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Kukkonen K, Taavitsainen S, Huhtala L, Uusi-Makela J, Granberg KJ, Nykter M, Urbanucci A. Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response. Cancers (Basel) 2021; 13:3325. [PMID: 34283056 PMCID: PMC8268970 DOI: 10.3390/cancers13133325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of chromatin and epigenetics has been defined as the overarching cancer hallmark. By disrupting transcriptional regulation in normal cells and mediating tumor progression by promoting cancer cell plasticity, this process has the ability to mediate all defined hallmarks of cancer. In this review, we collect and assess evidence on the contribution of chromatin and epigenetic dysregulation in prostate cancer. We highlight important mechanisms leading to prostate carcinogenesis, the emergence of castration-resistance upon treatment with androgen deprivation therapy, and resistance to antiandrogens. We examine in particular the contribution of chromatin structure and epigenetics to cell lineage commitment, which is dysregulated during tumorigenesis, and cell plasticity, which is altered during tumor progression.
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Affiliation(s)
- Konsta Kukkonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Laura Huhtala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Joonas Uusi-Makela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Kirsi J. Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
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2
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Gkountela S, Castro-Giner F, Szczerba BM, Vetter M, Landin J, Scherrer R, Krol I, Scheidmann MC, Beisel C, Stirnimann CU, Kurzeder C, Heinzelmann-Schwarz V, Rochlitz C, Weber WP, Aceto N. Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding. Cell 2019; 176:98-112.e14. [PMID: 30633912 PMCID: PMC6363966 DOI: 10.1016/j.cell.2018.11.046] [Citation(s) in RCA: 516] [Impact Index Per Article: 103.2] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/31/2018] [Accepted: 11/28/2018] [Indexed: 01/01/2023]
Abstract
The ability of circulating tumor cells (CTCs) to form clusters has been linked to increased metastatic potential. Yet biological features and vulnerabilities of CTC clusters remain largely unknown. Here, we profile the DNA methylation landscape of single CTCs and CTC clusters from breast cancer patients and mouse models on a genome-wide scale. We find that binding sites for stemness- and proliferation-associated transcription factors are specifically hypomethylated in CTC clusters, including binding sites for OCT4, NANOG, SOX2, and SIN3A, paralleling embryonic stem cell biology. Among 2,486 FDA-approved compounds, we identify Na+/K+ ATPase inhibitors that enable the dissociation of CTC clusters into single cells, leading to DNA methylation remodeling at critical sites and metastasis suppression. Thus, our results link CTC clustering to specific changes in DNA methylation that promote stemness and metastasis and point to cluster-targeting compounds to suppress the spread of cancer.
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Affiliation(s)
- Sofia Gkountela
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Francesc Castro-Giner
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Barbara Maria Szczerba
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Marcus Vetter
- Gynecologic Cancer Center, University Hospital Basel, 4056 Basel, Switzerland; Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland
| | - Julia Landin
- Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland; Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Ramona Scherrer
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Ilona Krol
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Manuel C Scheidmann
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | | | - Christian Kurzeder
- Gynecologic Cancer Center, University Hospital Basel, 4056 Basel, Switzerland; Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | | | - Christoph Rochlitz
- Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland
| | - Walter Paul Weber
- Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Nicola Aceto
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
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3
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Stelloo S, Bergman AM, Zwart W. Androgen receptor enhancer usage and the chromatin regulatory landscape in human prostate cancers. Endocr Relat Cancer 2019; 26:R267-R285. [PMID: 30865928 DOI: 10.1530/erc-19-0032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance. Genome-wide chromatin association studies revealed that transcriptional regulation by AR mainly depends on binding to distal regulatory enhancer elements that control gene expression through chromatin looping to gene promoters. Changes in the chromatin epigenetic landscape and DNA sequence can locally alter AR-DNA-binding capacity and consequently impact transcriptional output and disease outcome. The vast majority of reports describing AR chromatin interactions have been limited to cell lines, identifying numerous other factors and interacting transcription factors that impact AR chromatin interactions. Do these factors also impact AR cistromics - the genome-wide chromatin-binding landscape of AR - in vivo? Recent technological advances now enable researchers to identify AR chromatin-binding sites and their target genes in human specimens. In this review, we provide an overview of the different factors that influence AR chromatin binding in prostate cancer specimens, which is complemented with knowledge from cell line studies. Finally, we discuss novel perspectives on studying AR cistromics in clinical samples.
