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Sivapalan L, Kocher HM, Ross-Adams H, Chelala C. The molecular landscape of pancreatic ductal adenocarcinoma. Pancreatology 2022; 22:925-936. [PMID: 35927150 DOI: 10.1016/j.pan.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 06/30/2022] [Accepted: 07/17/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer-related mortality within the next decade, with limited effective treatment options and a dismal long-term prognosis for patients. Surgical resection of early, localised disease provides the only chance for potentially curative treatment; however, most patients with PDAC present with advanced disease and are not suitable for surgery. Genomic analyses of PDAC tumour lesions have identified a small number of recurrent alterations that are detected across most tumours, and beyond that a large number that either occur at a low (<5%) prevalence or are patient-specific in nature. This molecular heterogeneity has presented a significant challenge for the characterisation of tumour subtypes and effective molecular biomarkers, which have not yet manifested clinical benefits for diagnosis, treatment or prognosis in PDAC. These challenges are compounded by the overall lack of tumour biopsies for sequencing, the invasive nature of tissue sampling and the confounding effects of low tumour cellularity in many PDAC biopsy specimens, which have limited the applications of molecular profiling in unresectable patients and for longitudinal tumour monitoring. Further investigation into alternative sources of tumour analytes that can be sampled using minimally invasive methods and used to complement molecular analyses from tissue sequencing are required.
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Affiliation(s)
- L Sivapalan
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, UK
| | - H M Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, UK
| | - H Ross-Adams
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, UK.
| | - C Chelala
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, UK.
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Sivapalan L, Thorn GJ, Gadaleta E, Kocher HM, Ross-Adams H, Chelala C. Longitudinal profiling of circulating tumour DNA for tracking tumour dynamics in pancreatic cancer. BMC Cancer 2022; 22:369. [PMID: 35392854 PMCID: PMC8991893 DOI: 10.1186/s12885-022-09387-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The utility of circulating tumour DNA (ctDNA) for longitudinal tumour monitoring in pancreatic ductal adenocarcinoma (PDAC) has not been explored beyond mutations in the KRAS proto-oncogene. Here, we aimed to characterise and track patient-specific somatic ctDNA variants, to assess longitudinal changes in disease burden and explore the landscape of actionable alterations. METHODS We followed 3 patients with resectable disease and 4 patients with unresectable disease, including 4 patients with ≥ 3 serial follow-up samples, of whom 2 were rare long survivors (> 5 years). We performed whole exome sequencing of tumour gDNA and plasma ctDNA (n = 20) collected over a ~ 2-year period from diagnosis through treatment to death or final follow-up. Plasma from 3 chronic pancreatitis cases was used as a comparison for analysis of ctDNA mutations. RESULTS We detected > 55% concordance between somatic mutations in tumour tissues and matched serial plasma. Mutations in ctDNA were detected within known PDAC driver genes (KRAS, TP53, SMAD4, CDKN2A), in addition to patient-specific variants within alternative cancer drivers (NRAS, HRAS, MTOR, ERBB2, EGFR, PBRM1), with a trend towards higher overall mutation loads in advanced disease. ctDNA alterations with potential for therapeutic actionability were identified in all 7 patients, including DNA damage response (DDR) variants co-occurring with hypermutation signatures predictive of response to platinum chemotherapy. Longitudinal tracking in 4 patients with follow-up > 2 years demonstrated that ctDNA mutant allele fractions and clonal trends were consistent with CA19-9 measurements and/or clinically reported disease burden. The estimated prevalence of 'stem clones' was highest in an unresectable patient where changes in ctDNA dynamics preceded CA19-9 levels. Longitudinal evolutionary trajectories revealed ongoing subclonal evolution following chemotherapy. CONCLUSION These results provide proof-of-concept for the use of exome sequencing of serial plasma to characterise patient-specific ctDNA profiles, and demonstrate the sensitivity of ctDNA in monitoring disease burden in PDAC even in unresectable cases without matched tumour genotyping. They reveal the value of tracking clonal evolution in serial ctDNA to monitor treatment response, establishing the potential of applied precision medicine to guide stratified care by identifying and evaluating actionable opportunities for intervention aimed at optimising patient outcomes for an otherwise intractable disease.
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Affiliation(s)
- Lavanya Sivapalan
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Graeme J Thorn
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Emanuela Gadaleta
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Hemant M Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Helen Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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Gadaleta E, Thorn GJ, Ross-Adams H, Jones LJ, Chelala C. Field cancerization in breast cancer. J Pathol 2022; 257:561-574. [PMID: 35362092 PMCID: PMC9322418 DOI: 10.1002/path.5902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Breast cancer affects one in seven women worldwide during their lifetime. Widespread mammographic screening programs and education campaigns allow for early detection of the disease, often during its asymptomatic phase. Current practice in treatment and recurrence monitoring is based primarily on pathological evaluations but can also encompass genomic evaluations, both of which focus on the primary tumor. Although breast cancer is one of the most studied cancers, patients still recur at a rate of up to 15% within the first 10 years post‐surgery. Local recurrence was originally attributed to tumor cells contaminating histologically normal (HN) tissues beyond the surgical margin, but advances in technology have allowed for the identification of distinct aberrations that exist in the peri‐tumoral tissues themselves. One leading theory to explain this phenomenon is the field cancerization theory. Under this hypothesis, tumors arise from a field of molecularly altered cells that create a permissive environment for malignant evolution, which can occur with or without morphological changes. The traditional histopathology paradigm dictates that molecular alterations are reflected in the tissue phenotype. However, the spectrum of inter‐patient variability of normal breast tissue may obfuscate recognition of a cancerized field during routine diagnostics. In this review, we explore the concept of field cancerization focusing on HN peri‐tumoral tissues: we present the pathological and molecular features of field cancerization within these tissues and discuss how the use of peri‐tumoral tissues can affect research. Our observations suggest that pathological and molecular evaluations could be used synergistically to assess risk and guide the therapeutic management of patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Emanuela Gadaleta
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Graeme J Thorn
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helen Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Louise J Jones
- Centre for Tumour Biology Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
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Sivapalan L, Kocher H, Ross-Adams H, Chelala C. Molecular profiling of ctDNA in pancreatic cancer: Opportunities and challenges for clinical application. Pancreatology 2021; 21:363-378. [PMID: 33451936 PMCID: PMC7994018 DOI: 10.1016/j.pan.2020.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer-related mortality within the next decade, with limited effective treatment options and a dismal long-term prognosis for patients. Genomic profiling has not yet manifested clinical benefits for diagnosis, treatment or prognosis in PDAC, due to the lack of available tissues for sequencing and the confounding effects of low tumour cellularity in many biopsy specimens. Increasing focus is now turning to the use of minimally invasive liquid biopsies to enhance the characterisation of actionable PDAC tumour genomes. Circulating tumour DNA (ctDNA) is the most comprehensively studied liquid biopsy analyte in blood and can provide insight into the molecular profile and biological characteristics of individual PDAC tumours, in real-time and in advance of traditional imaging modalities. This can pave the way for identification of new therapeutic targets, novel risk variants and markers of tumour response, to supplement diagnostic screening and provide enhanced scrutiny in treatment stratification. In the roadmap towards the application of precision medicine for clinical management in PDAC, ctDNA analyses may serve a leading role in streamlining candidate biomarkers for clinical integration. In this review, we highlight recent developments in the use of ctDNA-based liquid biopsies for PDAC and provide new insights into the technical, analytical and biological challenges that must be overcome for this potential to be realised.
