1
|
MiRNAs in Lung Cancer: Diagnostic, Prognostic, and Therapeutic Potential. Diagnostics (Basel) 2022; 12:diagnostics12071610. [PMID: 35885514 PMCID: PMC9322918 DOI: 10.3390/diagnostics12071610] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the dominant emerging factor in cancer-related mortality around the globe. Therapeutic interventions for lung cancer are not up to par, mainly due to reoccurrence/relapse, chemoresistance, and late diagnosis. People are currently interested in miRNAs, which are small double-stranded (20–24 ribonucleotides) structures that regulate molecular targets (tumor suppressors, oncogenes) involved in tumorigeneses such as cell proliferation, apoptosis, metastasis, and angiogenesis via post-transcriptional regulation of mRNA. Many studies suggest the emerging role of miRNAs in lung cancer diagnostics, prognostics, and therapeutics. Therefore, it is necessary to intensely explore the miRNOME expression of lung tumors and the development of anti-cancer strategies. The current review focuses on the therapeutic, diagnostic, and prognostic potential of numerous miRNAs in lung cancer.
Collapse
|
2
|
Ramarao-Milne P, Kondrashova O, Barry S, Hooper JD, Lee JS, Waddell N. Histone Modifying Enzymes in Gynaecological Cancers. Cancers (Basel) 2021; 13:cancers13040816. [PMID: 33669182 PMCID: PMC7919659 DOI: 10.3390/cancers13040816] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Epigenetics is a process that allows genetic control, without the involvement of sequence changes to DNA or genes. In cancer, epigenetics is a key event in tumour development that can alter the expression of cancer driver genes and result in genomic instability. Due to the critical role of epigenetics in malignant transformation, therapies that target these processes have been developed to treat cancer. Here, we provide a summary of the epigenetic changes that have been described in a variety of gynaecological cancers. We then highlight how these changes are being targeted in preclinical models and clinical trials for gynaecological cancers. Abstract Genetic and epigenetic factors contribute to the development of cancer. Epigenetic dysregulation is common in gynaecological cancers and includes altered methylation at CpG islands in gene promoter regions, global demethylation that leads to genome instability and histone modifications. Histones are a major determinant of chromosomal conformation and stability, and unlike DNA methylation, which is generally associated with gene silencing, are amenable to post-translational modifications that induce facultative chromatin regions, or condensed transcriptionally silent regions that decondense resulting in global alteration of gene expression. In comparison, other components, crucial to the manipulation of chromatin dynamics, such as histone modifying enzymes, are not as well-studied. Inhibitors targeting DNA modifying enzymes, particularly histone modifying enzymes represent a potential cancer treatment. Due to the ability of epigenetic therapies to target multiple pathways simultaneously, tumours with complex mutational landscapes affected by multiple driver mutations may be most amenable to this type of inhibitor. Interrogation of the actionable landscape of different gynaecological cancer types has revealed that some patients have biomarkers which indicate potential sensitivity to epigenetic inhibitors. In this review we describe the role of epigenetics in gynaecological cancers and highlight how it may exploited for treatment.
Collapse
Affiliation(s)
- Priya Ramarao-Milne
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (P.R.-M.); (O.K.); (N.W.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Olga Kondrashova
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (P.R.-M.); (O.K.); (N.W.)
| | - Sinead Barry
- Department of Gynaecological Oncology, Mater Hospital Brisbane, Brisbane, QLD 4101, Australia;
- Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia;
| | - John D. Hooper
- Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia;
| | - Jason S. Lee
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
- Epigenetics and Disease Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Correspondence: ; Tel.: +61-7-38453951
| | - Nicola Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (P.R.-M.); (O.K.); (N.W.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| |
Collapse
|
3
|
Liu P, Tian W. Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis. PeerJ 2020; 8:e9654. [PMID: 32832275 PMCID: PMC7409785 DOI: 10.7717/peerj.9654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 12/30/2022] Open
Abstract
Background Tumorigenesis is highly heterogeneous, and using clinicopathological signatures only is not enough to effectively distinguish clear cell renal cell carcinoma (ccRCC) and improve risk stratification of patients. DNA methylation (DNAm) with the stability and reversibility often occurs in the early stage of tumorigenesis. Disorders of transcription and metabolism are also an important molecular mechanisms of tumorigenesis. Therefore, it is necessary to identify effective biomarkers involved in tumorigenesis through multi-omics analysis, and these biomarkers also provide new potential therapeutic targets. Method The discovery stage involved 160 pairs of ccRCC and matched normal tissues for investigation of DNAm and biomarkers as well as 318 cases of ccRCC including clinical signatures. Correlation analysis of epigenetic, transcriptomic and metabolomic data revealed the connection and discordance among multi-omics and the deregulated functional modules. Diagnostic or prognostic biomarkers were obtained by the correlation analysis, the Least Absolute Shrinkage and Selection Operator (LASSO) and the LASSO-Cox methods. Two classifiers were established based on random forest (RF) and LASSO-Cox algorithms in training datasets. Seven independent datasets were used to evaluate robustness and universality. The molecular biological function of biomarkers were investigated using DAVID and GeneMANIA. Results Based on multi-omics analysis, the epigenetic measurements uniquely identified DNAm dysregulation of cellular mechanisms resulting in transcriptomic alterations, including cell proliferation, immune response and inflammation. Combination of the gene co-expression network and metabolic network identified 134 CpG sites (CpGs) as potential biomarkers. Based on the LASSO and RF algorithms, five CpGs were obtained to build a diagnostic classifierwith better classification performance (AUC > 99%). A eight-CpG-based prognostic classifier was obtained to improve risk stratification (hazard ratio (HR) > 4; log-rank test, p-value < 0.01). Based on independent datasets and seven additional cancers, the diagnostic and prognostic classifiers also had better robustness and stability. The molecular biological function of genes with abnormal methylation were significantly associated with glycolysis/gluconeogenesis and signal transduction. Conclusion The present study provides a comprehensive analysis of ccRCC using multi-omics data. These findings indicated that multi-omics analysis could identify some novel epigenetic factors, which were the most important causes of advanced cancer and poor clinical prognosis. Diagnostic and prognostic biomarkers were identified, which provided a promising avenue to develop effective therapies for ccRCC.