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Affiliation(s)
- Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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4
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Abstract
Over the last decade, advancements in massively-parallel DNA sequencing and computational biology have allowed for unprecedented insights into the fundamental mutational processes that underlie virtually every major cancer type. Two major cancer genomics consortia-The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC)-have produced rich databases of mutational, pathological, and clinical data that can be mined through web-based portals, allowing for correlative studies and testing of novel hypotheses on well-powered patient cohorts.In this chapter, we will review the impact of these technological developments on the understanding of molecular subtypes that promote prostate cancer initiation, progression, metastasis, and clinical aggression. In particular, we will focus on molecular subtypes that define clinically-relevant patient cohorts and assess how a better understanding of how these subtypes-in both somatic and germline genomes-may influence the clinical course for individual men diagnosed with prostate cancer.
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5
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Berglund AE, Rounbehler RJ, Gerke T, Awasthi S, Cheng CH, Takhar M, Davicioni E, Alshalalfa M, Erho N, Klein EA, Freedland SJ, Ross AE, Schaeffer EM, Trock BJ, Den RB, Cleveland JL, Park JY, Dhillon J, Yamoah K. Distinct transcriptional repertoire of the androgen receptor in ETS fusion-negative prostate cancer. Prostate Cancer Prostatic Dis 2018; 22:292-302. [PMID: 30367117 PMCID: PMC6760558 DOI: 10.1038/s41391-018-0103-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/27/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Background Prostate cancer (PCa) tumors harboring translocations of ETS family genes with the androgen responsive TMPRSS2 gene (ETS+ tumors) provide a robust biomarker for detecting PCa in approximately 70% of patients. ETS+ PCa express high levels of the androgen receptor (AR), yet PCa tumors lacking ETS fusions (ETS−) also express AR and demonstrate androgen-regulated growth. In this study, we evaluate the differences in the AR-regulated transcriptomes between ETS+ and ETS− PCa tumors. Methods 10,608 patient tumors from three independent PCa datasets classified as ETS+ (samples overexpressing ERG or other ETS family members) or ETS− (all other PCa) were analyzed for differential gene expression using false-discovery-rate adjusted methods and gene-set enrichment analysis (GSEA). Results Based on the expression of AR-dependent genes and an unsupervised Principal Component Analysis (PCA) model, AR-regulated gene expression alone was able to separate PCa samples into groups based on ETS status in all PCa databases. ETS status distinguished several differentially expressed genes in both TCGA (6.9%) and GRID (6.6%) databases, with 413 genes overlapping in both databases. Importantly, GSEA showed enrichment of distinct androgen-responsive genes in both ETS− and ETS+ tumors, and AR ChIP-seq data identified 131 direct AR-target genes that are regulated in an ETS-specific fashion. Notably, dysregulation of ETS-dependent AR-target genes within the metabolic and non-canonical WNT pathways was associated with clinical outcomes. Conclusions ETS status influences the transcriptional repertoire of the AR, and ETS− PCa tumors appear to rely on distinctly different AR-dependent transcriptional programs to drive and sustain tumorigenesis.
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Affiliation(s)
- Anders E Berglund
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Robert J Rounbehler
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.,Department of Oncological Sciences, University of South Florida, Tampa, FL, USA
| | - Travis Gerke
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Shivanshu Awasthi
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Chia-Ho Cheng
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | | | | | | | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Stephen J Freedland
- Department of Surgery, Division of Urology, Center for Integrated Research on Cancer and Lifestyle, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Bruce J Trock
- Department of Urology, Johns Hopkins, Baltimore, MD, USA
| | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - John L Cleveland
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jasreman Dhillon
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA. .,Department of Radiation Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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6
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Liang Y, Xu P, Zou Q, Luo H, Yu W. An epigenetic perspective on tumorigenesis: Loss of cell identity, enhancer switching, and NamiRNA network. Semin Cancer Biol 2018; 57:1-9. [PMID: 30213688 DOI: 10.1016/j.semcancer.2018.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/26/2018] [Accepted: 09/06/2018] [Indexed: 02/09/2023]
Abstract
Various tumorigenic theories have been proposed in the past century, which contribute to the prevention and treatment of cancer clinically. However, the underlying mechanisms of the initiation of cancer, drug resistance, neoplasm relapse, and metastasis are still challenging to be panoramically addressed. Based on the abundant evidence provided by others and us, we postulate that Tumor Initiated by Loss of Cell Identity (LOCI), which is an inevitable initiating event of tumorigenesis. As a result, normal cells are transformed into the cancerous cell. In this process, epigenetic regulatory program, especially NamiRNA (Nuclear activating miRNA)-enhancer-gene activation network, is vital for the cell identity. The disorganization of NamiRNA-enhancer-gene activation network is a causal predisposition to the cell identity loss, and the altered cell identity is stabilized by genetic variations of the NamiRNA-enhancer-gene activation network. Furthermore, the additional genetic or epigenetic abnormities confer those cells to carcinogenic characteristics, such as growth advantage over normal cells, and finally yield cancer. In this review, we literally explain our tumor initiation hypothesis based on the corresponding evidence, which will not only help to refresh our understanding of tumorigenesis but also bring benefits to developing "cell identity reversing" based therapies.