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Affiliation(s)
- L. Sivapalan
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - H.M. Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - H. Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - C. Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK,Corresponding author.
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Marzec J, Ross-Adams H, Pirrò S, Wang J, Zhu Y, Mao X, Gadaleta E, Ahmad AS, North BV, Kammerer-Jacquet SF, Stankiewicz E, Kudahetti SC, Beltran L, Ren G, Berney DM, Lu YJ, Chelala C. The Transcriptomic Landscape of Prostate Cancer Development and Progression: An Integrative Analysis. Cancers (Basel) 2021; 13:345. [PMID: 33477882 PMCID: PMC7838904 DOI: 10.3390/cancers13020345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing of primary tumors is now standard for transcriptomic studies, but microarray-based data still constitute the majority of available information on other clinically valuable samples, including archive material. Using prostate cancer (PC) as a model, we developed a robust analytical framework to integrate data across different technical platforms and disease subtypes to connect distinct disease stages and reveal potentially relevant genes not identifiable from single studies alone. We reconstructed the molecular profile of PC to yield the first comprehensive insight into its development, by tracking changes in mRNA levels from normal prostate to high-grade prostatic intraepithelial neoplasia, and metastatic disease. A total of nine previously unreported stage-specific candidate genes with prognostic significance were also found. Here, we integrate gene expression data from disparate sample types, disease stages and technical platforms into one coherent whole, to give a global view of the expression changes associated with the development and progression of PC from normal tissue through to metastatic disease. Summary and individual data are available online at the Prostate Integrative Expression Database (PIXdb), a user-friendly interface designed for clinicians and laboratory researchers to facilitate translational research.
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Affiliation(s)
- Jacek Marzec
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Helen Ross-Adams
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Stefano Pirrò
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Jun Wang
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Yanan Zhu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Xueying Mao
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Emanuela Gadaleta
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Amar S. Ahmad
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK; (A.S.A.); (B.V.N.)
| | - Bernard V. North
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK; (A.S.A.); (B.V.N.)
| | - Solène-Florence Kammerer-Jacquet
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Elzbieta Stankiewicz
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Sakunthala C. Kudahetti
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Luis Beltran
- Department of Pathology, Barts Health NHS, London E1 F1R, UK;
| | - Guoping Ren
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou 310058, China;
| | - Daniel M. Berney
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
- Department of Pathology, Barts Health NHS, London E1 F1R, UK;
| | - Yong-Jie Lu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Claude Chelala
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University London, London EC1M 6BQ, UK
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Gadaleta E, Fourgoux P, Pirró S, Thorn GJ, Nelan R, Ironside A, Rajeeve V, Cutillas PR, Lobley AE, Wang J, Gea E, Ross-Adams H, Bessant C, Lemoine NR, Jones LJ, Chelala C. Characterization of four subtypes in morphologically normal tissue excised proximal and distal to breast cancer. NPJ Breast Cancer 2020; 6:38. [PMID: 32885042 PMCID: PMC7442642 DOI: 10.1038/s41523-020-00182-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/06/2020] [Indexed: 01/20/2023] Open
Abstract
Widespread mammographic screening programs and improved self-monitoring allow for breast cancer to be detected earlier than ever before. Breast-conserving surgery is a successful treatment for select women. However, up to 40% of women develop local recurrence after surgery despite apparently tumor-free margins. This suggests that morphologically normal breast may harbor early alterations that contribute to increased risk of cancer recurrence. We conducted a comprehensive transcriptomic and proteomic analysis to characterize 57 fresh-frozen tissues from breast cancers and matched histologically normal tissues resected proximal to (<2 cm) and distant from (5-10 cm) the primary tumor, using tissues from cosmetic reduction mammoplasties as baseline. Four distinct transcriptomic subtypes are identified within matched normal tissues: metabolic; immune; matrisome/epithelial-mesenchymal transition, and non-coding enriched. Key components of the subtypes are supported by proteomic and tissue composition analyses. We find that the metabolic subtype is associated with poor prognosis (p < 0.001, HR6.1). Examination of genes representing the metabolic signature identifies several genes able to prognosticate outcome from histologically normal tissues. A subset of these have been reported for their predictive ability in cancer but, to the best of our knowledge, these have not been reported altered in matched normal tissues. This study takes an important first step toward characterizing matched normal tissues resected at pre-defined margins from the primary tumor. Unlocking the predictive potential of unexcised tissue could prove key to driving the realization of personalized medicine for breast cancer patients, allowing for more biologically-driven analyses of tissue margins than morphology alone.
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Affiliation(s)
- Emanuela Gadaleta
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Pauline Fourgoux
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, EC1M 6BQ UK
| | - Stefano Pirró
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Graeme J. Thorn
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Rachel Nelan
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Alastair Ironside
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Vinothini Rajeeve
- Center for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Pedro R. Cutillas
- Center for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Anna E. Lobley
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Jun Wang
- Center for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Esteban Gea
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, EC1M 6BQ UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| | - Helen Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Conrad Bessant
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, EC1M 6BQ UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| | - Nicholas R. Lemoine
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Louise J. Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, EC1M 6BQ UK
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7
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Sangaralingam A, Dayem Ullah AZ, Marzec J, Gadaleta E, Nagano A, Ross-Adams H, Wang J, Lemoine NR, Chelala C. 'Multi-omic' data analysis using O-miner. Brief Bioinform 2019; 20:130-143. [PMID: 28981577 PMCID: PMC6357557 DOI: 10.1093/bib/bbx080] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
Innovations in -omics technologies have driven advances in biomedical research. However, integrating and analysing the large volumes of data generated from different high-throughput -omics technologies remain a significant challenge to basic and clinical scientists without bioinformatics skills or access to bioinformatics support. To address this demand, we have significantly updated our previous O-miner analytical suite, to incorporate several new features and data types to provide an efficient and easy-to-use Web tool for the automated analysis of data from '-omics' technologies. Created from a biologist's perspective, this tool allows for the automated analysis of large and complex transcriptomic, genomic and methylomic data sets, together with biological/clinical information, to identify significantly altered pathways and prioritize novel biomarkers/targets for biological validation. Our resource can be used to analyse both in-house data and the huge amount of publicly available information from array and sequencing platforms. Multiple data sets can be easily combined, allowing for meta-analyses. Here, we describe the analytical pipelines currently available in O-miner and present examples of use to demonstrate its utility and relevance in maximizing research output. O-miner Web server is free to use and is available at http://www.o-miner.org.