Collapse
Affiliation(s)
- Pengfei Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China.,Children's Hospital of Fudan University, Shanghai, China
| |
Collapse
|
4
|
Kong R, Sun G, Li X, Wu L, Li L, Li Y, Wang F, Xuan P, Yang S, Sun B, Hu J. Small Molecule Inhibitor C188-9 Synergistically Enhances the Demethylated Activity of Low-Dose 5-Aza-2'-Deoxycytidine Against Pancreatic Cancer. Front Oncol 2020; 10:612. [PMID: 32457835 PMCID: PMC7225308 DOI: 10.3389/fonc.2020.00612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/03/2020] [Indexed: 01/26/2023] Open
Abstract
Aberrant DNA methylation, especially hypermethylation of tumor suppressor genes, has been associated with many cancers' progression. 5-Aza-2′-deoxycytidine (DAC) can reverse hypermethylation-induced gene silencing via regulating DNA methyltransferases (DNMTs) activity, In addition, low-dose of DAC was proved to exert durable antitumor effects against solid tumor cells. Nevertheless, no clinical effect of DAC has been made when fighting against pancreatic cancer. Hence, it is necessary to raise a novel therapeutic strategy that further enhance the efficacy of DAC but not increase side effect, which impede the utilization of DAC. In the present study, we have discovered that C188-9, a novel signal transduction activator of transcription (STAT) inhibitor, could improve the antitumor effects of low-dose DAC in vivo and in vitro. Further study demonstrated that such improvement was attributed to re-expression of Ras association domain family member 1A (RASSF1A), a well-known tumor suppressor gene. Bisulfite sequencing PCR (BSP) assay showed that C188-9 combined with DAC treatment could significantly reverse the hypermethylation status of RASSF1A promoter, which indicated that C188-9 could enhance the demethylation efficacy of DAC. Our data demonstrated that DNA methyltransferase 1 (DNMT1) was the underlying mechanism that C188-9 regulates the demethylation efficacy of DAC. Overall, these findings provide a novel therapeutic strategy combining low-dose DAC and C188-9 to improve therapeutic efficacy by inhibiting DNMT1-inducing promoter methylation.
Collapse
Affiliation(s)
- Rui Kong
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Guangming Sun
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Xina Li
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Linfeng Wu
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Le Li
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Yilong Li
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Fei Wang
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Ping Xuan
- School of Computer Science and Technology, Heilongjiang University, Harbin, China
| | - Shifeng Yang
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Bei Sun
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| | - Jisheng Hu
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, China
| |
Collapse
|
5
|
Myasoedova VA, Sukhorukov V, Grechko AV, Zhang D, Romanenko E, Orekhov V, Orekhov AN. Inhibitors of DNA Methylation and Histone Deacetylation as Epigenetically Active Drugs for Anticancer Therapy. Curr Pharm Des 2020; 25:635-641. [PMID: 30950345 DOI: 10.2174/1381612825666190405144026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/29/2019] [Indexed: 12/12/2022]
Abstract
Gene expression is regulated and tightly controlled by epigenetic mechanisms. Alterations of these mechanisms are frequently observed in various diseases, particularly, in various types of cancer. Malignant transformation is caused by the impairment of the mechanisms of cell differentiation and cell cycle control associated with epigenetic changes. Altered patterns of epigenetic modification associated with malignancies can potentially be reversed by some agents that act on the key proteins responsible for DNA/histone modification and chromatin remodelling. Examples of such substances include the inhibitors of DNA methyltransferases or histone deacetylase. During the recent years, a number of such substances have been evaluated as potential therapeutic agents against certain types of cancer in preclinical and clinical studies, and some of them have been approved for treatment of hematological cancers. Application of epidrugs for therapy of solid tumors remains, however, more challenging. In this review, we summarize the current knowledge on the most studied mechanisms of epigenetic modification and the available epigenetically active drugs.
Collapse
Affiliation(s)
- Veronika A Myasoedova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Moscow 125315, Russian Federation
| | - Vasily Sukhorukov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Moscow 125315, Russian Federation.,Research Institute of Human Morphology, Moscow 117418, Russian Federation
| | - Andrey V Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow 109240, Russian Federation
| | - Dongwei Zhang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Elena Romanenko
- Belozersky Institute of Physical and Clinical Biology, Moscow, Russian Federation
| | - Vawain Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Moscow 125315, Russian Federation
| | - Alexander N Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Moscow 125315, Russian Federation.,Institute for Atherosclerosis Research, Skolkovo Innovative Center, Moscow 121609, Russian Federation
| |
Collapse
|
6
|
Singh S, Maurya PK. Nanomaterials-Based siRNA Delivery: Routes of Administration, Hurdles and Role of Nanocarriers. NANOTECHNOLOGY IN MODERN ANIMAL BIOTECHNOLOGY 2019. [PMCID: PMC7121101 DOI: 10.1007/978-981-13-6004-6_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Ribonucleic acid interference (RNAi) is a potential alternative therapeutic approach to knock down the overexpression of genes in several disorders especially cancers with underlying genetic dysfunctions. For silencing of specific genes involved in cell cycle, small/short interfering ribonucleic acids (siRNAs) are being used clinically. The siRNA-based RNAi is more efficient, specific and safe antisense technology than other RNAi approaches. The route of siRNA administration for siRNA therapy depends on the targeted site. However, certain hurdles like poor stability of siRNA, saturation, off-target effect, immunogenicity, anatomical barriers and non-targeted delivery restrict the successful siRNA therapy. Thus, advancement of an effective, secure, and long-term delivery system is prerequisite to the medical utilization of siRNA. Polycationic nanocarriers mediated targeted delivery system is an ideal system to remove these hurdles and to increase the blood retention time and rate of intracellular permeability. In this chapter, we will mainly discuss the different biocompatible, biodegradable, non-toxic (organic, inorganic and hybrid) nanocarriers that encapsulate and shield the siRNA from the different harsh environment and provides the increased systemic siRNA delivery.
Collapse
Affiliation(s)
- Sanjay Singh
- Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, Gujarat India
| | | |
Collapse
|
7
|
Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
Collapse
Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
| |
Collapse
|
8
|
Yuan Z, Sánchez Claros C, Suzuki M, Maggi EC, Kaner JD, Kinstlinger N, Gorecka J, Quinn TJ, Geha R, Corn A, Pastoriza J, Jing Q, Adem A, Wu H, Alemu G, Du YC, Zheng D, Greally JM, Libutti SK. Loss of MEN1 activates DNMT1 implicating DNA hypermethylation as a driver of MEN1 tumorigenesis. Oncotarget 2017; 7:12633-50. [PMID: 26871472 PMCID: PMC4914310 DOI: 10.18632/oncotarget.7279] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/24/2016] [Indexed: 12/12/2022] Open
Abstract
Multiple endocrine neoplasia type 1 (MEN1) syndrome results from mutations in the MEN1 gene and causes tumor formation via largely unknown mechanisms. Using a novel genome-wide methylation analysis, we studied tissues from MEN1-parathyroid tumors, Men1 knockout (KO) mice, and Men1 null mouse embryonic fibroblast (MEF) cell lines. We demonstrated that inactivation of menin (the protein product of MEN1) increases activity of DNA (cytosine-5)-methyltransferase 1 (DNMT1) by activating retinoblastoma-binding protein 5 (Rbbp5). The increased activity of DNMT1 mediates global DNA hypermethylation, which results in aberrant activation of the Wnt/β-catenin signaling pathway through inactivation of Sox regulatory genes. Our study provides important insights into the role of menin in DNA methylation and its impact on the pathogenesis of MEN1 tumor development.
