1, which shows that GREB1 is expressed in half of ER(+) cancers, and predicts good clinical outcome. These findings reveal an unexpected role for GREB1 as an estrogen-specific ER cofactor that is expressed in drug-sensitive contexts.
Collapse
Affiliation(s)
- Hisham Mohammed
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Clive D’Santos
- Proteomic core facility, Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Aurelien A. Serandour
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - H. Raza Ali
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge Breast Unit, Addenbrooke's hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
| | - Gordon. D. Brown
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Alan Atkins
- Thermo Fisher Scientific, Boundary way, Hemel Hempstead, HP2 7GE, UK
| | - Oscar M. Rueda
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Kelly A Holmes
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Vasiliki Theodorou
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jessica L. L. Robinson
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Wilbert Zwart
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Amel Saadi
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Caryn S. Ross-Innes
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Suraj Menon
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - John Stingl
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, CB2 0XZ, UK
| | - Carlo Palmieri
- Imperial College Healthcare NHS Trust, London, W12 0NN, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge Breast Unit, Addenbrooke's hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
- Department of Oncology, University of Cambridge, CB2 0XZ, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge, CB2 0RE
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, CB2 0XZ, UK
| |
Collapse
|
36
|
Koh GCKW, Schreiber MF, Bautista R, Maude RR, Dunachie S, Limmathurotsakul D, Day NPJ, Dougan G, Peacock SJ. Host responses to melioidosis and tuberculosis are both dominated by interferon-mediated signaling. PLoS One 2013; 8:e54961. [PMID: 23383015 PMCID: PMC3558488 DOI: 10.1371/journal.pone.0054961] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/18/2012] [Indexed: 01/08/2023] Open
Abstract
Melioidosis (Burkholderia pseudomallei infection) is a common cause of community-acquired sepsis in Northeast Thailand and northern Australia. B. pseudomallei is a soil saprophyte endemic to Southeast Asia and northern Australia. The clinical presentation of melioidosis may mimic tuberculosis (both cause chronic suppurative lesions unresponsive to conventional antibiotics and both commonly affect the lungs). The two diseases have overlapping risk profiles (e.g., diabetes, corticosteroid use), and both B. pseudomallei and Mycobacterium tuberculosis are intracellular pathogens. There are however important differences: the majority of melioidosis cases are acute, not chronic, and present with severe sepsis and a mortality rate that approaches 50% despite appropriate antimicrobial therapy. By contrast, tuberculosis is characteristically a chronic illness with mortality <2% with appropriate antimicrobial chemotherapy. We examined the gene expression profiles of total peripheral leukocytes in two cohorts of patients, one with acute melioidosis (30 patients and 30 controls) and another with tuberculosis (20 patients and 24 controls). Interferon-mediated responses dominate the host response to both infections, and both type 1 and type 2 interferon responses are important. An 86-gene signature previously thought to be specific for tuberculosis is also found in melioidosis. We conclude that the host responses to melioidosis and to tuberculosis are similar: both are dominated by interferon-signalling pathways and this similarity means gene expression signatures from whole blood do not distinguish between these two diseases.
Collapse
Affiliation(s)
- Gavin C K W Koh
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Lipina TV, Haque FN, McGirr A, Boutros PC, Berger T, Mak TW, Roder JC, Wong AHC. Prophylactic valproic acid treatment prevents schizophrenia-related behaviour in Disc1-L100P mutant mice. PLoS One 2012; 7:e51562. [PMID: 23272119 PMCID: PMC3525594 DOI: 10.1371/journal.pone.0051562] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 11/02/2012] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Schizophrenia is a neurodevelopmental disorder with onset early in adulthood. Disrupted-In-Schizophrenia-1 (DISC1) is a susceptibility gene for schizophrenia and other psychiatric disorders. Disc1-L100P mutant mice show behaviors relevant to schizophrenia at 12 weeks, but not at 8 weeks of age, and may be useful for investigating the onset of schizophrenia in early adulthood. METHODS We investigated whether early valproic acid treatment would prevent behavioral, cellular and gene expression abnormalities in Disc1-L100P mutants. RESULTS Valproic acid prevented hyperactivity and deficits in prepulse inhibition and latent inhibition in Disc1-L100P mice. Genome-wide transcription profiling identified Lcn2 (lipocalin2) transcripts as being elevated by the Disc1 mutation and corrected by valproate. Disc1-L100P mice also had increased glial cell numbers in the subventricular zone, which was normalized by valproate. Genetic deletion of Lcn2 normalized glial cell numbers and behavior in Disc1-L100P mutants. CONCLUSIONS Pharmacological treatments are a feasible way of preventing abnormal behaviour in a genetic model of schizophrenia. Lcn2 is a potential novel drug target for early intervention in schizophrenia.