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Affiliation(s)
- Ying Liang
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Peng Xu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Qingping Zou
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Huaibing Luo
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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7
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Liang Y, Xu P, Zou Q, Luo H, Yu W. An epigenetic perspective on tumorigenesis: Loss of cell identity, enhancer switching, and NamiRNA network. Semin Cancer Biol 2018; 83:596-604. [PMID: 30208341 DOI: 10.1016/j.semcancer.2018.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 02/09/2023]
Abstract
Various tumorigenic theories have been proposed in the past century, which contribute to the prevention and treatment of cancer clinically. However, the underlying mechanisms of the initiation of cancer, drug resistance, neoplasm relapse, and metastasis are still challenging to be panoramically addressed. Based on the abundant evidence provided by others and us, we postulate that Tumor Initiated by Loss of Cell Identity (LOCI), which is an inevitable initiating event of tumorigenesis. As a result, normal cells are transformed into the cancerous cell. In this process, epigenetic regulatory program, especially NamiRNA (Nuclear activating miRNA)-enhancer-gene activation network, is vital for the cell identity. The disorganization of NamiRNA-enhancer-gene activation network is a causal predisposition to the cell identity loss, and the altered cell identity is stabilized by genetic variations of the NamiRNA-enhancer-gene activation network. Furthermore, the additional genetic or epigenetic abnormities confer those cells to carcinogenic characteristics, such as growth advantage over normal cells, and finally yield cancer. In this review, we literally explain our tumor imitation hypothesis based on the corresponding evidence, which will not only help to refresh our understanding of tumorigenesis but also bring benefits to developing "cell identity reversing" based therapies.
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Affiliation(s)
- Ying Liang
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Peng Xu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Qingping Zou
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Huaibing Luo
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China; Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, Shanghai Medical College, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Molecular Biology, Fudan University, Shanghai, 200032, China; Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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Massie CE, Mills IG, Lynch AG. The importance of DNA methylation in prostate cancer development. J Steroid Biochem Mol Biol 2017; 166:1-15. [PMID: 27117390 DOI: 10.1016/j.jsbmb.2016.04.009] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/09/2016] [Accepted: 04/17/2016] [Indexed: 02/08/2023]
Abstract
After briefly reviewing the nature of DNA methylation, its general role in cancer and the tools available to interrogate it, we consider the literature surrounding DNA methylation as relating to prostate cancer. Specific consideration is given to recurrent alterations. A list of frequently reported genes is synthesized from 17 studies that have reported on methylation changes in malignant prostate tissue, and we chart the timing of those changes in the diseases history through amalgamation of several previously published data sets. We also review associations with genetic alterations and hormone signalling, before the practicalities of investigating prostate cancer methylation using cell lines are assessed. We conclude by outlining the interplay between DNA methylation and prostate cancer metabolism and their regulation by androgen receptor, with a specific discussion of the mitochondria and their associations with DNA methylation.
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Affiliation(s)
- Charles E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine (Norway), University of Oslo and Oslo University Hospitals, Gaustadalleen, Oslo, Norway; Department of Molecular Oncology, Oslo University Hospitals, Oslo, Norway; PCUK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK.
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9
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Yang Q, Liang X, Sun X, Zhang L, Fu X, Rogers CJ, Berim A, Zhang S, Wang S, Wang B, Foretz M, Viollet B, Gang DR, Rodgers BD, Zhu MJ, Du M. AMPK/α-Ketoglutarate Axis Dynamically Mediates DNA Demethylation in the Prdm16 Promoter and Brown Adipogenesis. Cell Metab 2016; 24:542-554. [PMID: 27641099 PMCID: PMC5061633 DOI: 10.1016/j.cmet.2016.08.010] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/06/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022]
Abstract
Promoting brown adipose tissue (BAT) development is an attractive strategy for the treatment of obesity, as activated BAT dissipates energy through thermogenesis; however, the mechanisms controlling BAT formation are not fully understood. We hypothesized that as a master regulator of energy metabolism, AMP-activated protein kinase (AMPK) may play a direct role in the process and found that AMPKα1 (PRKAA1) ablation reduced Prdm16 expression and impaired BAT development. During early brown adipogenesis, the cellular levels of α-ketoglutarate (αKG), a key metabolite required for TET-mediated DNA demethylation, were profoundly increased and required for active DNA demethylation of the Prdm16 promoter. AMPKα1 ablation reduced isocitrate dehydrogenase 2 activity and cellular αKG levels. Remarkably, postnatal AMPK activation with AICAR or metformin rescued obesity-induced suppression of brown adipogenesis and thermogenesis. In summary, AMPK is essential for the epigenetic control of BAT development through αKG, thus linking a metabolite to progenitor cell differentiation and thermogenesis.