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Affiliation(s)
| | | | - Jacek Marzec
- Barts Cancer Institute, Queen Mary University of London
| | | | - Ai Nagano
- Barts Cancer Institute, Queen Mary University of London
| | | | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London
| | | | - Claude Chelala
- Barts Cancer Institute, co-Lead of the Computational Biology Centre at the Life Science Initiative, Queen Mary University of London
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8
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Luca BA, Brewer DS, Edwards DR, Edward S, Whitaker HC, Merson S, Dennis N, Cooper RA, Hazell S, Warren AY, Eeles R, Lynch AG, Ross-Adams H, Lamb AD, Neal DE, Sethia K, Mills RD, Ball RY, Curley H, Clark J, Moulton V, Cooper CS. DESNT: A Poor Prognosis Category of Human Prostate Cancer. Eur Urol Focus 2018; 4:842-850. [PMID: 28753852 PMCID: PMC5669460 DOI: 10.1016/j.euf.2017.01.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/16/2017] [Accepted: 01/28/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND A critical problem in the clinical management of prostate cancer is that it is highly heterogeneous. Accurate prediction of individual cancer behaviour is therefore not achievable at the time of diagnosis leading to substantial overtreatment. It remains an enigma that, in contrast to breast cancer, unsupervised analyses of global expression profiles have not currently defined robust categories of prostate cancer with distinct clinical outcomes. OBJECTIVE To devise a novel classification framework for human prostate cancer based on unsupervised mathematical approaches. DESIGN, SETTING, AND PARTICIPANTS Our analyses are based on the hypothesis that previous attempts to classify prostate cancer have been unsuccessful because individual samples of prostate cancer frequently have heterogeneous compositions. To address this issue, we applied an unsupervised Bayesian procedure called Latent Process Decomposition to four independent prostate cancer transcriptome datasets obtained using samples from prostatectomy patients and containing between 78 and 182 participants. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Biochemical failure was assessed using log-rank analysis and Cox regression analysis. RESULTS AND LIMITATIONS Application of Latent Process Decomposition identified a common process in all four independent datasets examined. Cancers assigned to this process (designated DESNT cancers) are characterized by low expression of a core set of 45 genes, many encoding proteins involved in the cytoskeleton machinery, ion transport, and cell adhesion. For the three datasets with linked prostate-specific antigen failure data following prostatectomy, patients with DESNT cancer exhibited poor outcome relative to other patients (p=2.65×10-5, p=4.28×10-5, and p=2.98×10-8). When these three datasets were combined the independent predictive value of DESNT membership was p=1.61×10-7 compared with p=1.00×10-5 for Gleason sum. A limitation of the study is that only prediction of prostate-specific antigen failure was examined. CONCLUSIONS Our results demonstrate the existence of a novel poor prognosis category of human prostate cancer and will assist in the targeting of therapy, helping avoid treatment-associated morbidity in men with indolent disease. PATIENT SUMMARY Prostate cancer, unlike breast cancer, does not have a robust classification framework. We propose that this failure has occurred because prostate cancer samples selected for analysis frequently have heterozygous compositions (individual samples are made up of many different parts that each have different characteristics). Applying a mathematical approach that can overcome this problem we identify a novel poor prognosis category of human prostate cancer called DESNT.
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Affiliation(s)
- Bogdan-Alexandru Luca
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
- The Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - Dylan R Edwards
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sandra Edward
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, Sutton, UK
| | - Hayley C Whitaker
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Sue Merson
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, Sutton, UK
| | - Nening Dennis
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, Sutton, UK
| | - Rosalin A Cooper
- Department of Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - The CancerMap Group
- A list of participants and their affiliations appears in the Supplemental Information
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, Sutton, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Andy G Lynch
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Helen Ross-Adams
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Alastair D Lamb
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - David E Neal
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Krishna Sethia
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Robert D Mills
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Richard Y Ball
- Department of Histopathology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Helen Curley
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
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9
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Ross-Adams H, Ball S, Lawrenson K, Halim S, Russell R, Wells C, Strand SH, Ørntoft TF, Larson M, Armasu S, Massie CE, Asim M, Mortensen MM, Borre M, Woodfine K, Warren AY, Lamb AD, Kay J, Whitaker H, Ramos-Montoya A, Murrell A, Sørensen KD, Fridley BL, Goode EL, Gayther SA, Masters J, Neal DE, Mills IG. HNF1B variants associate with promoter methylation and regulate gene networks activated in prostate and ovarian cancer. Oncotarget 2018; 7:74734-74746. [PMID: 27732966 PMCID: PMC5342698 DOI: 10.18632/oncotarget.12543] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022] Open
Abstract
Two independent regions within HNF1B are consistently identified in prostate and ovarian cancer genome-wide association studies (GWAS); their functional roles are unclear. We link prostate cancer (PC) risk SNPs rs11649743 and rs3760511 with elevated HNF1B gene expression and allele-specific epigenetic silencing, and outline a mechanism by which common risk variants could effect functional changes that increase disease risk: functional assays suggest that HNF1B is a pro-differentiation factor that suppresses epithelial-to-mesenchymal transition (EMT) in unmethylated, healthy tissues. This tumor-suppressor activity is lost when HNF1B is silenced by promoter methylation in the progression to PC. Epigenetic inactivation of HNF1B in ovarian cancer also associates with known risk SNPs, with a similar impact on EMT. This represents one of the first comprehensive studies into the pleiotropic role of a GWAS-associated transcription factor across distinct cancer types, and is the first to describe a conserved role for a multi-cancer genetic risk factor.
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Affiliation(s)
- Helen Ross-Adams
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Stephen Ball
- Prostate Cancer Research Centre, University College London, London, UK
| | - Kate Lawrenson
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Silvia Halim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Roslin Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Claire Wells
- Division of Cancer Studies, King's College London, London, UK
| | - Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Torben F Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | | | | | - Charles E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Mohammad Asim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Kathryn Woodfine
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Jonathan Kay
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Hayley Whitaker
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | | | - Adele Murrell
- Department of Biology and Biochemistry, University of Bath, Centre for Regenerative Medicine, Claverton Down, Bath, UK
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Simon A Gayther
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - John Masters
- Prostate Cancer Research Centre, University College London, London, UK
| | - David E Neal
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Ian G Mills
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Departments of Cancer Prevention and Urology, Institute of Cancer Research and Department of Urology, Oslo University Hospital, Oslo, Norway.,Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, UK
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10
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Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, Massie CM, Egevad LA, Russell R, Ramos-Montoya A, Vowler SL, Sharma NL, Kay J, Whitaker H, Clark J, Hurst R, Gnanapragasam VJ, Shah NC, Warren AY, Cooper CS, Lynch AG, Stark R, Mills IG, Grönberg H, Neal DE. Corrigendum to "Integration of Copy Number and Transcriptomics Provides Risk Stratification in Prostate Cancer: A Discovery and Validation Cohort Study" [EBioMedicine 2 (9) (2015) 1133-1144]. EBioMedicine 2017; 17:238. [PMID: 28292578 PMCID: PMC5680481 DOI: 10.1016/j.ebiom.2017.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- H Ross-Adams
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - A D Lamb
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Department of Urology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK; Academic Urology Group, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - M J Dunning
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - S Halim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - J Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - C M Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - L A Egevad
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - R Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - A Ramos-Montoya
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - S L Vowler
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - N L Sharma
- Nuffield Department of Surgical Sciences, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - J Kay
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Molecular Diagnostics and Therapeutics Group, University College London, WC1E 6BT, UK.
| | - H Whitaker
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Molecular Diagnostics and Therapeutics Group, University College London, WC1E 6BT, UK.
| | - J Clark
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - R Hurst
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - V J Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK; Academic Urology Group, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - N C Shah
- Department of Urology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.
| | - A Y Warren
- Department of Pathology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.
| | - C S Cooper
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - A G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - R Stark
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| | - I G Mills
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, N-0318 Oslo, Norway; Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospitals, N-0424 Oslo, Norway; Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queen's University, Belfast, UK.
| | - H Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - D E Neal
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Department of Urology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.