Collapse
Affiliation(s)
- Tatiana V. Lipina
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Alexander McGirr
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Paul C. Boutros
- Informatics and Biocomputing Platform, Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Thorsten Berger
- Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Tak W. Mak
- Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - John C. Roder
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada
- Departments of Medical Biophysics and Molecular and Medical Genetics University of Toronto, Toronto, Ontario, Canada
| | - Albert H. C. Wong
- Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
38
|
Phan JH, Quo CF, Wang MD. Cardiovascular genomics: a biomarker identification pipeline. ACTA ACUST UNITED AC 2012; 16:809-22. [PMID: 22614726 DOI: 10.1109/titb.2012.2199570] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genomic biomarkers are essential for understanding the underlying molecular basis of human diseases such as cardiovascular disease. In this review, we describe a biomarker identification pipeline for cardiovascular disease, which includes 1) high-throughput genomic data acquisition, 2) preprocessing and normalization of data, 3) exploratory analysis, 4) feature selection, 5) classification, and 6) interpretation and validation of candidate biomarkers. We review each step in the pipeline, presenting current and widely used bioinformatics methods. Furthermore, we analyze several publicly available cardiovascular genomics datasets to illustrate the pipeline. Finally, we summarize the current challenges and opportunities for further research.
Collapse
Affiliation(s)
- John H Phan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
| | | | | |
Collapse
|
39
|
Rogers HA, Kilday JP, Mayne C, Ward J, Adamowicz-Brice M, Schwalbe EC, Clifford SC, Coyle B, Grundy RG. Supratentorial and spinal pediatric ependymomas display a hypermethylated phenotype which includes the loss of tumor suppressor genes involved in the control of cell growth and death. Acta Neuropathol 2012; 123:711-25. [PMID: 22109108 PMCID: PMC3316934 DOI: 10.1007/s00401-011-0904-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 10/26/2011] [Accepted: 10/27/2011] [Indexed: 01/19/2023]
Abstract
Epigenetic alterations, including methylation, have been shown to be an important mechanism of gene silencing in cancer. Ependymoma has been well characterized at the DNA copy number and mRNA expression levels. However little is known about DNA methylation changes. To gain a more global view of the methylation profile of ependymoma we conducted an array-based analysis. Our data demonstrated tumors to segregate according to their location in the CNS, which was associated with a difference in the global level of methylation. Supratentorial and spinal tumors displayed significantly more hypermethylated genes than posterior fossa tumors, similar to the ‘CpG island methylator phenotype’ (CIMP) identified in glioma and colon carcinoma. This hypermethylated profile was associated with an increase in expression of genes encoding for proteins involved in methylating DNA, suggesting an underlying mechanism. An integrated analysis of methylation and mRNA expression array data allowed us to identify methylation-induced expression changes. Most notably genes involved in the control of cell growth and death and the immune system were identified, including members of the JNK pathway and PPARG. In conclusion, we have generated a global view of the methylation profile of ependymoma. The data suggests epigenetic silencing of tumor suppressor genes is an important mechanism in the pathogenesis of supratentorial and spinal, but not posterior fossa ependymomas. Hypermethylation correlated with a decrease in expression of a number of tumor suppressor genes and pathways that could be playing an important role in tumor pathogenesis.