Collapse
Affiliation(s)
- Ziqiang Yuan
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Elaine C Maggi
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Justin D Kaner
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Noah Kinstlinger
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jolanta Gorecka
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Thomas J Quinn
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Rula Geha
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Amanda Corn
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jessica Pastoriza
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Qiang Jing
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Asha Adem
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Hao Wu
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Girum Alemu
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yi-Chieh Du
- Department of Pathology and Lab Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Steven K Libutti
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| |
Collapse
|
9
|
Sharma D, Koshy G, Gupta S, Sharma B, Grover S. Deciphering the Role of the Barr Body in Malignancy: An insight into head and neck cancer. Sultan Qaboos Univ Med J 2017; 17:e389-e397. [PMID: 29372079 PMCID: PMC5766293 DOI: 10.18295/squmj.2017.17.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 08/03/2017] [Accepted: 08/24/2017] [Indexed: 01/20/2023] Open
Abstract
X chromosome inactivation is the epitome of epigenetic regulation and long non-coding ribonucleic acid function. The differentiation status of cells has been ascribed to X chromosome activity, with two active X chromosomes generally only observed in undifferentiated or poorly differentiated cells. Recently, several studies have indicated that the reactivation of an inactive X chromosome or X chromosome multiplication correlates with the development of malignancy; however, this concept is still controversial. This review sought to shed light on the role of the X chromosome in cancer development. In particular, there is a need for further exploration of the expression patterns of X-linked genes in cancer cells, especially those in head and neck squamous cell carcinoma (HNSCC), in order to identify different prognostic subpopulations with distinct clinical implications. This article proposes a functional relationship between the loss of the Barr body and the disproportional expression of X-linked genes in HNSCC development.
Collapse
Affiliation(s)
- Deepti Sharma
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - George Koshy
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - Shruti Gupta
- Department of Oral Anatomy, Postgraduate Institute of Dental Sciences, Rohtak, Haryana, India
| | - Bhushan Sharma
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - Sonal Grover
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| |
Collapse
|
10
|
Reprimo, a Potential p53-Dependent Tumor Suppressor Gene, Is Frequently Hypermethylated in Estrogen Receptor α-Positive Breast Cancer. Int J Mol Sci 2017; 18:ijms18081525. [PMID: 28809778 PMCID: PMC5577992 DOI: 10.3390/ijms18081525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/01/2017] [Accepted: 07/05/2017] [Indexed: 01/31/2023] Open
Abstract
Aberrant DNA methylation is a hallmark of many cancers. Currently, there are four intrinsic molecular subtypes in breast cancer (BC): Luminal A, B, Her2-positive, and triple negative (TNBC). Recently, The Cancer Genome Atlas (TCGA) project has revealed that Luminal subtypes have higher levels of genome-wide methylation that may be a result of Estrogen/Estrogen receptor α (E2/ERα) signaling pathway activation. In this study, we analyze promoter CpG-island (CGIs) of the Reprimo (RPRM) gene in breast cancers (n = 77), cell lines (n = 38), and normal breast tissue (n = 10) using a MBDCap-seq database. Then, a validation cohort (n = 26) was used to confirm the results found in the MBDCap-seq platform. A differential methylation pattern was found between BC and cell lines compared to normal breast tissue. In BC, a higher DNA methylation was observed in tissues that were ERα-positive than in ERα-negative ones; more precisely, subtypes Luminal A compared to TNBC. Also, significant reverse correlation was observed between DNA methylation and RPRM mRNA expression in BC. Our data suggest that ERα expression in BC may affect the DNA methylation of CGIs in the RPRM gene. This approach suggests that DNA methylation status in CGIs of some tumor suppressor genes could be driven by E2 availability, subsequently inducing the activation of the ERα pathway.
Collapse
|
11
|
Delatola EI, Lebarbier E, Mary-Huard T, Radvanyi F, Robin S, Wong J. SegCorr a statistical procedure for the detection of genomic regions of correlated expression. BMC Bioinformatics 2017; 18:333. [PMID: 28697800 PMCID: PMC5504623 DOI: 10.1186/s12859-017-1742-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/26/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigenetic alterations as factors that may significantly alter expression in large chromosomal regions (gene silencing or gene activation). RESULTS The identification of correlated regions requires segmenting the gene expression correlation matrix into regions of homogeneously correlated genes and assessing whether the observed local correlation is significantly higher than the background chromosomal correlation. A unified statistical framework is proposed to achieve these two tasks, where optimal segmentation is efficiently performed using dynamic programming algorithm, and detection of highly correlated regions is then achieved using an exact test procedure. We also propose a simple and efficient procedure to correct the expression signal for mechanisms already known to impact expression correlation. The performance and robustness of the proposed procedure, called SegCorr, are evaluated on simulated data. The procedure is illustrated on cancer data, where the signal is corrected for correlations caused by copy number variation. It permitted the detection of regions with high correlations linked to epigenetic marks like DNA methylation. CONCLUSIONS SegCorr is a novel method that performs correlation matrix segmentation and applies a test procedure in order to detect highly correlated regions in gene expression.
Collapse
Affiliation(s)
- Eleni Ioanna Delatola
- AgroParisTech UMR518, Paris, 75005, France.
- INRA UMR518, Paris, 75005, France.
- Institut Curie, PSL Research University, Cedex 05, Paris, 75248, France.
- CNRS UMR144, Equipe Labellisee par La Ligue Nationale contre le Cancer, Cedex 05, Paris, 75248, France.