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11
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Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Boutros P, Mills IG, Lynch AG, Lamb AD. Mining Human Prostate Cancer Datasets: The "camcAPP" Shiny App. EBioMedicine 2017; 17:5-6. [PMID: 28286059 PMCID: PMC5360593 DOI: 10.1016/j.ebiom.2017.02.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 01/27/2023] Open
Affiliation(s)
- Mark J Dunning
- Cancer Research UK Cambridge Institute, Cambridge Biomedical Campus, UK
| | - Sarah L Vowler
- Cancer Research UK Cambridge Institute, Cambridge Biomedical Campus, UK
| | - Emilie Lalonde
- Department of Medical Biophysics, University of Toronto, Canada; Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Helen Ross-Adams
- Bioinformatics Unit, Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University London, UK
| | - Paul Boutros
- Department of Medical Biophysics, University of Toronto, Canada; Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Ian G Mills
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University of Belfast, 97 Lisburn Road, Belfast, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge Institute, Cambridge Biomedical Campus, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge Institute, Cambridge Biomedical Campus, UK; Department of Genito-urinary Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Academic Urology Group, Department of Surgery, University of Cambridge, UK.
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12
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Shaw GL, Whitaker H, Corcoran M, Dunning MJ, Luxton H, Kay J, Massie CE, Miller JL, Lamb AD, Ross-Adams H, Russell R, Nelson AW, Eldridge MD, Lynch AG, Ramos-Montoya A, Mills IG, Taylor AE, Arlt W, Shah N, Warren AY, Neal DE. The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer. Eur Urol 2016; 70:214-8. [PMID: 26572708 PMCID: PMC4926724 DOI: 10.1016/j.eururo.2015.10.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 10/20/2015] [Indexed: 12/03/2022]
Abstract
UNLABELLED The androgen receptor (AR) is the dominant growth factor in prostate cancer (PCa). Therefore, understanding how ARs regulate the human transcriptome is of paramount importance. The early effects of castration on human PCa have not previously been studied 27 patients medically castrated with degarelix 7 d before radical prostatectomy. We used mass spectrometry, immunohistochemistry, and gene expression array (validated by reverse transcription-polymerase chain reaction) to compare resected tumour with matched, controlled, untreated PCa tissue. All patients had levels of serum androgen, with reduced levels of intraprostatic androgen at prostatectomy. We observed differential expression of known androgen-regulated genes (TMPRSS2, KLK3, CAMKK2, FKBP5). We identified 749 genes downregulated and 908 genes upregulated following castration. AR regulation of α-methylacyl-CoA racemase expression and three other genes (FAM129A, RAB27A, and KIAA0101) was confirmed. Upregulation of oestrogen receptor 1 (ESR1) expression was observed in malignant epithelia and was associated with differential expression of ESR1-regulated genes and correlated with proliferation (Ki-67 expression). PATIENT SUMMARY This first-in-man study defines the rapid gene expression changes taking place in prostate cancer (PCa) following castration. Expression levels of the genes that the androgen receptor regulates are predictive of treatment outcome. Upregulation of oestrogen receptor 1 is a mechanism by which PCa cells may survive despite castration.
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Affiliation(s)
- Greg L Shaw
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, UK; University College Hospitals NHS Trust, UK.
| | - Hayley Whitaker
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; University College London, London, UK
| | - Marie Corcoran
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Mark J Dunning
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Hayley Luxton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; University College London, London, UK
| | - Jonathan Kay
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; University College London, London, UK
| | - Charlie E Massie
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jodi L Miller
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Helen Ross-Adams
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Roslin Russell
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Adam W Nelson
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Andrew G Lynch
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | | | - Ian G Mills
- Prostate Cancer Research Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway; Departments of Cancer Prevention and Urology, Institute of Cancer Research and Oslo University Hospitals, Oslo, Norway; Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, UK
| | - Angela E Taylor
- Centre for Endocrinology, Diabetes and Metabolism, University of Birmingham, Egbaston, Birmingham, UK
| | - Wiebke Arlt
- Centre for Endocrinology, Diabetes and Metabolism, University of Birmingham, Egbaston, Birmingham, UK
| | - Nimish Shah
- Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - David E Neal
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Trust, Cambridge, UK; Nuffield Department of Surgery, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
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13
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Marzec J, Mao X, Li M, Wang M, Feng N, Gou X, Wang G, Sun Z, Xu J, Xu H, Zhang X, Zhao SC, Ren G, Yu Y, Wu Y, Wu J, Xue Y, Zhou B, Zhang Y, Xu X, Li J, He W, Benlloch S, Ross-Adams H, Chen L, Li J, Hong Y, Kote-Jarai Z, Cui X, Hou J, Guo J, Xu L, Yin C, Zhou Y, Neal DE, Oliver T, Cao G, Zhang Z, Easton DF, Chelala C, Olama AAA, Eeles RA, Zhang H, Lu YJ. A genetic study and meta-analysis of the genetic predisposition of prostate cancer in a Chinese population. Oncotarget 2016; 7:21393-403. [PMID: 26881390 PMCID: PMC5008293 DOI: 10.18632/oncotarget.7250] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/23/2016] [Indexed: 11/25/2022] Open
Abstract
Prostate cancer predisposition has been extensively investigated in European populations, but there have been few studies of other ethnic groups. To investigate prostate cancer susceptibility in the under-investigated Chinese population, we performed single-nucleotide polymorphism (SNP) array analysis on a cohort of Chinese cases and controls and then meta-analysis with data from the existing Chinese prostate cancer genome-wide association study (GWAS). Genotyping 211,155 SNPs in 495 cases and 640 controls of Chinese ancestry identified several new suggestive Chinese prostate cancer predisposition loci. However, none of them reached genome-wide significance level either by meta-analysis or replication study. The meta-analysis with the Chinese GWAS data revealed that four 8q24 loci are the main contributors to Chinese prostate cancer risk and the risk alleles from three of them exist at much higher frequencies in Chinese than European populations. We also found that several predisposition loci reported in Western populations have different effect on Chinese men. Therefore, this first extensive single-nucleotide polymorphism study of Chinese prostate cancer in comparison with European population indicates that four loci on 8q24 contribute to a great risk of prostate cancer in a considerable large proportion of Chinese men. Based on those four loci, the top 10% of the population have six- or two-fold prostate cancer risk compared with men of the bottom 10% or median risk respectively, which may facilitate the design of prostate cancer genetic risk screening and prevention in Chinese men. These findings also provide additional insights into the etiology and pathogenesis of prostate cancer.