Collapse
Affiliation(s)
- Hazel A. Rogers
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - John-Paul Kilday
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Cerys Mayne
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Jennifer Ward
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Martyna Adamowicz-Brice
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Ed C. Schwalbe
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Steven C. Clifford
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Beth Coyle
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Richard G. Grundy
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| |
Collapse
|
40
|
Maia AT, Antoniou AC, O'Reilly M, Samarajiwa S, Dunning M, Kartsonaki C, Chin SF, Curtis CN, McGuffog L, Domchek SM, EMBRACE, Easton DF, Peock S, Frost D, Evans DG, Eeles R, Izatt L, Adlard J, Eccles D, GEMO Study Collaborators , Sinilnikova OM, Mazoyer S, Stoppa-Lyonnet D, Gauthier-Villars M, Faivre L, Venat-Bouvet L, Delnatte C, Nevanlinna H, Couch FJ, Godwin AK, Caligo MA, SWE-BRCA, Barkardottir RB, kConFab Investigators, Chen X, Beesley J, Healey S, Caldas C, Chenevix-Trench G, Ponder BAJ. Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers. Breast Cancer Res 2012; 14:R63. [PMID: 22513257 PMCID: PMC3446398 DOI: 10.1186/bcr3169] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 01/30/2012] [Accepted: 04/18/2012] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION Cis-acting regulatory single nucleotide polymorphisms (SNPs) at specific loci may modulate penetrance of germline mutations at the same loci by introducing different levels of expression of the wild-type allele. We have previously reported that BRCA2 shows differential allelic expression and we hypothesize that the known variable penetrance of BRCA2 mutations might be associated with this mechanism. METHODS We combined haplotype analysis and differential allelic expression of BRCA2 in breast tissue to identify expression haplotypes and candidate cis-regulatory variants. These candidate variants underwent selection based on in silico predictions for regulatory potential and disruption of transcription factor binding, and were functionally analyzed in vitro and in vivo in normal and breast cancer cell lines. SNPs tagging the expression haplotypes were correlated with the total expression of several genes in breast tissue measured by Taqman and microarray technologies. The effect of the expression haplotypes on breast cancer risk in BRCA2 mutation carriers was investigated in 2,754 carriers. RESULTS We identified common haplotypes associated with differences in the levels of BRCA2 expression in human breast cells. We characterized three cis-regulatory SNPs located at the promoter and two intronic regulatory elements which affect the binding of the transcription factors C/EBPα, HMGA1, D-binding protein (DBP) and ZF5. We showed that the expression haplotypes also correlated with changes in the expression of other genes in normal breast. Furthermore, there was suggestive evidence that the minor allele of SNP rs4942440, which is associated with higher BRCA2 expression, is also associated with a reduced risk of breast cancer (per-allele hazard ratio (HR) = 0.85, 95% confidence interval (CI) = 0.72 to 1.00, P-trend = 0.048). CONCLUSIONS Our work provides further insights into the role of cis-regulatory variation in the penetrance of disease-causing mutations. We identified small-effect genetic variants associated with allelic expression differences in BRCA2 which could possibly affect the risk in mutation carriers through altering expression levels of the wild-type allele.
Collapse
Affiliation(s)
- Ana-Teresa Maia
- Cambridge Research Institute - CRUK, Li Ka Shing Centre, Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Robinson Way, Cambridge, CB2 0RE, UK
- Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine, Department of Biomedical Sciences and Medicine, Gambelas Campus, Building 7, University of Algarve, 8005-139 Faro, Portugal
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Martin O'Reilly
- Cambridge Research Institute - CRUK, Li Ka Shing Centre, Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shamith Samarajiwa
- Cambridge Research Institute - CRUK, Li Ka Shing Centre, Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Robinson Way, Cambridge, CB2 0RE, UK
| | - Mark Dunning
- Cambridge Research Institute - CRUK, Li Ka Shing Centre, Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
| | - Christiana Kartsonaki
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Suet-Feung Chin
- Cambridge Research Institute - CRUK, Li Ka Shing Centre, Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Robinson Way, Cambridge, CB2 0RE, UK
| | - Christina N Curtis
- Cambridge Research Institute - CRUK, Li Ka Shing Centre, Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Robinson Way, Cambridge, CB2 0RE, UK
- Institute for Biotechnology and Bioengineering, Centre for Molecular and Structural Biomedicine, Department of Biomedical Sciences and Medicine, University of Algarve, Portugal