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Affiliation(s)
- Qiyuan Yang
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Xingwei Liang
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Xiaofei Sun
- School of Food Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lupei Zhang
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Fu
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Carl J Rogers
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Shuming Zhang
- School of Food Sciences, Washington State University, Pullman, WA 99164, USA
| | - Songbo Wang
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Bo Wang
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Marc Foretz
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Benoit Viollet
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Buel D Rodgers
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Mei-Jun Zhu
- School of Food Sciences, Washington State University, Pullman, WA 99164, USA
| | - Min Du
- Washington Center for Muscle Biology and Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA; Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100194, China.
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10
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ERG expression in prostate cancer: biological relevance and clinical implication. J Cancer Res Clin Oncol 2015; 142:1781-93. [DOI: 10.1007/s00432-015-2096-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/10/2015] [Indexed: 01/09/2023]
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11
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Strand SH, Hoyer S, Lynnerup AS, Haldrup C, Storebjerg TM, Borre M, Orntoft TF, Sorensen KD. High levels of 5-hydroxymethylcytosine (5hmC) is an adverse predictor of biochemical recurrence after prostatectomy in ERG-negative prostate cancer. Clin Epigenetics 2015; 7:111. [PMID: 26478752 PMCID: PMC4608326 DOI: 10.1186/s13148-015-0146-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/02/2015] [Indexed: 12/14/2022] Open
Abstract
Background Prostate cancer (PC) can be stratified into distinct molecular subtypes based on TMPRSS2-ERG gene fusion status, but its potential prognostic value remains controversial. Likewise, routine clinicopathological features cannot clearly distinguish aggressive from indolent tumors at the time of diagnosis; thus, new prognostic biomarkers are urgently needed. The DNA methylation variant 5-hydroxymethylcytosine (5hmC, an oxidized derivative of 5-methylcytosine) has recently emerged as a new diagnostic and/or prognostic biomarker candidate for several human malignancies. However, this remains to be systematically investigated for PC. In this study, we determined 5hmC levels in 311 PC (stratified by ERG status) and 228 adjacent non-malignant (NM) prostate tissue specimens by immunohistochemical analysis of a tissue microarray, representing a large radical prostatectomy (RP) cohort with long clinical follow-up. We investigated possible correlations between 5hmC and routine clinicopathological variables and assessed the prognostic potential of 5hmC by Kaplan-Meier and uni- and multivariate Cox regression analyses in ERG+ (n = 178) vs. ERG− (n = 133) PCs using biochemical recurrence (BCR) as endpoint. Results We observed a borderline significant (p = 0.06) reduction in 5hmC levels in PC compared to NM tissue samples, which was explained by a highly significant (p < 0.001) loss of 5hmC in ERG− PCs. ERG status was not predictive of BCR in this cohort (p = 0.73), and no significant association was found between BCR and 5hmC levels in ERG+ PCs (p = 0.98). In contrast, high 5hmC immunoreactivity was a significant adverse predictor of BCR after RP in ERG− PCs, independent of Gleason score, pathological tumor stage, surgical margin status, and pre-operative prostate-specific antigen (PSA) level (hazard ratio (HR) (95 % confidence interval (CI)): 1.62 (1.15–2.28), p = 0.006). Conclusions This is the first study to demonstrate a prognostic potential for 5hmC in PC. Our findings highlight the importance of ERG stratification in PC biomarker studies and suggest that epigenetic mechanisms involving 5hmC are important for the development and/or progression of ERG− PC. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0146-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Soren Hoyer
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Anne-Sofie Lynnerup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark ; Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark ; Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Tine Maj Storebjerg
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark ; Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark ; Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben F Orntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Karina D Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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12
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Johansson I, Lauss M, Holm K, Staaf J, Nilsson C, Fjällskog ML, Ringnér M, Hedenfalk I. Genome methylation patterns in male breast cancer - Identification of an epitype with hypermethylation of polycomb target genes. Mol Oncol 2015; 9:1565-79. [PMID: 25990542 PMCID: PMC5528783 DOI: 10.1016/j.molonc.2015.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/13/2015] [Accepted: 04/28/2015] [Indexed: 11/03/2022] Open
Abstract
