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Super-enhancer in prostate cancer: transcriptional disorders and therapeutic targets. NPJ Precis Oncol 2020; 4:31. [PMID: 33299103 PMCID: PMC7677538 DOI: 10.1038/s41698-020-00137-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Abnormal activity of oncogenic and tumor-suppressor signaling pathways contributes to cancer and cancer risk in humans. Transcriptional dysregulation of these pathways is commonly associated with tumorigenesis and the development of cancer. Genetic and epigenetic alterations may mediate dysregulated transcriptional activity. One of the most important epigenetic alternations is the non-coding regulatory element, which includes both enhancers and super-enhancers (SEs). SEs, characterized as large clusters of enhancers with aberrant high levels of transcription factor binding, have been considered as key drivers of gene expression in controlling and maintaining cancer cell identity. In cancer cells, oncogenes acquire SEs and the cancer phenotype relies on these abnormal transcription programs driven by SEs, which leads to cancer cells often becoming addicted to the SEs-related transcription programs, including prostate cancer. Here, we summarize recent findings of SEs and SEs-related gene regulation in prostate cancer and review the potential pharmacological inhibitors in basic research and clinical trials.
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Ordoñez R, Martínez-Calle N, Agirre X, Prosper F. DNA Methylation of Enhancer Elements in Myeloid Neoplasms: Think Outside the Promoters? Cancers (Basel) 2019; 11:cancers11101424. [PMID: 31554341 PMCID: PMC6827153 DOI: 10.3390/cancers11101424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/15/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022] Open
Abstract
Gene regulation through DNA methylation is a well described phenomenon that has a prominent role in physiological and pathological cell-states. This epigenetic modification is usually grouped in regions denominated CpG islands, which frequently co-localize with gene promoters, silencing the transcription of those genes. Recent genome-wide DNA methylation studies have challenged this paradigm, demonstrating that DNA methylation of regulatory regions outside promoters is able to influence cell-type specific gene expression programs under physiologic or pathologic conditions. Coupling genome-wide DNA methylation assays with histone mark annotation has allowed for the identification of specific epigenomic changes that affect enhancer regulatory regions, revealing an additional layer of complexity to the epigenetic regulation of gene expression. In this review, we summarize the novel evidence for the molecular and biological regulation of DNA methylation in enhancer regions and the dynamism of these changes contributing to the fine-tuning of gene expression. We also analyze the contribution of enhancer DNA methylation on the expression of relevant genes in acute myeloid leukemia and chronic myeloproliferative neoplasms. The characterization of the aberrant enhancer DNA methylation provides not only a novel pathogenic mechanism for different tumors but also highlights novel potential therapeutic targets for myeloid derived neoplasms.
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Affiliation(s)
- Raquel Ordoñez
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Nicolás Martínez-Calle
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Xabier Agirre
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain.
| | - Felipe Prosper
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain.
- Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Avenida Pío XII-36, 31008 Pamplona, Spain.
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Wen W, Wu P, Gong J, Zhao M, Zhang Z, Chen R, Chen H, Sun J. Association of Pioglitazone with Increased Risk of Prostate Cancer and Pancreatic Cancer: A Functional Network Study. Diabetes Ther 2018; 9:2229-2243. [PMID: 30255424 PMCID: PMC6250638 DOI: 10.1007/s13300-018-0509-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The question of whether pioglitazone, an antidiabetic drug, increases the risk of cancer has been debated for some time. Recent studies have shown that pioglitazone use can increase the risk of prostate cancer as well as pancreatic cancer. However, it is unclear whether pioglitazone is a causal risk factor for these cancers. METHODS In this study, we aimed to explore the direct targets of pioglitazone and genes associated with this drug by querying open platforms in order to construct a biological function network, and then to further evaluate the relationships of pioglitazone with prostate cancer and pancreatic cancer. RESULTS We first tested our hypothesis using DrugBank and STRING. We identified four direct targets of pioglitazone and 50 pioglitazone-associated genes, which were then selected for KEGG pathway analysis using STRING and WebGestalt. This analysis generated the top 25 KEGG pathways, among which four pathways were related to site-specific cancers, including prostate cancer and pancreatic cancer. Finally, a genomic study using cBioPortal indicated that genomic alterations of two gene sets related to the prostate cancer and pancreatic cancer pathways, respectively, are associated with the acceleration of carcinogenesis. CONCLUSIONS Pioglitazone is likely to be a causal risk factor for prostate cancer and pancreatic cancer, so this drug should be used with caution. The present research also demonstrates the use of biological function network analysis to effectively explore drug interactions and drug safety profiles.
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Affiliation(s)
- Weiheng Wen
- Department of Endocrinology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Peili Wu
- Department of Endocrinology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jinru Gong
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Min Zhao
- Department of Endocrinology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Zhen Zhang
- Department of Endocrinology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Rongping Chen
- Department of Endocrinology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Hong Chen
- Department of Endocrinology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
| | - Jia Sun
- Department of Endocrinology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
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Cai Y, Tsai HC, Yen RWC, Zhang YW, Kong X, Wang W, Xia L, Baylin SB. Critical threshold levels of DNA methyltransferase 1 are required to maintain DNA methylation across the genome in human cancer cells. Genome Res 2017; 27:533-544. [PMID: 28232479 PMCID: PMC5378172 DOI: 10.1101/gr.208108.116] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 02/22/2017] [Indexed: 11/18/2022]
Abstract
Reversing DNA methylation abnormalities and associated gene silencing, through inhibiting DNA methyltransferases (DNMTs) is an important potential cancer therapy paradigm. Maximizing this potential requires defining precisely how these enzymes maintain genome-wide, cancer-specific DNA methylation. To date, there is incomplete understanding of precisely how the three DNMTs, 1, 3A, and 3B, interact for maintaining DNA methylation abnormalities in cancer. By combining genetic and shRNA depletion strategies, we define not only a dominant role for DNA methyltransferase 1 (DNMT1) but also distinct roles of 3A and 3B in genome-wide DNA methylation maintenance. Lowering DNMT1 below a threshold level is required for maximal loss of DNA methylation at all genomic regions, including gene body and enhancer regions, and for maximally reversing abnormal promoter DNA hypermethylation and associated gene silencing to reexpress key genes. It is difficult to reach this threshold with patient-tolerable doses of current DNMT inhibitors (DNMTIs). We show that new approaches, like decreasing the DNMT targeting protein, UHRF1, can augment the DNA demethylation capacities of existing DNA methylation inhibitors for fully realizing their therapeutic potential.