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Susan M Domchek
- Department of Medicine, Hematology-Oncology, Abramson Cancer Center, University of Pennsylvania, 3400 Spruce St, Philadelphia, PA 19104, USA
| | - EMBRACE
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Susan Peock
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - D Gareth Evans
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Brunswick Street, Manchester, M13 9PL, UK
| | - Ros Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, 15 Cotswold Rd, Belmont, Sutton Surrey SM2 5NG, UK
| | - Louise Izatt
- Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, 7th floor, Borough Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Julian Adlard
- Yorkshire Regional Genetics Service, Ward 10, 3rd Floor, Chapel Allerton Hospital Chapeltown Road, Leeds, LS7 4SA, UK
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA, UK
| | - GEMO Study Collaborators
- GEMO Study Collaborators: Cancer Genetics Network "Groupe Génétique et Cancer", Fédération Nationale des Centres de Lutte Contre le Cancer, France
| | - Olga M Sinilnikova
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Cancer Research Center of Lyon, Lyon, 7 rue Guillaume Paradin, 69008 Lyon, France
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Centre Hospitalier Universitaire de Lyon/Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Cancer Research Center of Lyon, Lyon, 7 rue Guillaume Paradin, 69008 Lyon, France
| | - Dominique Stoppa-Lyonnet
- Service de Génétique Oncologique, Institut Curie, 26 rue d'Ulm 75248 Paris cedex 05, France
- Unité INSERM U830, Institut Curie, 26 rue d'Ulm 75248 Paris cedex 05, France
- Université Paris Descartes, Faculté de Médecine, 12, rue de l'Ecole de Médecine 75270 Paris Cedex 06, France
| | | | - Laurence Faivre
- Centre de Génétique, CHU Dijon, Université de Bourgogne, Dijon F-21000, France
- Centre Georges François Leclerc, 1 Rue Professeur Marion 21000 Dijon, France
| | - Laurence Venat-Bouvet
- Department of Medical Oncology, Centre Hospitalier Universitaire Dupuytren, Limoges, France
| | - Capucine Delnatte
- Centre René Gauducheau, Boulevard Jacques Monod 44805 St Herblain Cedex, Nantes, France
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, P.O. BOX 700, 00029 HUS, Finland
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest Rochester, MN 55905, USA
| | - Andrew K Godwin
- University of Kansas Medical Center, 3901 Rainbow Boulevard, KS City, KS 66160, USA
| | - Maria Adelaide Caligo
- Division of Surgical, Molecular and Ultrastructural Pathology, Department of Oncology, University of Pisa and Pisa University Hospital, Lungarno Antonio Pacinotti, 43 56126 Pisa, Italy
| | | | - Rosa B Barkardottir
- Department of Pathology, Landspitali University Hospital, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, level 4 Reykjavik, Iceland
| | - kConFab Investigators
- Peter MacCallum Cancer Institute, Locked Bag 1, A'Beckett Street, Melbourne, VIC 8006, Australia
| | - Xiaoqing Chen
- Queensland Institute of Medical Research, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Jonathan Beesley
- Queensland Institute of Medical Research, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Sue Healey
- Queensland Institute of Medical Research, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Carlos Caldas
- Cambridge Research Institute - CRUK, Li Ka Shing Centre, Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge Experimental Cancer Medicine Centre, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Georgia Chenevix-Trench
- Queensland Institute of Medical Research, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Bruce AJ Ponder
- Cambridge Research Institute - CRUK, Li Ka Shing Centre, Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Robinson Way, Cambridge, CB2 0RE, UK
| |
Collapse
|
41
|
Holmes KA, Hurtado A, Brown GD, Launchbury R, Ross-Innes CS, Hadfield J, Odom DT, Carroll JS. Transducin-like enhancer protein 1 mediates estrogen receptor binding and transcriptional activity in breast cancer cells. Proc Natl Acad Sci U S A 2012; 109:2748-53. [PMID: 21536917 PMCID: PMC3286936 DOI: 10.1073/pnas.1018863108] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Estrogen receptor (ER) binds to distal enhancers within the genome and requires additional factors, such as the Forkhead protein FoxA1, for mediating chromatin interactions. We now show that the human Groucho protein, Transducin-like enhancer protein 1 (TLE1), positively assists some ER-chromatin interactions, a role that is distinct from its general role as a transcriptional repressor. We show that specific silencing of TLE1 inhibits the ability of ER to bind to a subset of ER binding sites within the genome, a phenomenon that results in perturbations in phospho-RNA Pol II recruitment. Furthermore, TLE1 is essential for effective ER-mediated cell division. We have discovered a distinct role for TLE1, as a necessary transcriptional component of the ER complex, where it facilitates ER-chromatin interactions.