Male breast cancer (MBC) is a rare disease that shares both similarities and differences with female breast cancer (FBC). The aim of this study was to assess genome-wide DNA methylation profiles in MBC and compare them with the previously identified transcriptional subgroups of MBC, luminal M1 and M2, as well as the intrinsic subtypes of FBC. Illumina's 450K Infinium arrays were applied to 47 MBC and 188 FBC tumors. Unsupervised clustering of the most variable CpGs among MBC tumors revealed two stable epitypes, designated ME1 and ME2. The methylation patterns differed significantly between the groups and were closely associated with the transcriptional subgroups luminal M1 and M2. Tumors in the ME1 group were more proliferative and aggressive than ME2 tumors, and showed a tendency toward inferior survival. ME1 tumors also displayed hypermethylation of PRC2 target genes and high expression of EZH2, one of the core components of PRC2. Upon combined analysis of MBC and FBC tumors, ME1 MBCs clustered among luminal B FBC tumors and ME2 MBCs clustered within the predominantly luminal A FBC cluster. The majority of the MBC tumors remained grouped together within the clusters rather than being interspersed among the FBC tumors. Differences in the genomic location of methylated CpGs, as well as in the regulation of central canonical pathways may explain the separation between MBC and FBC tumors in the respective clusters. These findings further suggest that MBC is not readily defined using conventional criteria applied to FBC.
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Affiliation(s)
- Ida Johansson
- Department of Oncology and Pathology, Clinical Sciences, and CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Martin Lauss
- Department of Oncology and Pathology, Clinical Sciences, and CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Karolina Holm
- Department of Oncology and Pathology, Clinical Sciences, and CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Johan Staaf
- Department of Oncology and Pathology, Clinical Sciences, and CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | | | | | - Markus Ringnér
- Department of Oncology and Pathology, Clinical Sciences, and CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Department of Oncology and Pathology, Clinical Sciences, and CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden.
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13
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Clermont PL, Lin D, Crea F, Wu R, Xue H, Wang Y, Thu KL, Lam WL, Collins CC, Wang Y, Helgason CD. Polycomb-mediated silencing in neuroendocrine prostate cancer. Clin Epigenetics 2015; 7:40. [PMID: 25859291 PMCID: PMC4391120 DOI: 10.1186/s13148-015-0074-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/13/2015] [Indexed: 02/06/2023] Open
Abstract
Background Neuroendocrine prostate cancer (NEPC) is a highly aggressive subtype of prostate cancer (PCa) for which the median survival remains less than a year. Current treatments are only palliative in nature, and the lack of suitable pre-clinical models has hampered previous efforts to develop novel therapeutic strategies. Addressing this need, we have recently established the first in vivo model of complete neuroendocrine transdifferentiation using patient-derived xenografts. Few genetic differences were observed between parental PCa and relapsed NEPC, suggesting that NEPC likely results from alterations that are epigenetic in nature. Thus, we sought to identify targetable epigenetic regulators whose expression was elevated in NEPC using genome-wide profiling of patient-derived xenografts and clinical samples. Results Our data indicate that multiple members of the polycomb group (PcG) family of transcriptional repressors were selectively upregulated in NEPC. Notably, CBX2 and EZH2 were consistently the most highly overexpressed epigenetic regulators across multiple datasets from clinical and xenograft tumor tissues. Given the striking upregulation of PcG genes and other transcriptional repressors, we derived a 185-gene list termed ‘neuroendocrine-associated repression signature’ (NEARS) by overlapping transcripts downregulated across multiple in vivo NEPC models. In line with the striking upregulation of PcG family members, NEARS was preferentially enriched with PcG target genes, suggesting a driving role for PcG silencing in NEPC. Importantly, NEARS was significantly associated with high-grade tumors, metastatic progression, and poor outcome in multiple clinical datasets, consistent with extensive literature linking PcG genes and aggressive disease progression. Conclusions We have explored the epigenetic landscape of NEPC and provided evidence of increased PcG-mediated silencing associated with aberrant transcriptional regulation of key differentiation genes. Our results position CBX2 and EZH2 as potential therapeutic targets in NEPC, providing opportunities to explore novel strategies aimed at reversing epigenetic alterations driving this lethal disease. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0074-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pier-Luc Clermont
- Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada ; Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada
| | - Dong Lin
- Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada ; Vancouver Prostate Centre, 899 West 12th Avenue, Vancouver, BC V5Z 1 M9 Canada
| | - Francesco Crea
- Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada ; Vancouver Prostate Centre, 899 West 12th Avenue, Vancouver, BC V5Z 1 M9 Canada ; Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, 2775 Laurel Street, Vancouver, BC V5Z 1 M9 Canada
| | - Rebecca Wu
- Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada
| | - Hui Xue
- Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada
| | - Yuwei Wang
- Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada
| | - Kelsie L Thu
- Department of Integrative Oncology, Genetics Unit, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada
| | - Wan L Lam
- Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada ; Department of Integrative Oncology, Genetics Unit, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada
| | - Colin C Collins
- Vancouver Prostate Centre, 899 West 12th Avenue, Vancouver, BC V5Z 1 M9 Canada ; Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, 2775 Laurel Street, Vancouver, BC V5Z 1 M9 Canada
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada ; Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada ; Vancouver Prostate Centre, 899 West 12th Avenue, Vancouver, BC V5Z 1 M9 Canada ; Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, 2775 Laurel Street, Vancouver, BC V5Z 1 M9 Canada
| | - Cheryl D Helgason
- Department of Experimental Therapeutics, British Columbia Cancer Research Centre, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada ; Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, 675 W 10th Avenue, Vancouver, BC V5Z 1 L3 Canada ; Department of Surgery, University of British Columbia, 910 W 10th Avenue, Vancouver, BC V5Z 4E3 Canada
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14
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Liang YX, Mo RJ, He HC, Chen JH, Zou J, Han ZD, Lu JM, Cai C, Zeng YR, Zhong WD, Wu CL. Aberrant hypomethylation-mediated CD147 overexpression promotes aggressive tumor progression in human prostate cancer. Oncol Rep 2015; 33:2648-54. [PMID: 25813864 DOI: 10.3892/or.2015.3870] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/05/2015] [Indexed: 12/31/2022] Open
Abstract
Our previous study revealed the potential role of CD147 in human prostate cancer (PCa). Here, we investigated the CD147 promoter methylation status and the correlation with tumorigenicity in human PCa. CD147 mRNA and protein expression levels were both significantly higher in the 4 PCa cell lines, than in the 2 non-tumorigenic benign human prostatic epithelial cell lines (all P<0.01). We showed hypomethylation of promoter regions of CD147 in PCa cell lines with significant CD147 expression as compared to non-tumorigenic benign human prostatic epithelial cell lines slowly expressing CD147. Additionally, the treatment of methylated cell lines with 5-aza-2'-deoxycytidine increased CD147 expression significantly in low-expressing cell lines and also activated the expression of matrix metalloproteinase (MMP)-2, which may be one of the most important downstream targets of CD147. Furthermore, PCa tissues displayed decreased DNA methylation in the promoter region of CD147 compared to the corresponding non-cancerous prostate tissues, and methylation intensity correlated inversely with the CD147 mRNA levels. There was a significant negative correlation between CD147 mRNA levels and the number of methylated sites in PCa tissues (r=-0.467, P<0.01). In conclusion, our data offer convincing evidence for the first time that the DNA promoter hypomethylation of CD147 may be one of the regulatory mechanisms involved in the cancer-related overexpression of CD147 and may play a crucial role in the tumorigenesis of PCa.
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Affiliation(s)
- Yu-Xiang Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Ru-Jun Mo
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Hui-Chan He
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Jia-Hong Chen
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Jun Zou
- Department of Urology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Zhao-Dong Han
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Jian-Ming Lu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Chao Cai
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Yan-Ru Zeng
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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15
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Savio AJ, Bapat B. Beyond the island: epigenetic biomarkers of colorectal and prostate cancer. Methods Mol Biol 2015; 1238:103-24. [PMID: 25421657 DOI: 10.1007/978-1-4939-1804-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Epigenetic dysregulation is a common feature across all cancer types. Epigenetic mechanisms, from DNA methylation to histone modifications, allow for a vast number of cellular phenotypes to be created from the same genetic material. Just as certain genetic changes play a key role in tumor initiation and progression, epigenetic changes may also set the course of tumor development and be required for malignant transformation. The most frequently studied epigenetic changes investigated thus far are global genomic DNA hypomethylation along with specific hypermethylation, predominantly at promoter CpG islands of tumor suppressor genes. In addition to DNA methylation changes at CpG islands, there is an abundance of other epigenetic alterations occurring within cancer cells including DNA methylation alterations outside of CpG islands, non-CpG methylation, changes in cytosine oxidative species (hydroxymethylcytosine, formylcytosine, carboxylcytosine) levels, and histone modifications. This chapter examines epigenetic alterations beyond the island, and summarizes recent findings in DNA-based epigenetic regulation of the two most commonly diagnosed cancers in the Western world: colorectal cancer and prostate cancer.