| | - Emilie Lebarbier
- AgroParisTech UMR518, Paris, 75005, France
- INRA UMR518, Paris, 75005, France
| | - Tristan Mary-Huard
- AgroParisTech UMR518, Paris, 75005, France
- INRA UMR518, Paris, 75005, France
- INRA, UMR 0320 - UMR 8120 Genetique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, F-91190, France
| | - François Radvanyi
- Institut Curie, PSL Research University, Cedex 05, Paris, 75248, France
- CNRS UMR144, Equipe Labellisee par La Ligue Nationale contre le Cancer, Cedex 05, Paris, 75248, France
| | - Stéphane Robin
- AgroParisTech UMR518, Paris, 75005, France
- INRA UMR518, Paris, 75005, France
| | - Jennifer Wong
- Institut Curie, PSL Research University, Cedex 05, Paris, 75248, France
- CNRS UMR144, Equipe Labellisee par La Ligue Nationale contre le Cancer, Cedex 05, Paris, 75248, France
- Molecular Oncology Unit, Department of Biochemistry, Hospital Saint Louis, AP-HP, Cedex 10, Paris, 75475, France
- Université Paris Diderot, Sorbonne Paris Cité, CNRS UMR7212/INSERM U944, Cedex 10, Paris, 75475, France
| |
Collapse
|
12
|
Babu D, Fullwood MJ. 3D genome organization in health and disease: emerging opportunities in cancer translational medicine. Nucleus 2016; 6:382-93. [PMID: 26553406 PMCID: PMC4915485 DOI: 10.1080/19491034.2015.1106676] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Organizing the DNA to fit inside a spatially constrained nucleus is a challenging problem that has attracted the attention of scientists across all disciplines of science. Increasing evidence has demonstrated the importance of genome geometry in several cellular contexts that affect human health. Among several approaches, the application of sequencing technologies has substantially increased our understanding of this intricate organization, also known as chromatin interactions. These structures are involved in transcriptional control of gene expression by connecting distal regulatory elements with their target genes and regulating co-transcriptional splicing. In addition, chromatin interactions play pivotal roles in the organization of the genome, the formation of structural variants, recombination, DNA replication and cell division. Mutations in factors that regulate chromatin interactions lead to the development of pathological conditions, for example, cancer. In this review, we discuss key findings that have shed light on the importance of these structures in the context of cancers, and highlight the applicability of chromatin interactions as potential biomarkers in molecular medicine as well as therapeutic implications of chromatin interactions.
Collapse
Affiliation(s)
- Deepak Babu
- a Cancer Science Institute of Singapore: Singapore; National University of Singapore ; Singapore
| | - Melissa J Fullwood
- a Cancer Science Institute of Singapore: Singapore; National University of Singapore ; Singapore.,b School of Biological Sciences; Nanyang Technological University ; Singapore.,c Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR) ; Singapore.,d Yale-NUS Liberal Arts College ; Singapore
| |
Collapse
|
13
|
Verma M. Genome-wide association studies and epigenome-wide association studies go together in cancer control. Future Oncol 2016; 12:1645-64. [PMID: 27079684 PMCID: PMC5551540 DOI: 10.2217/fon-2015-0035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023] Open
Abstract
Completion of the human genome a decade ago laid the foundation for: using genetic information in assessing risk to identify individuals and populations that are likely to develop cancer, and designing treatments based on a person's genetic profiling (precision medicine). Genome-wide association studies (GWAS) completed during the past few years have identified risk-associated single nucleotide polymorphisms that can be used as screening tools in epidemiologic studies of a variety of tumor types. This led to the conduct of epigenome-wide association studies (EWAS). This article discusses the current status, challenges and research opportunities in GWAS and EWAS. Information gained from GWAS and EWAS has potential applications in cancer control and treatment.
Collapse
Affiliation(s)
- Mukesh Verma
- Methods & Technologies Branch, Epidemiology & Genomics Research Program, Division of Cancer Control & Population Sciences, National Cancer Institute (NCI), NIH, 9609 Medical Center Drive, Suite 4E102, Rockville, MD 20850, USA
| |
Collapse
|
14
|
Kirschner SA, Hunewald O, Mériaux SB, Brunnhoefer R, Muller CP, Turner JD. Focussing reduced representation CpG sequencing through judicious restriction enzyme choice. Genomics 2016; 107:109-19. [PMID: 26945642 DOI: 10.1016/j.ygeno.2016.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 01/01/2023]
Abstract
Current restriction enzyme based reduced representation methylation analyses aim for limited, but unbiased, methylome coverage. As the current best estimate suggests that only ~20% of CpGs are dynamically regulated, we characterised the CpG and genomic context surrounding all suitable restriction enzyme sites to identify those that were located in regions rich in dynamically methylated CpGs. The restriction-site distributions for MspI, BstUI, and HhaI were non-random. CpGs in CGI and shelf+shore could be enriched, particularly in gene bodies for all genomic regions, promoters (TSS1500, TSS200), intra- (1st exon, gene body, 3'UTR, 5'UTR) and inter-genic regions. HpyCH4IV enriched CpG elements in the open sea for all genomic elements. Judicious restriction enzyme choice improves the focus of reduced representation approaches by avoiding the monopolization of read coverage by genomic regions that are irrelevant, unwanted or difficult to map, and only sequencing the most informative fraction of CpGs.
Collapse
Affiliation(s)
- Sophie A Kirschner
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg; Department of Immunology, Research Institute of Psychobiology, University of Trier, D-54290, Germany
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Sophie B Mériaux
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Regina Brunnhoefer
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg; Department of Immunology, Research Institute of Psychobiology, University of Trier, D-54290, Germany
| | - Jonathan D Turner
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg.
| |
Collapse
|
15
|
Nervi C, De Marinis E, Codacci-Pisanelli G. Epigenetic treatment of solid tumours: a review of clinical trials. Clin Epigenetics 2015; 7:127. [PMID: 26692909 PMCID: PMC4676165 DOI: 10.1186/s13148-015-0157-2] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 11/10/2015] [Indexed: 12/12/2022] Open
Abstract
Epigenetic treatment has been approved by regulatory agencies for haematological malignancies. The success observed in cutaneous lymphomas represents a proof of principle that similar results may be obtained in solid tumours. Several agents that interfere with DNA methylation-demethylation and histones acetylation/deacetylation have been studied, and some (such as azacytidine, decitabine, valproic acid and vorinostat) are already in clinical use. The aim of this review is to provide a brief overview of the molecular events underlying the antitumour effects of epigenetic treatments and to summarise data available on clinical trials that tested the use of epigenetic agents against solid tumours. We not only list results but also try to indicate how the proper evaluation of this treatment might result in a better selection of effective agents and in a more rapid development. We divided compounds in demethylating agents and HDAC inhibitors. For each class, we report the antitumour activity and the toxic side effects. When available, we describe plasma pharmacokinetics and pharmacodynamic evaluation in tumours and in surrogate tissues (generally white blood cells). Epigenetic treatment is a reality in haematological malignancies and deserves adequate attention in solid tumours. A careful consideration of available clinical data however is required for faster drug development and possibly to re-evaluate some molecules that were perhaps discarded too early.