Collapse
Affiliation(s)
- Kelly A. Holmes
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Antoni Hurtado
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Gordon D. Brown
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Rosalind Launchbury
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Caryn S. Ross-Innes
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - James Hadfield
- Genomics Core, Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom; and
| | - Duncan T. Odom
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, CB2 0RE, United Kingdom
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, CB2 0RE, United Kingdom
| |
Collapse
|
42
|
Eftang LL, Esbensen Y, Tannæs TM, Bukholm IRK, Bukholm G. Interleukin-8 is the single most up-regulated gene in whole genome profiling of H. pylori exposed gastric epithelial cells. BMC Microbiol 2012; 12:9. [PMID: 22248188 PMCID: PMC3292955 DOI: 10.1186/1471-2180-12-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 01/17/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The association between Helicobacter pylori infection and upper gastrointestinal disease is well established. However, only a small fraction of H. pylori carriers develop disease, and there are great geographical differences in disease penetrance. The explanation to this enigma lies in the interaction between the bacterium and the host. H. pylori Outer Membrane Phospholipase A (OMPLA) has been suggested to play a role in the virulence of this bacterium. The aim of this study was to profile the most significant cellular pathways and biological processes affected in gastric epithelial cells during 24 h of H. pylori exposure, and to study the inflammatory response to OMPLA⁺ and OMPLA⁻ H. pylori variants. RESULTS Interleukin-8 was the most significantly up-regulated gene and appears to play a paramount role in the epithelial cell response to H. pylori infection and in the pathological processes leading to gastric disease. MAPK and NF-kappaB cellular pathways were powerfully activated, but did not seem to explain the impressive IL-8 response. There was marked up-regulation of TP53BP2, whose corresponding protein ASPP2 may interact with H. pylori CagA and cause marked p53 suppression of apoptosis. Other regulators of apoptosis also showed abberant regulation. We also identified up-regulation of several oncogenes and down-regulation of tumor suppressor genes as early as during the first 24 h of infection. H. pylori OMPLA phase variation did not seem to influence the inflammatory epithelial cell gene response in this experiment. CONCLUSION In whole genome analysis of the epithelial response to H. pylori exposure, IL-8 demonstrated the most marked up-regulation, and was involved in many of the most important cellular response processes to the infection. There was dysregulation of apoptosis, tumor suppressor genes and oncogenes as early as in the first 24 h of H. pylori infection, which may represent early signs of gastric tumorigenesis. OMPLA⁺/⁻ did not affect the acute inflammatory response to H. pylori.
Collapse
Affiliation(s)
- Lars L Eftang
- Department of Clinical Molecular Biology (Epigen), Institute of Clinical Medicine, University of Oslo, Akershus University Hospital, Lørenskog, Norway
- Department of Gastroenterological Surgery, Akershus University Hospital, Lørenskog, Norway
| | - Ying Esbensen
- Department of Clinical Molecular Biology (Epigen), Institute of Clinical Medicine, University of Oslo, Akershus University Hospital, Lørenskog, Norway
| | - Tone M Tannæs
- Department of Clinical Molecular Biology (Epigen), Akershus University Hospital, Lørenskog, Norway
| | - Ida RK Bukholm
- Department of Gastroenterological Surgery, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Akershus University Hospital, University of Oslo, Lørenskog, Norway
| | - Geir Bukholm
- Institute of Health and Society, University of Oslo, Oslo, Norway
| |
Collapse
|
43
|
Abstract
Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered.