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Affiliation(s)
- Jacek Marzec
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Meiling Li
- Department of Epidemiology, Second Military Medical University, Shanghai, 200433, China
| | - Meilin Wang
- Department of Molecular and Genetic Toxicology, The Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, 210029, China
| | - Ninghan Feng
- Department of Urology, Wuxi Second People's Hospital, Nanjing Medical University, Wuxi, 214002, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xin Gou
- Department of Urology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Guomin Wang
- Department of Urology, Zhongshan Hospital, Fudan University Medical College, Shanghai, 200032, China
| | - Zan Sun
- Liaoning People's Hospital and Center of Experiment and Technology, China Medical University, Shenyang, 110001, China
| | - Jianfeng Xu
- Program for Personalized Cancer Care, North Shore University Health System, Evanston, IL 60201, U.S.A
- Fudan Institute of Urology, Huashang Hospital, Fudan University, Shanghai, 200040, China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Huazhong Science and Technology University, Wuhan, 430030, China
| | - Xiaoping Zhang
- Department of Urology, Xiehe Hospital, Huazhong Science and Technology University, Wuhan, 430022, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Guoping Ren
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou, 310009, China
| | - Yongwei Yu
- Department of Pathology, Changhai Hospital, The Second Military Medical University, Shanghai, 200433, China
| | - Yudong Wu
- Department of Urology, First Affiliated Hospital, Medical College, Zhengzhou University, Zhengzhou, 450003, China
| | - Ji Wu
- Department of Urology, North Sichuan Medical College, Nanchong, 637000, China
| | - Yao Xue
- Department of Molecular and Genetic Toxicology, The Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, 210029, China
| | - Bo Zhou
- Department of Nutrition Science, Shenyang Medical College, Shenyang, 110034, China
| | - Yanling Zhang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou, 310009, China
| | - Xingxing Xu
- Department of Epidemiology, Second Military Medical University, Shanghai, 200433, China
| | - Jie Li
- Department of Urology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Weiyang He
- Department of Urology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge–Strangeways Research Laboratory, Cambridge, CB1 8RN, UK
| | - Helen Ross-Adams
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Li Chen
- Department of Urology, Xiehe Hospital, Huazhong Science and Technology University, Wuhan, 430022, China
| | - Jucong Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yingqia Hong
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Xingang Cui
- Department of Urology, Changzheng Hospital, The Second Military Medical University, Shanghai, 200003, China
| | - Jianguo Hou
- Department of Urology, Changhai Hospital, The Second Military Medical University, Shanghai, 200433, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University Medical College, Shanghai, 200032, China
| | - Lei Xu
- Department of Urology, Zhongshan Hospital, Fudan University Medical College, Shanghai, 200032, China
| | - Changjun Yin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yuanping Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - David E. Neal
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tim Oliver
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, 200433, China
| | - Zhengdong Zhang
- Department of Molecular and Genetic Toxicology, The Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, 210029, China
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge–Strangeways Research Laboratory, Cambridge, CB1 8RN, UK
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | | | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge–Strangeways Research Laboratory, Cambridge, CB1 8RN, UK
| | - Rosalind A. Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- The Royal Marsden NHS Foundation Trust, London and Surrey, SM2 5NG, UK
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, 200433, China
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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14
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Whitington T, Gao P, Song W, Ross-Adams H, Lamb AD, Yang Y, Svezia I, Klevebring D, Mills IG, Karlsson R, Halim S, Dunning MJ, Egevad L, Warren AY, Neal DE, Grönberg H, Lindberg J, Wei GH, Wiklund F. Gene regulatory mechanisms underpinning prostate cancer susceptibility. Nat Genet 2016; 48:387-97. [PMID: 26950096 DOI: 10.1038/ng.3523] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/08/2016] [Indexed: 12/29/2022]
Abstract
Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development.
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Affiliation(s)
- Thomas Whitington
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ping Gao
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Wei Song
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Helen Ross-Adams
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Yuehong Yang
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ilaria Svezia
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Daniel Klevebring
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.,Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Silvia Halim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Beatson Institute, Glasgow, UK
| | - Mark J Dunning
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Lars Egevad
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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15
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Affiliation(s)
- Helen Ross-Adams
- Institute of Cancer & Genetics, Cardiff University, Cardiff, CF14 4XN, UK.,Academic Urology Group, CamPARI Clinic, Department of Urology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge Institute, Cambridge Biomedical Campus, Robinson Way, Cambridge, CB2 0RE, UK.,Academic Urology Group, CamPARI Clinic, Department of Urology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
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16
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Ross-Adams H, Lamb A, Dunning M, Halim S, Lindberg J, Massie C, Egevad L, Russell R, Ramos-Montoya A, Vowler S, Sharma N, Kay J, Whitaker H, Clark J, Hurst R, Gnanapragasam V, Shah N, Warren A, Cooper C, Lynch A, Stark R, Mills I, Grönberg H, Neal D. Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study. EBioMedicine 2015; 2:1133-44. [PMID: 26501111 PMCID: PMC4588396 DOI: 10.1016/j.ebiom.2015.07.017] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/10/2015] [Accepted: 07/14/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. METHODS In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone. FINDINGS We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions. INTERPRETATION For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.
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Affiliation(s)
- H. Ross-Adams
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - A.D. Lamb
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
- Academic Urology Group, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - M.J. Dunning
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - S. Halim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - J. Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - C.M. Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - L.A. Egevad
- Department of Oncology–Pathology, Karolinska Institutet, Stockholm, Sweden
| | - R. Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - A. Ramos-Montoya
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - S.L. Vowler
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - N.L. Sharma
- Nuffield Department of Surgical Sciences, University of Oxford, Roosevelt Drive, Oxford, UK
| | - J. Kay
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Molecular Diagnostics and Therapeutics Group, University College London, WC1E 6BT, UK
| | - H. Whitaker
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Molecular Diagnostics and Therapeutics Group, University College London, WC1E 6BT, UK
| | - J. Clark
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - R. Hurst
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - V.J. Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
- Academic Urology Group, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - N.C. Shah
- Department of Urology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - A.Y. Warren
- Department of Pathology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - C.S. Cooper
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - A.G. Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - R. Stark
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - I.G. Mills
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, N-0318 Oslo, Norway
- Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospitals, N-0424 Oslo, Norway
- Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queen's University, Belfast, UK
| | - H. Grönberg
- Academic Urology Group, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - D.E. Neal
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
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17
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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: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [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.
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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
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18
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Bon H, Wadhwa K, Schreiner A, Osborne M, Carroll T, Ramos-Montoya A, Ross-Adams H, Visser M, Hoffmann R, Ahmed AA, Neal DE, Mills IG. Salt-inducible kinase 2 regulates mitotic progression and transcription in prostate cancer. Mol Cancer Res 2014; 13:620-635. [PMID: 25548099 DOI: 10.1158/1541-7786.mcr-13-0182-t] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 12/02/2014] [Indexed: 11/16/2022]
Abstract
UNLABELLED Salt-inducible kinase 2 (SIK2) is a multifunctional kinase of the AMPK family that plays a role in CREB1-mediated gene transcription and was recently reported to have therapeutic potential in ovarian cancer. The expression of this kinase was investigated in prostate cancer clinical specimens. Interestingly, auto-antibodies against SIK2 were increased in the plasma of patients with aggressive disease. Examination of SIK2 in prostate cancer cells found that it functions both as a positive regulator of cell-cycle progression and a negative regulator of CREB1 activity. Knockdown of SIK2 inhibited cell growth, delayed cell-cycle progression, induced cell death, and enhanced CREB1 activity. Expression of a kinase-dead mutant of SIK2 also inhibited cell growth, induced cell death, and enhanced CREB1 activity. Treatment with a small-molecule SIK2 inhibitor (ARN-3236), currently in preclinical development, also led to enhanced CREB1 activity in a dose- and time-dependent manner. Because CREB1 is a transcription factor and proto-oncogene, it was posited that the effects of SIK2 on cell proliferation and viability might be mediated by changes in gene expression. To test this, gene expression array profiling was performed and while SIK2 knockdown or overexpression of the kinase-dead mutant affected established CREB1 target genes; the overlap with transcripts regulated by forskolin (FSK), the adenylate cyclase/CREB1 pathway activator, was incomplete. IMPLICATIONS This study demonstrates that targeting SIK2 genetically or therapeutically will have pleiotropic effects on cell-cycle progression and transcription factor activation, which should be accounted for when characterizing SIK2 inhibitors.