Collapse
Affiliation(s)
- Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnology, University of Rome "la Sapienza", Corso della Repubblica, 97, 04100 Latina, Italy
| | - Elisabetta De Marinis
- Department of Medical and Surgical Sciences and Biotechnology, University of Rome "la Sapienza", Corso della Repubblica, 97, 04100 Latina, Italy
| | - Giovanni Codacci-Pisanelli
- Department of Medical and Surgical Sciences and Biotechnology, University of Rome "la Sapienza", Corso della Repubblica, 97, 04100 Latina, Italy
| |
Collapse
|
16
|
Marks H, Kerstens HHD, Barakat TS, Splinter E, Dirks RAM, van Mierlo G, Joshi O, Wang SY, Babak T, Albers CA, Kalkan T, Smith A, Jouneau A, de Laat W, Gribnau J, Stunnenberg HG. Dynamics of gene silencing during X inactivation using allele-specific RNA-seq. Genome Biol 2015; 16:149. [PMID: 26235224 PMCID: PMC4546214 DOI: 10.1186/s13059-015-0698-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/18/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells, which contain a single X chromosome. Here, we use mouse female embryonic stem cells (ESCs) with non-random X chromosome inactivation (XCI) and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome by high-resolution allele-specific RNA-seq. RESULTS Induction of XCI by differentiation of female ESCs shows that genes proximal to the X-inactivation center are silenced earlier than distal genes, while lowly expressed genes show faster XCI dynamics than highly expressed genes. The active X chromosome shows a minor but significant increase in gene activity during differentiation, resulting in complete dosage compensation in differentiated cell types. Genes escaping XCI show little or no silencing during early propagation of XCI. Allele-specific RNA-seq of neural progenitor cells generated from the female ESCs identifies three regions distal to the X-inactivation center that escape XCI. These regions, which stably escape during propagation and maintenance of XCI, coincide with topologically associating domains (TADs) as present in the female ESCs. Also, the previously characterized gene clusters escaping XCI in human fibroblasts correlate with TADs. CONCLUSIONS The gene silencing observed during XCI provides further insight in the establishment of the repressive complex formed by the inactive X chromosome. The association of escape regions with TADs, in mouse and human, suggests that TADs are the primary targets during propagation of XCI over the X chromosome.
Collapse
Affiliation(s)
- Hendrik Marks
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Hindrik H D Kerstens
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tahsin Stefan Barakat
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Erik Splinter
- Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
| | - René A M Dirks
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Guido van Mierlo
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Onkar Joshi
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Shuang-Yin Wang
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tomas Babak
- Biology Department, Queen's University, Kingston, ON, Canada.
| | - Cornelis A Albers
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| | - Tüzer Kalkan
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Alice Jouneau
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Wouter de Laat
- Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Hendrik G Stunnenberg
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.
| |
Collapse
|
17
|
Rafique S, Thomas JS, Sproul D, Bickmore WA. Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer. Genome Biol 2015; 16:145. [PMID: 26235388 PMCID: PMC4536608 DOI: 10.1186/s13059-015-0719-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/06/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers. RESULTS We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen. CONCLUSIONS Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells.
Collapse
Affiliation(s)
- Sehrish Rafique
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. .,Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Jeremy S Thomas
- Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. .,Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
| |
Collapse
|
18
|
Forn M, Díez-Villanueva A, Merlos-Suárez A, Muñoz M, Lois S, Carriò E, Jordà M, Bigas A, Batlle E, Peinado MA. Overlapping DNA methylation dynamics in mouse intestinal cell differentiation and early stages of malignant progression. PLoS One 2015; 10:e0123263. [PMID: 25933092 PMCID: PMC4416816 DOI: 10.1371/journal.pone.0123263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
Mouse models of intestinal crypt cell differentiation and tumorigenesis have been used to characterize the molecular mechanisms underlying both processes. DNA methylation is a key epigenetic mark and plays an important role in cell identity and differentiation programs and cancer. To get insights into the dynamics of cell differentiation and malignant transformation we have compared the DNA methylation profiles along the mouse small intestine crypt and early stages of tumorigenesis. Genome-scale analysis of DNA methylation together with microarray gene expression have been applied to compare intestinal crypt stem cells (EphB2high), differentiated cells (EphB2negative), ApcMin/+ adenomas and the corresponding non-tumor adjacent tissue, together with small and large intestine samples and the colon cancer cell line CT26. Compared with late stages, small intestine crypt differentiation and early stages of tumorigenesis display few and relatively small changes in DNA methylation. Hypermethylated loci are largely shared by the two processes and affect the proximities of promoter and enhancer regions, with enrichment in genes associated with the intestinal stem cell signature and the PRC2 complex. The hypermethylation is progressive, with minute levels in differentiated cells, as compared with intestinal stem cells, and reaching full methylation in advanced stages. Hypomethylation shows different signatures in differentiation and cancer and is already present in the non-tumor tissue adjacent to the adenomas in ApcMin/+ mice, but at lower levels than advanced cancers. This study provides a reference framework to decipher the mechanisms driving mouse intestinal tumorigenesis and also the human counterpart.
Collapse
Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Díez-Villanueva
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Merlos-Suárez
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
| | - Mar Muñoz
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Sergi Lois
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Elvira Carriò
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Mireia Jordà
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Bigas
- Institut Hospital del Mar d’Investigació Mèdica (IMIM) 08003 Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miguel A. Peinado
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
- * E-mail:
| |
Collapse
|
19
|
Jadhav RR, Ye Z, Huang RL, Liu J, Hsu PY, Huang YW, Rangel LB, Lai HC, Roa JC, Kirma NB, Huang THM, Jin VX. Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer. Clin Epigenetics 2015; 7:13. [PMID: 25763113 PMCID: PMC4355986 DOI: 10.1186/s13148-015-0045-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022] Open
Abstract
Background Recent genome-wide analysis has shown that DNA methylation spans long stretches of chromosome regions consisting of clusters of contiguous CpG islands or gene families. Hypermethylation of various gene clusters has been reported in many types of cancer. In this study, we conducted methyl-binding domain capture (MBDCap) sequencing (MBD-seq) analysis on a breast cancer cohort consisting of 77 patients and 10 normal controls, as well as a panel of 38 breast cancer cell lines. Results Bioinformatics analysis determined seven gene clusters with a significant difference in overall survival (OS) and further revealed a distinct feature that the conservation of a large gene cluster (approximately 70 kb) metallothionein-1 (MT1) among 45 species is much lower than the average of all RefSeq genes. Furthermore, we found that DNA methylation is an important epigenetic regulator contributing to gene repression of MT1 gene cluster in both ERα positive (ERα+) and ERα negative (ERα−) breast tumors. In silico analysis revealed much lower gene expression of this cluster in The Cancer Genome Atlas (TCGA) cohort for ERα + tumors. To further investigate the role of estrogen, we conducted 17β-estradiol (E2) and demethylating agent 5-aza-2′-deoxycytidine (DAC) treatment in various breast cancer cell types. Cell proliferation and invasion assays suggested MT1F and MT1M may play an anti-oncogenic role in breast cancer. Conclusions Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer. Further investigation of these clusters revealed that estrogen mediates epigenetic repression of MT1 cluster in ERα + breast cancer cell lines. In all, our studies identify thousands of breast tumor hypermethylated regions for the first time, in particular, discovering seven large contiguous hypermethylated gene clusters. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0045-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rohit R Jadhav