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Affiliation(s)
- Andrea J Savio
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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16
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Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M, Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R. BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nat Genet 2014; 47:22-30. [PMID: 25485837 DOI: 10.1038/ng.3165] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/17/2014] [Indexed: 12/14/2022]
Abstract
Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show that the gene encoding BAZ2A (TIP5), a factor previously implicated in epigenetic rRNA gene silencing, is overexpressed in prostate cancer and is paradoxically involved in maintaining prostate cancer cell growth, a feature specific to cancer cells. BAZ2A regulates numerous protein-coding genes and directly interacts with EZH2 to maintain epigenetic silencing at genes repressed in metastasis. BAZ2A overexpression is tightly associated with a molecular subtype displaying a CpG island methylator phenotype (CIMP). Finally, high BAZ2A levels serve as an independent predictor of biochemical recurrence in a cohort of 7,682 individuals with prostate cancer. This work identifies a new aberrant role for the epigenetic regulator BAZ2A, which can also serve as a useful marker for metastatic potential in prostate cancer.
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Affiliation(s)
- Lei Gu
- 1] Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra C Frommel
- 1] Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland. [2] Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Christopher C Oakes
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Grupp
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cristina Y Gerig
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Dominik Bär
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- 1] Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. [2] Swiss Institute of Bioinformatics (SIB), University of Zurich, Zurich, Switzerland
| | - Constance Baer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Weiss
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthieu Schapira
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Ruprecht Kuner
- Unit of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center of Tumour Diseases, Heidelberg, Germany
| | - Holger Sültmann
- Unit of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center of Tumour Diseases, Heidelberg, Germany
| | - Maurizio Provenzano
- Oncology Research Unit, Division of Urology, University Hospital of Zurich, Zurich, Switzerland
| | | | | | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thorsten Schlomm
- Martini Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roland Eils
- 1] Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raffaella Santoro
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
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17
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Grupp K, Ospina-Klinck D, Tsourlakis MC, Koop C, Wilczak W, Adam M, Simon R, Sauter G, Izbicki JR, Graefen M, Huland H, Steurer S, Schlomm T, Minner S, Quaas A. NY-ESO-1 expression is tightly linked to TMPRSS2-ERG fusion in prostate cancer. Prostate 2014; 74:1012-22. [PMID: 24789172 DOI: 10.1002/pros.22816] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/02/2014] [Indexed: 11/07/2022]
Abstract
BACKGROUND NY-ESO-1 has been suggested as therapeutic cancer vaccine in prostate cancer. This study was undertaken to explore the relationship of NY-ESO-1 with tumor phenotype, biochemical recurrence, and molecular subgroups in hormone-naive prostate cancers. METHODS NY-ESO-1 immunohistochemistry was analyzed on a tissue microarray containing 11,152 prostate cancer samples. Results were compared to clinically follow-up data, ERG status, and deletions on PTEN, 3p13, 5q21, and 6q15. RESULTS NY-ESO-1 expression was absent in benign prostate glands. In prostate cancer, NY-ESO-1 positivity was found 8.8% of our 8,761 interpretable tumors including 5.8% with weak, 2.5% with moderate, and 0.5% with strong expression. There was a threefold higher rate of NY-ESO-1 expression in ERG fusion positive tumors than in ERG negative cancers (P < 0.0001). There was a significant association with early PSA recurrence, which was largely limited to ERG positive cancers. Within the ERG positive subgroup, high NY-ESO-1 expression was associated with early biochemical recurrence (P = 0.0002) and high Gleason grade (P < 0.0001). In ERG negative cancers, NY-ESO-1 expression was also linked to PTEN (P = 0.0012) and 6q15 deletions (P = 0.0005). CONCLUSIONS Our observations indicate a tight link of NY-ESO-1 expression to ERG activation and (to a lesser extent) PTEN- and 6q15-deletions in prostate cancer. The impact of these interactions on the likelihood of response to immunotherapy is unclear. The prognostic impact of NY-ESO-1 expression is little and not independent of histologic variables.