Collapse
Affiliation(s)
- Matthew E. Ritchie
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (MR); (MD)
| | - Mark J. Dunning
- Cancer Research UK, Cambridge Research Institute, Cambridge, United Kingdom
- * E-mail: (MR); (MD)
| | - Mike L. Smith
- Cancer Research UK, Cambridge Research Institute, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Wei Shi
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Computer Science and Software Engineering, The University of Melbourne, Parkville, Victoria, Australia
| | - Andy G. Lynch
- Cancer Research UK, Cambridge Research Institute, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
44
|
Lawson MH, Cummings NM, Rassl DM, Russell R, Brenton JD, Rintoul RC, Murphy G. Two novel determinants of etoposide resistance in small cell lung cancer. Cancer Res 2011; 71:4877-87. [PMID: 21642373 PMCID: PMC3145147 DOI: 10.1158/0008-5472.can-11-0080] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Patient survival in small cell lung cancer (SCLC) is limited by acquired chemoresistance. Here we report the use of a biologically relevant model to identify novel candidate genes mediating in vivo acquired resistance to etoposide. Candidate genes derived from a cDNA microarray analysis were cloned and transiently overexpressed to evaluate their potential functional roles. We identified two promising genes in the DNA repair enzyme DNA polymerase β and in the neuroendocrine transcription factor NKX2.2. Specific inhibition of DNA polymerase β reduced the numbers of cells surviving treatment with etoposide and increased the amount of DNA damage in cells. Conversely, stable overexpression of NKX2.2 increased cell survival in response to etoposide in SCLC cell lines. Consistent with these findings, we found that an absence of nuclear staining for NKX2.2 in SCLC primary tumors was an independent predictor of improved outcomes in chemotherapy-treated patients. Taken together, our findings justify future prospective studies to confirm the roles of these molecules in mediating chemotherapy resistance in SCLC.
Collapse
Affiliation(s)
- Malcolm H Lawson
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE
- Department of Thoracic Oncology, Papworth Hospital NHS Foundation Trust, Papworth Everard, Cambridgeshire, CB23 3RE
- Department of Oncology, University of Cambridge
| | - Natalie M Cummings
- Department of Thoracic Oncology, Papworth Hospital NHS Foundation Trust, Papworth Everard, Cambridgeshire, CB23 3RE
- Department of Oncology, University of Cambridge
| | - Doris M Rassl
- Department of Thoracic Oncology, Papworth Hospital NHS Foundation Trust, Papworth Everard, Cambridgeshire, CB23 3RE
| | - Roslin Russell
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE
| | - James D Brenton
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE
- Department of Oncology, University of Cambridge
| | - Robert C Rintoul
- Department of Thoracic Oncology, Papworth Hospital NHS Foundation Trust, Papworth Everard, Cambridgeshire, CB23 3RE
| | - Gillian Murphy
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE
- Department of Oncology, University of Cambridge
| |
Collapse
|
45
|
Robinson JLL, MacArthur S, Ross-Innes CS, Tilley WD, Neal DE, Mills IG, Carroll JS. Androgen receptor driven transcription in molecular apocrine breast cancer is mediated by FoxA1. EMBO J 2011; 30:3019-27. [PMID: 21701558 PMCID: PMC3160190 DOI: 10.1038/emboj.2011.216] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 06/09/2011] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is a heterogeneous disease and several distinct subtypes exist based on differential gene expression patterns. Molecular apocrine tumours were recently identified as an additional subgroup, characterised as oestrogen receptor negative and androgen receptor positive (ER- AR+), but with an expression profile resembling ER+ luminal breast cancer. One possible explanation for the apparent incongruity is that ER gene expression programmes could be recapitulated by AR. Using a cell line model of ER- AR+ molecular apocrine tumours (termed MDA-MB-453 cells), we map global AR binding events and find a binding profile that is similar to ER binding in breast cancer cells. We find that AR binding is a near-perfect subset of FoxA1 binding regions, a level of concordance never previously seen with a nuclear receptor. AR functionality is dependent on FoxA1, since silencing of FoxA1 inhibits AR binding, expression of the majority of the molecular apocrine gene signature and growth cell growth. These findings show that AR binds and regulates ER cis-regulatory elements in molecular apocrine tumours, resulting in a transcriptional programme reminiscent of ER-mediated transcription in luminal breast cancers.