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Zhenqing Ye
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, Taipei Medical University Shuang Ho Hospital, New Taipei City, 23561 Taiwan
| | - Joseph Liu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Pei-Yin Hsu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 9200 West Wisconsin Avenue, Froedtert Medical College Lab Building (FMCLB) 258, Milwaukee, 53226 WI USA
| | - Leticia B Rangel
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Pharmaceutical Sciences, Biotechnology Program/RENORBIO, Health Sciences Center, Universidade Federal do Espirito Santo, Av. Marechal Campos, 1468, Maruipe, 29040-090 Vitoria ES Brazil ; Programa Ciencias Sem Fronteiras, CNPq, Brasilia, Brazil
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Taipei Medical University Shuang Ho Hospital, New Taipei City, 23561 Taiwan ; School of Medicine, Taipei Medical University, No. 250, Wu-Hsing Street, Taipei, 110 Taiwan ; Graduate Institute of Life Sciences, Department and Graduate Institute of Biochemistry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Juan Carlos Roa
- Departamento de Pathologı'a, Universidad de la Frontera, Claro Solar 115, Temuco, Chile
| | - Nameer B Kirma
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Victor X Jin
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| |
Collapse
|
20
|
Identification of long-range epigenetic silencing on chromosome 15q25 and its clinical implication in gastric cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:666-78. [PMID: 25576785 DOI: 10.1016/j.ajpath.2014.11.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/19/2014] [Accepted: 11/04/2014] [Indexed: 12/12/2022]
Abstract
Recent genome-wide epigenomic and transcription profiling studies have demonstrated that epigenetic silencing can encompass multiple neighboring genes, termed as long-range epigenetic silencing (LRES). Herein, we identified a novel LRES region by comparing gene expression of human colon cancer HCT116 cells with their DNA methyltransferase 1 and DNA methyltransferase 3B double-knockout derivative double-knockout cells. Ten consecutive genes spanning 3 Mb of chromosome 15q25 were coordinately silenced, with eight genes showing promoter CpG island hypermethylation and enrichment of repressive histone marks, which were evaluated by bisulfite sequencing analysis and chromatin immunoprecipitation assay. Comparison of primary gastric tumor specimens with normal tissue confirmed that the long-range silencing of this region was tumor specific. Methylation of genes within the LRES region was evaluated in 190 gastric tumor tissues using the MethyLight assay, and their association with clinicopathological features, such as older age, high-grade differentiation, and diffuse or mixed-type histology, was determined. LRES-positive gastric cancer patients (six or more methylated genes) showed lower recurrence and better survival. Our findings emphasize the differential dynamics of DNA methylation and histone modification, indicating the importance of studying the relationship of each epigenetic modification in the context of chromatin domains. Patients with LRES showed lower recurrence and better prognosis, indicating that stratifying patients according to underlying molecular features, such as LRES regions, may better predict recurrence and survival.
Collapse
|
21
|
Abstract
Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Research has shown that epigenetic mechanisms provide an "extra" layer of transcriptional control that regulates how genes are expressed. These mechanisms are critical components in the normal development and growth of cells. Epigenetic abnormalities have been found to be causative factors in cancer, genetic disorders, and pediatric syndromes. Head and neck cancers are a group of malignancies with diverse biological behaviors and a strong, well-established association with environmental effects. Although the hunt for genetic alterations in head and neck cancer has continued in the past two decades, with unequivocal proof of a genetic role in multistage head and neck carcinogenesis, epigenetic alteration in association with promoter CpG islands hypermethylation has emerged in the past few years as one of the most active areas of cancer research. Silencing of the genes by hypermethylation or induction of oncogenes by promoter hypomethylation is a frequent mechanism in head and neck cancer and achieves increasing diagnostic and therapeutic importance. In this context it is important for clinicians to understand the principles of epigenetic mechanisms and how these principles relate to human health and disease. It is important to address the use of epigenetic pathways in new approaches to molecular diagnosis and novel targeted treatments across the clinical spectrum.
Collapse
Affiliation(s)
- Syeda Marriam Bakhtiar
- Department of Bioinformatics, Faculty of Computing, Mohammad Ali Jinnah University, Islamabad, Pakistan
| | | | | |
Collapse
|
22
|
Draz MS, Fang BA, Zhang P, Hu Z, Gu S, Weng KC, Gray JW, Chen FF. Nanoparticle-mediated systemic delivery of siRNA for treatment of cancers and viral infections. Am J Cancer Res 2014; 4:872-92. [PMID: 25057313 PMCID: PMC4107289 DOI: 10.7150/thno.9404] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/27/2014] [Indexed: 12/17/2022] Open
Abstract
RNA interference (RNAi) is an endogenous post-transcriptional gene regulatory mechanism, where non-coding, double-stranded RNA molecules interfere with the expression of certain genes in order to silence it. Since its discovery, this phenomenon has evolved as powerful technology to diagnose and treat diseases at cellular and molecular levels. With a lot of attention, short interfering RNA (siRNA) therapeutics has brought a great hope for treatment of various undruggable diseases, including genetic diseases, cancer, and resistant viral infections. However, the challenge of their systemic delivery and on how they are integrated to exhibit the desired properties and functions remains a key bottleneck for realizing its full potential. Nanoparticles are currently well known to exhibit a number of unique properties that could be strategically tailored into new advanced siRNA delivery systems. This review summarizes the various nanoparticulate systems developed so far in the literature for systemic delivery of siRNA, which include silica and silicon-based nanoparticles, metal and metal oxides nanoparticles, carbon nanotubes, graphene, dendrimers, polymers, cyclodextrins, lipids, hydrogels, and semiconductor nanocrystals. Challenges and barriers to the delivery of siRNA and the role of different nanoparticles to surmount these challenges are also included in the review.
Collapse
|
23
|
Frydecka D, Karpiński P, Misiak B. Unravelling immune alterations in schizophrenia: can DNA methylation provide clues? Epigenomics 2014; 6:245-7. [DOI: 10.2217/epi.14.26] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Dorota Frydecka
- Department of Psychiatry, Wroclaw Medical University, 10 Pasteur Street, 50–367 Wroclaw, Poland
| | - Paweł Karpiński
- Department of Genetics, Wroclaw Medical University, 10 Pasteur Street, 50–367 Wroclaw, Poland
| | - Błażej Misiak
- Department of Psychiatry, Wroclaw Medical University, 10 Pasteur Street, 50–367 Wroclaw, Poland
- Department of Genetics, Wroclaw Medical University, 10 Pasteur Street, 50–367 Wroclaw, Poland
| |
Collapse
|
24
|
Precursor lesions for sporadic pancreatic cancer: PanIN, IPMN, and MCN. BIOMED RESEARCH INTERNATIONAL 2014; 2014:474905. [PMID: 24783207 PMCID: PMC3982269 DOI: 10.1155/2014/474905] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 02/08/2014] [Accepted: 02/10/2014] [Indexed: 12/20/2022]
Abstract
Pancreatic cancer is still a dismal disease. The high mortality rate is mainly caused by the lack of highly sensitive and specific diagnostic tools, and most of the patients are diagnosed in an advanced and incurable stage. Knowledge about precursor lesions for pancreatic cancer has grown significantly over the last decade, and nowadays we know that mainly three lesions (PanIN, and IPMN, MCN) are responsible for the development of pancreatic cancer. The early detection of these lesions is still challenging but provides the chance to cure patients before they might get an invasive pancreatic carcinoma. This paper focuses on PanIN, IPMN, and MCN lesions and reviews the current level of knowledge and clinical measures.