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Affiliation(s)
- Katharina Grupp
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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18
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Yang YA, Kim J, Yu J. Influence of oncogenic transcription factors on chromatin conformation and implications in prostate cancer. APPLICATION OF CLINICAL GENETICS 2014; 7:81-91. [PMID: 24876790 PMCID: PMC4036145 DOI: 10.2147/tacg.s35598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In recent years, facilitated by rapid technological advances, we are becoming more adept at probing the molecular processes, which take place in the nucleus, that are crucial for the hierarchical regulation and organization of chromatin architecture. With an unprecedented level of resolution, a detailed atlas of chromosomal structures (histone displacement, variants, modifications, chromosome territories, and DNA looping) and mechanisms underlying their establishment, provides invaluable insight into physiological as well as pathological phenomena. In this review, we will focus on prostate cancer, a prevalent malignancy in men worldwide, and for which a curative treatment strategy is yet to be attained. We aim to catalog the most frequently observed oncogenic alterations associated with chromatin conformation, while emphasizing the TMPRSS2-ERG fusion, which is found in more than one-half of prostate cancer patients and its functions in compromising the chromatin landscape in prostate cancer.
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Affiliation(s)
- Yeqing Angela Yang
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Jung Kim
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Jindan Yu
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA ; Robert H Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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19
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Fraser M, Berlin A, Bristow RG, van der Kwast T. Genomic, pathological, and clinical heterogeneity as drivers of personalized medicine in prostate cancer. Urol Oncol 2014; 33:85-94. [PMID: 24768356 DOI: 10.1016/j.urolonc.2013.10.020] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 12/23/2022]
Abstract
Prostate cancer (CaP) is the most commonly diagnosed malignancy in men in the Western world. In North America, more than 275,000 men are diagnosed annually, whereby approximately 1 in 6 men will be diagnosed with CaP in their lifetime, and 1 in 34 men will die from castration-resistant metastatic disease. Unfortunately, current clinical prognostic factors explain only a proportion of the observed variation in clinical outcome from patient to patient. Furthermore, overtreatment of indolent and low-risk cancers leads to inappropriate morbidity following radiotherapy or surgery. As such, better predictors of individualized prognosis and treatment response are urgently needed to triage patients to customized and intensified CaP treatment. Recent developments in next-generation sequencing have made it possible to identify prognostic and predictive signatures based on genomic profiles. We discuss the genetic basis of CaP progression from localized to systemic disease (e.g., point mutations, copy-number alterations, and structural variants) in relation with unique features of CaP biology, including intraprostatic and interprostatic heterogeneity, multifocality and multiclonality, TMPRSS2:ERG, and other ETS-family gene fusions. Finally, we focus on the use of genomic markers as prognostic factors for local failure and for systemic disease, as novel risk-stratification tools, in triaging patients to existing treatment options, and ultimately the potential of genomics for the identification of molecular targets for therapy of CaP.
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Affiliation(s)
- Michael Fraser
- Ontario Cancer Institute and Princess Margaret Cancer Center (University Health Network), Toronto, Ontario, Canada
| | - Alejandro Berlin
- Ontario Cancer Institute and Princess Margaret Cancer Center (University Health Network), Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Robert G Bristow
- Ontario Cancer Institute and Princess Margaret Cancer Center (University Health Network), Toronto, Ontario, Canada; Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital (University Health Network), Toronto, Ontario, Canada.
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20
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Bristow RG, Berlin A, Dal Pra A. An arranged marriage for precision medicine: hypoxia and genomic assays in localized prostate cancer radiotherapy. Br J Radiol 2014; 87:20130753. [PMID: 24588670 DOI: 10.1259/bjr.20130753] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Prostate cancer (CaP) is the most commonly diagnosed malignancy in males in the Western world with one in six males diagnosed in their lifetime. Current clinical prognostication groupings use pathologic Gleason score, pre-treatment prostatic-specific antigen and Union for International Cancer Control-TNM staging to place patients with localized CaP into low-, intermediate- and high-risk categories. These categories represent an increasing risk of biochemical failure and CaP-specific mortality rates, they also reflect the need for increasing treatment intensity and justification for increased side effects. In this article, we point out that 30-50% of patients will still fail image-guided radiotherapy or surgery despite the judicious use of clinical risk categories owing to interpatient heterogeneity in treatment response. To improve treatment individualization, better predictors of prognosis and radiotherapy treatment response are needed to triage patients to bespoke and intensified CaP treatment protocols. These should include the use of pre-treatment genomic tests based on DNA or RNA indices and/or assays that reflect cancer metabolism, such as hypoxia assays, to define patient-specific CaP progression and aggression. More importantly, it is argued that these novel prognostic assays could be even more useful if combined together to drive forward precision cancer medicine for localized CaP.
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Affiliation(s)
- R G Bristow
- Princess Margaret Cancer Center (University Health Network), Toronto, ON, Canada
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