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Affiliation(s)
- Yi Cai
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Hsing-Chen Tsai
- Graduate Institute of Toxicology, National Taiwan University, Taipei, 10051, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, 10002, Taiwan
| | - Ray-Whay Chiu Yen
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Yang W Zhang
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Xiangqian Kong
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Wei Wang
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Limin Xia
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephen B Baylin
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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TGFβ promotes mesenchymal phenotype of pancreatic cancer cells, in part, through epigenetic activation of VAV1. Oncogene 2016; 36:2202-2214. [PMID: 27893715 DOI: 10.1038/onc.2016.378] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/14/2016] [Accepted: 08/29/2016] [Indexed: 02/06/2023]
Abstract
The highly homeostasis-resistant nature of cancer cells leads to their escape from treatment and to liver metastasis, which in turn makes pancreatic ductal adenocarcinoma (PDAC) difficult to treat, especially the squamous/epithelial-to-mesenchymal transition (EMT)-like subtype. As the molecular mechanisms underlying tumour heterogeneity remain elusive, we investigated whether epigenetic regulation might explain inter-individual differences in the progression of specific subtypes. DNA methylation profiling performed on cancer tissues prior to chemo/radiotherapy identified one hypermethylated CpG site (CpG6882469) in the VAV1 gene body that was correlated with demethylation of two promoter CpGs (CpG6772370/CpG6772811) in both PDAC and peripheral blood. Transforming growth factor β treatment induced gene-body hypermethylation, dissociation of DNMT1 from the promoter, and VAV1 expression via SMAD4 and mutant KrasG12D. Pharmacological inhibition of TGFβ-VAV1 signalling decreased the squamous/EMT-like cancer cells, promoted nuclear VAV1 localization, and enhanced the efficacy of gemcitabine in prolonging the survival of KPfl/flC mice. Together, the three VAV1 CpGs serve as biomarkers for prognosis and early detection, and the TGFβ-VAV1 axis represents a therapeutic target.
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The MYC 3' Wnt-Responsive Element Drives Oncogenic MYC Expression in Human Colorectal Cancer Cells. Cancers (Basel) 2016; 8:cancers8050052. [PMID: 27223305 PMCID: PMC4880869 DOI: 10.3390/cancers8050052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/11/2016] [Accepted: 05/18/2016] [Indexed: 12/11/2022] Open
Abstract
Mutations in components of the Wnt/β-catenin signaling pathway drive colorectal cancer (CRC) by deregulating expression of downstream target genes including the c-MYC proto-oncogene (MYC). The critical regulatory DNA enhancer elements that control oncogenic MYC expression in CRC have yet to be fully elucidated. In previous reports, we correlated T-cell factor (TCF) and β-catenin binding to the MYC 3′ Wnt responsive DNA element (MYC 3′ WRE) with MYC expression in HCT116 cells. Here we used CRISPR/Cas9 to determine whether this element is a critical driver of MYC. We isolated a clonal population of cells that contained a deletion of a single TCF binding element (TBE) within the MYC 3′ WRE. This deletion reduced TCF/β-catenin binding to this regulatory element and decreased MYC expression. Using RNA-Seq analysis, we found altered expression of genes that regulate metabolic processes, many of which are known MYC target genes. We found that 3′ WRE-Mut cells displayed a reduced proliferative capacity, diminished clonogenic growth, and a decreased potential to form tumors in vivo. These findings indicate that the MYC 3′ WRE is a critical driver of oncogenic MYC expression and suggest that this element may serve as a therapeutic target for CRC.
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Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Res 2014; 42:10856-68. [PMID: 25122745 PMCID: PMC4176344 DOI: 10.1093/nar/gku708] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have created six-finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB domain (SKD) that interacts with a complex containing repressive histone methyltransferases. ChIP-seq analysis of the effector-free ATFs in MCF7 breast cancer cells identified thousands of binding sites, mostly in promoter regions; the addition of an SKD domain increased the number of binding sites ∼5-fold, with a majority of the new sites located outside of promoters. De novo motif analyses suggest that the lack of binding specificity is due to subsets of the finger domains being used for genomic interactions. Although the ATFs display widespread binding, few genes showed expression differences; genes repressed by the ATF-SKD have stronger binding sites and are more enriched for a 12 nt motif. Interestingly, epigenetic analyses indicate that the transcriptional repression caused by the ATF-SKD is not due to changes in active histone modifications.
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Affiliation(s)
- Matthew R Grimmer
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA Integrated Genetics and Genomics, University of California-Davis, Davis, CA 95616, USA
| | - Sabine Stolzenburg
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia
| | - Pilar Blancafort
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Crawley, WA 6009, Australia Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Nedlands, WA 6008, Australia
| | - Peggy J Farnham
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
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