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Affiliation(s)
- Hélène Bon
- Uro-oncology Research Group, Cambridge Research Institute, Cambridge, CB2 0RE, UK
| | - Karan Wadhwa
- Uro-oncology Research Group, Cambridge Research Institute, Cambridge, CB2 0RE, UK
| | - Alexander Schreiner
- Microscopy and Imaging Core, Cambridge Research Institute, Cambridge, CB2 0RE, UK
| | - Michelle Osborne
- Genomics Core, Cambridge Research Institute, Cambridge, CB2 ORE, UK
| | - Thomas Carroll
- Bioinformatics Core, Cambridge Research Institute, Cambridge, CB2 0RE, UK
| | | | - Helen Ross-Adams
- Uro-oncology Research Group, Cambridge Research Institute, Cambridge, CB2 0RE, UK
| | - Matthieu Visser
- Health Care Innovation, Philips Research, Eidhoven, Netherlands
| | - Ralf Hoffmann
- Molecular Diagnostics, Philips Research, Eindhoven, Netherlands
| | - Ahmed Ashour Ahmed
- Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS and Nuffield Department of Obstetrics and Gynaecology, University of Oxford, OX3 9DU, UK
| | - David E Neal
- Uro-oncology Research Group, Cambridge Research Institute, Cambridge, CB2 0RE, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, CB2 2QQ, UK.,Department of Oncology, University of Cambridge, Cambridge, CB2 2QQ, UK
| | - Ian G Mills
- Uro-oncology Research Group, Cambridge Research Institute, Cambridge, CB2 0RE, UK.,Department of Urology, Oslo University Hospital, 0424 Oslo, Norway.,Department of Cancer Prevention, Oslo University Hospital, 0424 Oslo, Norway.,Prostate Cancer Research Group, Centre for Molecular Medicine Norway, University of Oslo and Oslo University Hospital, N-0349, Oslo, Norway
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19
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Lalonde E, Ishkanian AS, Sykes J, Fraser M, Ross-Adams H, Erho N, Dunning MJ, Halim S, Lamb AD, Moon NC, Zafarana G, Warren AY, Meng X, Thoms J, Grzadkowski MR, Berlin A, Have CL, Ramnarine VR, Yao CQ, Malloff CA, Lam LL, Xie H, Harding NJ, Mak DYF, Chu KC, Chong LC, Sendorek DH, P'ng C, Collins CC, Squire JA, Jurisica I, Cooper C, Eeles R, Pintilie M, Dal Pra A, Davicioni E, Lam WL, Milosevic M, Neal DE, van der Kwast T, Boutros PC, Bristow RG. Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study. Lancet Oncol 2014; 15:1521-1532. [PMID: 25456371 DOI: 10.1016/s1470-2045(14)71021-6] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Clinical prognostic groupings for localised prostate cancers are imprecise, with 30-50% of patients recurring after image-guided radiotherapy or radical prostatectomy. We aimed to test combined genomic and microenvironmental indices in prostate cancer to improve risk stratification and complement clinical prognostic factors. METHODS We used DNA-based indices alone or in combination with intra-prostatic hypoxia measurements to develop four prognostic indices in 126 low-risk to intermediate-risk patients (Toronto cohort) who will receive image-guided radiotherapy. We validated these indices in two independent cohorts of 154 (Memorial Sloan Kettering Cancer Center cohort [MSKCC] cohort) and 117 (Cambridge cohort) radical prostatectomy specimens from low-risk to high-risk patients. We applied unsupervised and supervised machine learning techniques to the copy-number profiles of 126 pre-image-guided radiotherapy diagnostic biopsies to develop prognostic signatures. Our primary endpoint was the development of a set of prognostic measures capable of stratifying patients for risk of biochemical relapse 5 years after primary treatment. FINDINGS Biochemical relapse was associated with indices of tumour hypoxia, genomic instability, and genomic subtypes based on multivariate analyses. We identified four genomic subtypes for prostate cancer, which had different 5-year biochemical relapse-free survival. Genomic instability is prognostic for relapse in both image-guided radiotherapy (multivariate analysis hazard ratio [HR] 4·5 [95% CI 2·1-9·8]; p=0·00013; area under the receiver operator curve [AUC] 0·70 [95% CI 0·65-0·76]) and radical prostatectomy (4·0 [1·6-9·7]; p=0·0024; AUC 0·57 [0·52-0·61]) patients with prostate cancer, and its effect is magnified by intratumoral hypoxia (3·8 [1·2-12]; p=0·019; AUC 0·67 [0·61-0·73]). A novel 100-loci DNA signature accurately classified treatment outcome in the MSKCC low-risk to intermediate-risk cohort (multivariate analysis HR 6·1 [95% CI 2·0-19]; p=0·0015; AUC 0·74 [95% CI 0·65-0·83]). In the independent MSKCC and Cambridge cohorts, this signature identified low-risk to high-risk patients who were most likely to fail treatment within 18 months (combined cohorts multivariate analysis HR 2·9 [95% CI 1·4-6·0]; p=0·0039; AUC 0·68 [95% CI 0·63-0·73]), and was better at predicting biochemical relapse than 23 previously published RNA signatures. INTERPRETATION This is the first study of cancer outcome to integrate DNA-based and microenvironment-based failure indices to predict patient outcome. Patients exhibiting these aggressive features after biopsy should be entered into treatment intensification trials. FUNDING Movember Foundation, Prostate Cancer Canada, Ontario Institute for Cancer Research, Canadian Institute for Health Research, NIHR Cambridge Biomedical Research Centre, The University of Cambridge, Cancer Research UK, Cambridge Cancer Charity, Prostate Cancer UK, Hutchison Whampoa Limited, Terry Fox Research Institute, Princess Margaret Cancer Centre Foundation, PMH-Radiation Medicine Program Academic Enrichment Fund, Motorcycle Ride for Dad (Durham), Canadian Cancer Society.
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Affiliation(s)
- Emilie Lalonde
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Adrian S Ishkanian
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, USA
| | - Jenna Sykes
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Fraser
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Helen Ross-Adams
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Nicholas Erho
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Mark J Dunning
- Bioinformatics Core, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Silvia Halim
- Bioinformatics Core, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alastair D Lamb
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, UK
| | - Nathalie C Moon
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gaetano Zafarana
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - Xianyue Meng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - John Thoms
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michal R Grzadkowski
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Alejandro Berlin
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Cherry L Have
- Department of Pathology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Varune R Ramnarine
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Vancouver Prostate Centre and Department of Urological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cindy Q Yao
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Chad A Malloff
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Lucia L Lam
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Honglei Xie
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Nicholas J Harding
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Denise Y F Mak
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Center for Addiction and Mental Health, Toronto, ON, Canada
| | - Kenneth C Chu
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lauren C Chong
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Dorota H Sendorek
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Christine P'ng
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Colin C Collins
- Vancouver Prostate Centre and Department of Urological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jeremy A Squire
- Department of Pathology and Forensic Medicine, University of São Paulo at Ribeirão Preto, Ribeirão Preto, Brazil
| | - Igor Jurisica
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Colin Cooper
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK; Department of Biological Sciences and School of Medicine, University of East Anglia, Norwich, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK; Royal Marsden National Health Service Foundation Trust, London, UK
| | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alan Dal Pra
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Radiation Oncology, Bern University Hospital, Bern, Switzerland
| | - Elai Davicioni
- Research and Development, GenomeDx Biosciences, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Michael Milosevic
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, UK
| | - Theodorus van der Kwast
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Department of Pathology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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Ramos-Montoya A, Lamb AD, Russell R, Carroll T, Jurmeister S, Galeano-Dalmau N, Massie CE, Boren J, Bon H, Theodorou V, Vias M, Shaw GL, Sharma NL, Ross-Adams H, Scott HE, Vowler SL, Howat WJ, Warren AY, Wooster RF, Mills IG, Neal DE. HES6 drives a critical AR transcriptional programme to induce castration-resistant prostate cancer through activation of an E2F1-mediated cell cycle network. EMBO Mol Med 2014; 6:651-61. [PMID: 24737870 PMCID: PMC4023887 DOI: 10.1002/emmm.201303581] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Castrate-resistant prostate cancer (CRPC) is poorly characterized and heterogeneous and while the androgen receptor (AR) is of singular importance, other factors such as c-Myc and the E2F family also play a role in later stage disease. HES6 is a transcription co-factor associated with stem cell characteristics in neural tissue. Here we show that HES6 is up-regulated in aggressive human prostate cancer and drives castration-resistant tumour growth in the absence of ligand binding by enhancing the transcriptional activity of the AR, which is preferentially directed to a regulatory network enriched for transcription factors such as E2F1. In the clinical setting, we have uncovered a HES6-associated signature that predicts poor outcome in prostate cancer, which can be pharmacologically targeted by inhibition of PLK1 with restoration of sensitivity to castration. We have therefore shown for the first time the critical role of HES6 in the development of CRPC and identified its potential in patient-specific therapeutic strategies.