Collapse
Affiliation(s)
- Jessica L L Robinson
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Stewart MacArthur
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Caryn S Ross-Innes
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Hanson Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - David E Neal
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Ian G Mills
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
- Centre for Molecular Medicine Norway, Blindern, Oslo, Norway
| | - Jason S Carroll
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| |
Collapse
|
46
|
Massie CE, Lynch A, Ramos-Montoya A, Boren J, Stark R, Fazli L, Warren A, Scott H, Madhu B, Sharma N, Bon H, Zecchini V, Smith DM, DeNicola GM, Mathews N, Osborne M, Hadfield J, MacArthur S, Adryan B, Lyons SK, Brindle KM, Griffiths J, Gleave ME, Rennie PS, Neal DE, Mills IG. The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis. EMBO J 2011; 30:2719-33. [PMID: 21602788 PMCID: PMC3155295 DOI: 10.1038/emboj.2011.158] [Citation(s) in RCA: 503] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/21/2011] [Indexed: 11/09/2022] Open
Abstract
The androgen receptor (AR) is a key regulator of prostate growth and the principal drug target for the treatment of prostate cancer. Previous studies have mapped AR targets and identified some candidates which may contribute to cancer progression, but did not characterize AR biology in an integrated manner. In this study, we took an interdisciplinary approach, integrating detailed genomic studies with metabolomic profiling and identify an anabolic transcriptional network involving AR as the core regulator. Restricting flux through anabolic pathways is an attractive approach to deprive tumours of the building blocks needed to sustain tumour growth. Therefore, we searched for targets of the AR that may contribute to these anabolic processes and could be amenable to therapeutic intervention by virtue of differential expression in prostate tumours. This highlighted calcium/calmodulin-dependent protein kinase kinase 2, which we show is overexpressed in prostate cancer and regulates cancer cell growth via its unexpected role as a hormone-dependent modulator of anabolic metabolism. In conclusion, it is possible to progress from transcriptional studies to a promising therapeutic target by taking an unbiased interdisciplinary approach.
Collapse
Affiliation(s)
| | - Andy Lynch
- CRUK Cambridge Research Institute, Cambridge, UK
| | | | - Joan Boren
- CRUK Cambridge Research Institute, Cambridge, UK
| | - Rory Stark
- CRUK Cambridge Research Institute, Cambridge, UK
| | - Ladan Fazli
- The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Anne Warren
- Department of Pathology, Addenbrookes Hospital, Cambridge, UK
| | - Helen Scott
- CRUK Cambridge Research Institute, Cambridge, UK
| | | | - Naomi Sharma
- CRUK Cambridge Research Institute, Cambridge, UK
| | - Helene Bon
- CRUK Cambridge Research Institute, Cambridge, UK
| | | | | | | | - Nik Mathews
- CRUK Cambridge Research Institute, Cambridge, UK
| | | | | | | | - Boris Adryan
- Cambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | | | - Martin E Gleave
- The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Paul S Rennie
- The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - David E Neal
- CRUK Cambridge Research Institute, Cambridge, UK
| | - Ian G Mills
- CRUK Cambridge Research Institute, Cambridge, UK
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, University of Oslo, Oslo, Norway
| |
Collapse
|
47
|
Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F. NGSQC: cross-platform quality analysis pipeline for deep sequencing data. BMC Genomics 2010; 11 Suppl 4:S7. [PMID: 21143816 PMCID: PMC3005923 DOI: 10.1186/1471-2164-11-s4-s7] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background While the accuracy and precision of deep sequencing data is significantly better than those obtained by the earlier generation of hybridization-based high throughput technologies, the digital nature of deep sequencing output often leads to unwarranted confidence in their reliability. Results The NGSQC (Next Generation Sequencing Quality Control) pipeline provides a set of novel quality control measures for quickly detecting a wide variety of quality issues in deep sequencing data derived from two dimensional surfaces, regardless of the assay technology used. It also enables researchers to determine whether sequencing data related to their most interesting biological discoveries are caused by sequencing quality issues. Conclusions Next generation sequencing platforms have their own share of quality issues and there can be significant lab-to-lab, batch-to-batch and even within chip/slide variations. NGSQC can help to ensure that biological conclusions, in particular those based on relatively rare sequence alterations, are not caused by low quality sequencing.
Collapse
Affiliation(s)
- Manhong Dai
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA.