Collapse
|
25
|
Ilmjärv S, Hundahl CA, Reimets R, Niitsoo M, Kolde R, Vilo J, Vasar E, Luuk H. Estimating differential expression from multiple indicators. Nucleic Acids Res 2014; 42:e72. [PMID: 24586062 PMCID: PMC4005682 DOI: 10.1093/nar/gku158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Regardless of the advent of high-throughput sequencing, microarrays remain central in current biomedical research. Conventional microarray analysis pipelines apply data reduction before the estimation of differential expression, which is likely to render the estimates susceptible to noise from signal summarization and reduce statistical power. We present a probe-level framework, which capitalizes on the high number of concurrent measurements to provide more robust differential expression estimates. The framework naturally extends to various experimental designs and target categories (e.g. transcripts, genes, genomic regions) as well as small sample sizes. Benchmarking in relation to popular microarray and RNA-sequencing data-analysis pipelines indicated high and stable performance on the Microarray Quality Control dataset and in a cell-culture model of hypoxia. Experimental-data-exhibiting long-range epigenetic silencing of gene expression was used to demonstrate the efficacy of detecting differential expression of genomic regions, a level of analysis not embraced by conventional workflows. Finally, we designed and conducted an experiment to identify hypothermia-responsive genes in terms of monotonic time-response. As a novel insight, hypothermia-dependent up-regulation of multiple genes of two major antioxidant pathways was identified and verified by quantitative real-time PCR.
Collapse
Affiliation(s)
- Sten Ilmjärv
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia, Quretec Ltd, Tartu, Estonia, Centre for Excellence in Translational Medicine, University of Tartu, Tartu, Estonia, Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark and Department of Computer Science, University of Tartu, Tartu, Estonia
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Gloss B, Moran-Jones K, Lin V, Gonzalez M, Scurry J, Hacker NF, Sutherland RL, Clark SJ, Samimi G. ZNF300P1 encodes a lincRNA that regulates cell polarity and is epigenetically silenced in type II epithelial ovarian cancer. Mol Cancer 2014; 13:3. [PMID: 24393131 PMCID: PMC3895665 DOI: 10.1186/1476-4598-13-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 01/02/2014] [Indexed: 12/24/2022] Open
Abstract
Background We previously identified that the CpG island-associated promoter of the novel lincRNA ZNF300P1 (also known as LOC134466) is frequently hypermethylated and silenced in ovarian cancer tissues. However, the function of ZNF300P1 was unknown. In this report we demonstrate that ZNF300P1 is involved in the regulation of key cell cycle and cell motility networks in human ovarian surface epithelial cells, and may play a role in promoting metastasis in ovarian cancer cells. Methods We applied methylated DNA immunoprecipitation on whole genome promoter tiling arrays and Sequenom assays to examine methylation status of ZNF300P1 in multiple ovarian cancer cell lines, as well as in normal ovarian and ovarian tumor tissues. Transcript profiling was used to investigate the effects of ZNF300P1 suppression in ovarian cancer cells. We utilized siRNA knockdown in normal ovarian surface epithelial cells and performed cellular proliferation, migration and adhesion assays to validate and explore the profiling results. Results We demonstrate that ZNF300P1 is methylated in multiple ovarian cancer cell lines. Loss of ZNF300P1 results in decreased cell proliferation and colony formation. In addition, knockdown of the ZNF300P1 transcript results in aberrant and less persistent migration in wound healing assays due to a loss of cellular polarity. Using an ex vivo peritoneal adhesion assay, we also reveal a role for ZNF300P1 in the attachment of ovarian cancer cells to peritoneal membranes, indicating a potential function of ZNF300P1 expression in metastasis of ovarian cancer cells to sites within the peritoneal cavity. Conclusion Our findings further support ZNF300P1 as frequently methylated in ovarian cancer and reveal a novel function for ZNF300P1 lincRNA expression in regulating cell polarity, motility, and adhesion and loss of expression may contribute to the metastatic potential of ovarian cancer cells.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Goli Samimi
- Kinghorn Cancer Centre and Cancer Research Program, Garvan Institute of Medical Research, 370 Victoria Street, 2010, Darlinghurst, NSW, Australia.
| |
Collapse
|
27
|
Methylation profiling defines an extensive field defect in histologically normal prostate tissues associated with prostate cancer. Neoplasia 2013; 15:399-408. [PMID: 23555185 DOI: 10.1593/neo.13280] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/11/2013] [Accepted: 02/13/2013] [Indexed: 01/30/2023] Open
Abstract
Prostate cancer (PCa) is typically found as a multifocal disease suggesting the potential for molecular defects within the morphologically normal tissue. The frequency and spatial extent of DNA methylation changes encompassing a potential field defect are unknown. A comparison of non-tumor-associated (NTA) prostate to histologically indistinguishable tumor-associated (TA) prostate tissues detected a distinct profile of DNA methylation alterations (0.2%) using genome-wide DNA arrays based on the Encyclopedia of DNA Elements 18 sequence that tile both gene-rich and poor regions. Hypomethylation (87%) occurred more frequently than hypermethylation (13%). Several of the most significantly altered loci (CAV1, EVX1, MCF2L, and FGF1) were then used as probes to map the extent of these DNA methylation changes in normal tissues from prostates containing cancer. In TA tissues, the extent of methylation was similar both adjacent (2 mm) and at a distance (>1 cm) from tumor foci. These loci were also able to distinguish NTA from TA tissues in a validation set of patient samples. These mapping studies indicate that a spatially widespread epigenetic defect occurs in the peripheral prostate tissues of men who have PCa that may be useful in the detection of this disease.