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Affiliation(s)
- Antonio Ramos-Montoya
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Alastair D Lamb
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK,Department of Urology, Addenbrooke's HospitalCambridge, UK,*Corresponding author. Tel: +44 1223 331940; Fax: +44 1223 769007; E-mail:
| | - Roslin Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Thomas Carroll
- Bioinformatics Core Facility, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Sarah Jurmeister
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Nuria Galeano-Dalmau
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Joan Boren
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Helene Bon
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Vasiliki Theodorou
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Maria Vias
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Greg L Shaw
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK,Department of Urology, Addenbrooke's HospitalCambridge, UK
| | - Naomi L Sharma
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK,Department of Urology, Addenbrooke's HospitalCambridge, UK
| | - Helen Ross-Adams
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Helen E Scott
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Sarah L Vowler
- Bioinformatics Core Facility, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - William J Howat
- Histopathology/ISH Core Facility, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK
| | - Anne Y Warren
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK,Department of Pathology, Addenbrooke's HospitalCambridge, UK
| | | | - Ian G Mills
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK,Prostate Cancer Research Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of OsloOslo, Norway,Departments of Cancer Prevention and Urology, Institute of Cancer Research and Oslo University HospitalsOslo, Norway
| | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridge, UK,Department of Urology, Addenbrooke's HospitalCambridge, UK,Department of Oncology, University of CambridgeCambridge, UK,**Corresponding author. Tel: +44 1223 331940; Fax: +44 1223 769007; E-mail:
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Kote-Jarai Z, Saunders EJ, Leongamornlert DA, Tymrakiewicz M, Dadaev T, Jugurnauth-Little S, Ross-Adams H, Al Olama AA, Benlloch S, Halim S, Russell R, Russel R, Dunning AM, Luccarini C, Dennis J, Neal DE, Hamdy FC, Donovan JL, Muir K, Giles GG, Severi G, Wiklund F, Gronberg H, Haiman CA, Schumacher F, Henderson BE, Le Marchand L, Lindstrom S, Kraft P, Hunter DJ, Gapstur S, Chanock S, Berndt SI, Albanes D, Andriole G, Schleutker J, Weischer M, Canzian F, Riboli E, Key TJ, Travis RC, Campa D, Ingles SA, John EM, Hayes RB, Pharoah P, Khaw KT, Stanford JL, Ostrander EA, Signorello LB, Thibodeau SN, Schaid D, Maier C, Vogel W, Kibel AS, Cybulski C, Lubinski J, Cannon-Albright L, Brenner H, Park JY, Kaneva R, Batra J, Spurdle A, Clements JA, Teixeira MR, Govindasami K, Guy M, Wilkinson RA, Sawyer EJ, Morgan A, Dicks E, Baynes C, Conroy D, Bojesen SE, Kaaks R, Vincent D, Bacot F, Tessier DC, Easton DF, Eeles RA. Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression. Hum Mol Genet 2013; 22:2520-8. [PMID: 23535824 PMCID: PMC3658165 DOI: 10.1093/hmg/ddt086] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 02/18/2013] [Indexed: 01/18/2023] Open
Abstract
Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease.
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Affiliation(s)
- Zsofia Kote-Jarai
- The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.
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22
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Kote-Jarai Z, Saunders E, Leongamornlert D, Tymrakiewicz M, Dadaev T, Jugurnauth S, Benlloch S, Amin Al Olama A, Ross-Adams H, Neal D, Eeles R. Abstract 2546: Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-2546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We have previously reported an association between prostate cancer (PrCa) risk and rs2242652 on 5p15. rs2242652 lies in intron 4 of TERT, which encodes telomerase reverse transcriptase, the catalytic subunit of the telomerase ribonucleoprotein complex. Telomerase catalyzes the de novo addition of telomere repeat sequences on to chromosome ends and thereby counterbalances telomere-dependent replicative senescence. Associations between SNPs in the TERT region and multiple cancer types have been reported; however no correlation has been observed thus far between the cancer-associated SNPs in TERT and gene expression or telomere length. To comprehensively evaluate the association between genetic variation across this region and PrCa we performed a fine-mapping analysis by direct genotyping using either a custom Illumina iSelect array (114 SNPs on iCOGS) or Sequenom MassArray iPlex (25 SNPs) followed by imputation of 1,094 SNPs in 22,301 PrCa cases and 22,320 controls in the PRACTICAL consortium. To determine independently associated variants in this region, we performed multiple stepwise logistic regression analysis; SNPs were included in the model if they were significant at P<10−4 after adjustment for other SNPs. Regression models identified multiple independent associations, reflecting the complexity of this region. These SNPs fall into four regions consisting of clusters of highly or moderately correlated variants, and there is only weak LD between SNPs in different regions. To investigate whether SNPs in any of these regions were associated with TERT gene expression, we performed qPCR assays on RNA from benign prostate tissue samples using the Fluidigm Biomark™ HD system. We found evidence that the risk reducing alleles of several variants in region one associated with elevated TERT expression, providing a plausible mechanism for the differential effect of SNPs on PrCa risk. Deep re-sequencing of these loci may help to further refine this region and facilitate selection of prospective causal variants for functional validation studies.