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Lynch AG, Hadfield J, Dunning MJ, Osborne M, Thorne NP, Tavaré S. The cost of reducing starting RNA quantity for Illumina BeadArrays: a bead-level dilution experiment. BMC Genomics 2010; 11:540. [PMID: 20925945 PMCID: PMC3091689 DOI: 10.1186/1471-2164-11-540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 10/06/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The demands of microarray expression technologies for quantities of RNA place a limit on the questions they can address. As a consequence, the RNA requirements have reduced over time as technologies have improved. In this paper we investigate the costs of reducing the starting quantity of RNA for the Illumina BeadArray platform. This we do via a dilution data set generated from two reference RNA sources that have become the standard for investigations into microarray and sequencing technologies. RESULTS We find that the starting quantity of RNA has an effect on observed intensities despite the fact that the quantity of cRNA being hybridized remains constant. We see a loss of sensitivity when using lower quantities of RNA, but no great rise in the false positive rate. Even with 10 ng of starting RNA, the positive results are reliable although many differentially expressed genes are missed. We see that there is some scope for combining data from samples that have contributed differing quantities of RNA, but note also that sample sizes should increase to compensate for the loss of signal-to-noise when using low quantities of starting RNA. CONCLUSIONS The BeadArray platform maintains a low false discovery rate even when small amounts of starting RNA are used. In contrast, the sensitivity of the platform drops off noticeably over the same range. Thus, those conducting experiments should not opt for low quantities of starting RNA without consideration of the costs of doing so. The implications for experimental design, and the integration of data from different starting quantities, are complex.
Collapse
Affiliation(s)
- Andy G Lynch
- Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK - CRI, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - James Hadfield
- Cancer Research UK - CRI, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Mark J Dunning
- Cancer Research UK - CRI, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Michelle Osborne
- Cancer Research UK - CRI, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Natalie P Thorne
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville Victoria 3052, Australia
| | - Simon Tavaré
- Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK - CRI, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| |
Collapse
|
49
|
Smith ML, Lynch AG. BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies. Cancer Inform 2010; 9:217-27. [PMID: 20981138 PMCID: PMC2956622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microarray technologies have been an increasingly important tool in cancer research in the last decade, and a number of initiatives have sought to stress the importance of the provision and sharing of raw microarray data. Illumina BeadArrays provide a particular problem in this regard, as their random construction simultaneously adds value to analysis of the raw data and obstructs the sharing of those data.We present a compression scheme for raw Illumina BeadArray data, designed to ease the burdens of sharing and storing such data, that is implemented in the BeadDataPackR BioConductor package (http://bioconductor.org/packages/release/bioc/html/BeadDataPackR.html). It offers two key advantages over off-the-peg compression tools. First it uses knowledge of the data formats to achieve greater compression than other approaches, and second it does not need to be decompressed for analysis, but rather the values held within can be directly accessed.
Collapse
Affiliation(s)
- Mike L. Smith
- Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK
| | - Andy G. Lynch
- Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK
| |
Collapse
|
50
|
Chai HS, Therneau TM, Bailey KR, Kocher JPA. Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. BMC Bioinformatics 2010; 11:356. [PMID: 20587065 PMCID: PMC2910027 DOI: 10.1186/1471-2105-11-356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 06/29/2010] [Indexed: 12/05/2022] Open
Abstract
Background Microarray measurements are susceptible to a variety of experimental artifacts, some of which give rise to systematic biases that are spatially dependent in a unique way on each chip. It is likely that such artifacts affect many SNP arrays, but the normalization methods used in currently available genotyping algorithms make no attempt at spatial bias correction. Here, we propose an effective single-chip spatial bias removal procedure for Affymetrix 6.0 SNP arrays or platforms with similar design features. This procedure deals with both extreme and subtle biases and is intended to be applied before standard genotype calling algorithms. Results Application of the spatial bias adjustments on HapMap samples resulted in higher genotype call rates with equal or even better accuracy for thousands of SNPs. Consequently the normalization procedure is expected to lead to more meaningful biological inferences and could be valuable for genome-wide SNP analysis. Conclusions Spatial normalization can potentially rescue thousands of SNPs in a genetic study at the small cost of computational time. The approach is implemented in R and available from the authors upon request.
Collapse
Affiliation(s)
- High Seng Chai
- Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | | | | |
Collapse
|