Citation Format: Zsofia Kote-Jarai, Edward Saunders, Daniel Leongamornlert, Malgorzata Tymrakiewicz, Tokhir Dadaev, Sarah Jugurnauth, Sara Benlloch, Ali Amin Al Olama, Helen Ross-Adams, David Neal, The UKGPCS Collaborators and The PRACTICAL Consortium, Douglas Easton, Rosalind Eeles. Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2546. doi:10.1158/1538-7445.AM2013-2546
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Affiliation(s)
| | | | | | | | - Tokhir Dadaev
- 1The Institute of Cancer Research, Sutton, United Kingdom
| | | | | | | | | | - David Neal
- 2University of Cambridge, Cambridge, United Kingdom
| | - Rosalind Eeles
- 1The Institute of Cancer Research, Sutton, United Kingdom
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23
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Whitaker HC, Kote-Jarai Z, Ross-Adams H, Warren AY, Burge J, George A, Bancroft E, Jhavar S, Leongamornlert D, Tymrakiewicz M, Saunders E, Page E, Mitra A, Mitchell G, Lindeman GJ, Evans DG, Blanco I, Mercer C, Rubinstein WS, Clowes V, Douglas F, Hodgson S, Walker L, Donaldson A, Izatt L, Dorkins H, Male A, Tucker K, Stapleton A, Lam J, Kirk J, Lilja H, Easton D, Cooper C, Eeles R, Neal DE. The rs10993994 risk allele for prostate cancer results in clinically relevant changes in microseminoprotein-beta expression in tissue and urine. PLoS One 2010; 5:e13363. [PMID: 20967219 PMCID: PMC2954177 DOI: 10.1371/journal.pone.0013363] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/01/2010] [Indexed: 11/19/2022] Open
Abstract
Background Microseminoprotein-beta (MSMB) regulates apoptosis and using genome-wide association studies the rs10993994 single nucleotide polymorphism in the MSMB promoter has been linked to an increased risk of developing prostate cancer. The promoter location of the risk allele, and its ability to reduce promoter activity, suggested that the rs10993994 risk allele could result in lowered MSMB in benign tissue leading to increased prostate cancer risk. Methodology/Principal Findings MSMB expression in benign and malignant prostate tissue was examined using immunohistochemistry and compared with the rs10993994 genotype. Urinary MSMB concentrations were determined by ELISA and correlated with urinary PSA, the presence or absence of cancer, rs10993994 genotype and age of onset. MSMB levels in prostate tissue and urine were greatly reduced with tumourigenesis. Urinary MSMB was better than urinary PSA at differentiating men with prostate cancer at all Gleason grades. The high risk allele was associated with heterogeneity of MSMB staining and loss of MSMB in both tissue and urine in benign prostate. Conclusions These data show that some high risk alleles discovered using genome-wide association studies produce phenotypic effects with potential clinical utility. We provide the first link between a low penetrance polymorphism for prostate cancer and a potential test in human tissue and bodily fluids. There is potential to develop tissue and urinary MSMB for a biomarker of prostate cancer risk, diagnosis and disease monitoring.
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Affiliation(s)
- Hayley C Whitaker
- Uro-Oncology Research Group, CRUK Cambridge Research Institute, Cambridge, United Kingdom.
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Gschwendtner A, Bevan S, Cole JW, Plourde A, Matarin M, Ross-Adams H, Meitinger T, Wichmann E, Mitchell BD, Furie K, Slowik A, Rich SS, Syme PD, MacLeod MJ, Meschia JF, Rosand J, Kittner SJ, Markus HS, Müller-Myhsok B, Dichgans M. Sequence variants on chromosome 9p21.3 confer risk for atherosclerotic stroke. Ann Neurol 2009; 65:531-9. [PMID: 19475673 DOI: 10.1002/ana.21590] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Recent studies have identified a major locus for risk for coronary artery disease and myocardial infarction on chromosome 9p21.3. Stroke, in particular, ischemic stroke caused by atherosclerotic disease, shares common mechanisms with myocardial infarction. We investigated whether the 9p21 region contributes to ischemic stroke risk. METHODS In an initial screen, 15 single nucleotide polymorphisms (SNPs) covering the critical genetic interval on 9p21 were genotyped in samples from Southern Germany (1,090 cases, 1,244 control subjects) and the United Kingdom (758 cases, 872 control subjects, 3 SNPs). SNPs significantly associated with ischemic stroke or individual stroke subtypes in either of the screening samples were subsequently genotyped in 2,528 additional cases and 2,189 additional control subjects from Europe and North America. RESULTS Genotyping of the screening samples demonstrated associations between seven SNPs and atherosclerotic stroke (all p < 0.05). Analysis of the full sample confirmed associations between six SNPs and atherosclerotic stroke in multivariate analyses controlling for demographic variables, coronary artery disease, myocardial infarction, and vascular risk factors (all p < 0.05). The odds ratios for the lead SNP (rs1537378-C) were similar in the various subsamples with a pooled odds ratio of 1.21 (95% confidence interval, 1.07-1.37) under both fixed- and random-effects models (p = 0.002). The point estimate for the population attributable risk is 20.1% for atherosclerotic stroke. INTERPRETATION The chromosome 9p21.3 region represents a major risk locus for atherosclerotic stroke. The effect of this locus on stroke appears to be independent of its relation to coronary artery disease and other stroke risk factors. Our findings support a broad role of the 9p21 region in arterial disease.
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Affiliation(s)
- Andreas Gschwendtner
- Department of Neurology, Klinikum Grosshadern, Ludwig-Maximilians-Universität, Marchioninistrasse 15, Munich, Germany
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25
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Pasdar A, Ross-Adams H, Cumming A, Cheung J, Whalley L, St Clair D, MacLeod MJ. Paraoxonase gene polymorphisms and haplotype analysis in a stroke population. BMC Med Genet 2006; 7:28. [PMID: 16551349 PMCID: PMC1435875 DOI: 10.1186/1471-2350-7-28] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 03/21/2006] [Indexed: 11/10/2022]
Abstract
BACKGROUND Paraoxonase (PON) has anti-atherogenic activity due to its protective function against low density lipoprotein (LDL) oxidation. Alteration of enzyme activity due to polymorphisms in the PON genes may influence the development of atheroma and thus affect stroke risk. Three PON genes (PON1, PON2 and PON3) have been identifiedand mapped to chromosome 7. METHODS We looked at the distribution of paraoxonase polymorphisms and haplotype arrangement in 397 Caucasian ischaemic stroke patients and 405 controls. We investigated 6 different common single nucleotide polymorphisms (SNP) in PON genes; two substitutions in PON1 ["A/G": Gln (Q)/Arg (R)] at codon 192 and ["T/A": Leu (L)/Met (M)] at codon 55, two in PON2 at codon 311 ["G/A": Cys (C)/Ser (S)] and codon 148 ["C/G": Ala (A)/Gly (G)] and two SNPs, both "A" to "G" substitutions, in PON3--intronic rs2074353, which we designated PON3-1 and [Ala (A)/Ala (A)] at codon 99, designated as PON3-3. Dynamic Allele Specific Hybridisation (DASH) was used as the genotyping assay. Haplotype analysis was performed using both PHASE and EHPLUS programs. RESULTS Genotype and allele frequencies were similar in cases and controls. Lipid profiles were not influenced by PON genotype. Haplotype frequencies for the six loci (PON2-148, PON2-311, PON3-3, PON3-1, PON1-55 and PON1-192) were estimated. Comparison of the two programs showed a significant difference in haplotype arrangements with EHPLUS (p-value = 0.005) but not with PHASE Ver.2 (p-value = 0.12). The 112211 (1 = frequent allele, 2 = rare allele) haplotype arrangement was commoner in cases than controls (p = 0.015), and the 111121 haplotype was commoner in controls (p = 0.006). CONCLUSION Our study did not identify a role for individual paraoxonase gene polymorphisms in the pathogenesis of ischaemic stroke. Findings of haplotype differences should be confirmed in large scale studies. The importance of using a well-validated haplotype analysis program is also underlined.
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Affiliation(s)
| | | | - Alastair Cumming
- Department of Molecular and Cell Biology, University of Aberdeen, UK
| | - John Cheung
- Department of Mental Health, University of Aberdeen, UK
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