Collapse
|
28
|
Forn M, Muñoz M, Tauriello DVF, Merlos-Suárez A, Rodilla V, Bigas A, Batlle E, Jordà M, Peinado MA. Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells. Mol Oncol 2013; 7:1129-41. [PMID: 24035705 DOI: 10.1016/j.molonc.2013.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 01/08/2023] Open
Abstract
DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and has been described in different human cancer types. However, it is unknown whether there is a coordinated regulation of the genes embedded in these regions in normal cells and in early stages of tumor progression. To better characterize the molecular events associated with the regulation and remodeling of these regions we analyzed two regions undergoing LRES in human colon cancer in the mouse model. We demonstrate that LRES also occurs in murine cancer in vivo and mimics the molecular features of the human phenomenon, namely, downregulation of gene expression, acquisition of inactive histone marks, and DNA hypermethylation of specific CpG islands. The genes embedded in these regions showed a dynamic and autonomous regulation during mouse intestinal cell differentiation, indicating that, in the framework considered here, the coordinated regulation in LRES is restricted to cancer. Unexpectedly, benign adenomas in Apc(Min/+) mice showed overexpression of most of the genes affected by LRES in cancer, which suggests that the repressive remodeling of the region is a late event. Chromatin immunoprecipitation analysis of the transcriptional insulator CTCF in mouse colon cancer cells revealed disrupted chromatin domain boundaries as compared with normal cells. Malignant regression of cancer cells by in vitro differentiation resulted in partial reversion of LRES and gain of CTCF binding. We conclude that genes in LRES regions are plastically regulated in cell differentiation and hyperproliferation, but are constrained to a coordinated repression by abolishing boundaries and the autonomous regulation of chromatin domains in cancer cells.
Collapse
Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C. Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer. Nucleic Acids Res 2013; 41:6857-69. [PMID: 23703216 PMCID: PMC3737543 DOI: 10.1093/nar/gkt438] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/29/2013] [Accepted: 04/29/2013] [Indexed: 12/18/2022] Open
Abstract
LINE-1 retrotransposons are abundant repetitive elements of viral origin, which in normal cells are kept quiescent through epigenetic mechanisms. Activation of LINE-1 occurs frequently in cancer and can enable LINE-1 mobilization but also has retrotransposition-independent consequences. We previously reported that in cancer, aberrantly active LINE-1 promoters can drive transcription of flanking unique sequences giving rise to LINE-1 chimeric transcripts (LCTs). Here, we show that one such LCT, LCT13, is a large transcript (>300 kb) running antisense to the metastasis-suppressor gene TFPI-2. We have modelled antisense RNA expression at TFPI-2 in transgenic mouse embryonic stem (ES) cells and demonstrate that antisense RNA induces silencing and deposition of repressive histone modifications implying a causal link. Consistent with this, LCT13 expression in breast and colon cancer cell lines is associated with silencing and repressive chromatin at TFPI-2. Furthermore, we detected LCT13 transcripts in 56% of colorectal tumours exhibiting reduced TFPI-2 expression. Our findings implicate activation of LINE-1 elements in subsequent epigenetic remodelling of surrounding genes, thus hinting a novel retrotransposition-independent role for LINE-1 elements in malignancy.
Collapse
Affiliation(s)
- Hazel A. Cruickshanks
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Natasha Vafadar-Isfahani
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Donncha S. Dunican
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Andy Lee
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Duncan Sproul
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Jonathan N. Lund
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Richard R. Meehan
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Cristina Tufarelli
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| |
Collapse
|
30
|
Abstract
Cancer arises as a consequence of cumulative disruptions to cellular growth control with Darwinian selection for those heritable changes that provide the greatest clonal advantage. These traits can be acquired and stably maintained by either genetic or epigenetic means. Here, we explore the ways in which alterations in the genome and epigenome influence each other and cooperate to promote oncogenic transformation. Disruption of epigenomic control is pervasive in malignancy and can be classified as an enabling characteristic of cancer cells, akin to genome instability and mutation.
Collapse
Affiliation(s)
- Hui Shen
- USC Epigenome Center, University of Southern California, Room G511B, 1450 Biggy Street, Los Angeles, CA 90089-9061, USA
| | | |
Collapse
|
31
|
Monoallelic chromatin conformation flanking long-range silenced domains in cancer-derived and normal cells. PLoS One 2013; 8:e63190. [PMID: 23696799 PMCID: PMC3655995 DOI: 10.1371/journal.pone.0063190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 03/27/2013] [Indexed: 11/25/2022] Open
Abstract
Epigenetic inactivation of chromatin plays an important role in determining cell phenotype in both normal and cancer cells, but our knowledge is still incomplete with respect to any potential monoallelic nature of the phenomenon. We have genotyped DNA isolated from chromatin of two colorectal cancer-derived lines and a culture of normal human intestinal epithelial cells (HIEC), which was immunoprecipitated with antibodies to acetylated vs. methylated histone H3K9, and presented the data as B allele frequency differences over multiple single-nucleotide polymorphism (SNP) moving window averages. [B allele is an arbitrary term defined as one of the two alleles at any given SNP, named A and B]. Three different validation tests confirmed that peaks exhibiting differences represented monoallelic domains. These complementary tests confirmed the following: 1) genes in the regions of high B allele frequency difference were expressed monoallelically; 2) in normal cells all five imprinting control regions which carried heterozygous SNPs were characterized by B allele difference peaks; and 3) the haplotypes in the B allele difference peaks were faithfully maintained in the chromatin immunoprecipitated with the respective antibodies. In both samples most of the monoallelic domains were found at the boundaries between regions of open and closed chromatin. With respect to the cancer line, this supports the established concept of conformation spreading, but the results from the normal cells were unexpected. Since these cells were polyclonal, the monoallelic structures were probably not determined by random choice as occurs in X-inactivation, so we propose that epigenetic inactivation in some domains may be heritable and polymorphic in normal human cells.
Collapse
|
32
|
Hong Q, Hsu LJ, Chou PY, Chou YT, Lu CY, Chen YA, Chang NS. Self-aggregating TIAF1 in lung cancer progression. TRANSLATIONAL RESPIRATORY MEDICINE 2013; 1:5. [PMID: 27234387 PMCID: PMC6733429 DOI: 10.1186/2213-0802-1-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 02/19/2013] [Indexed: 11/10/2022]
Abstract
Recent studies have demonstrated that transforming growth factor beta (TGF-β1)-induced antiapoptotic factor (TIAF1) is able to form aggregates in the hippocampi of middle-aged normal individuals. The aggregating TIAF1 induces generation of amyloid beta (Aβ) for causing neurodegeneration. Intriguingly, TIAF1 aggregates are shown, together with Smad4 and Aβ, in the cancer stroma and peritumor capsules of many solid tumors. During lung cancer progression, for example, TIAF1 and amyloid fibrils are significantly upregulated in the cancer stroma. Aggregates of TIAF1 and Aβ are shown on the interface between metastatic lung cancer cells and the brain tissues. Conceivably, these peritumor materials are needed for cancer cells to survive. In vitro experiments revealed that TIAF1 is a crucial component for tumor suppressors p53 and WWOX-mediated tumor suppression and apoptosis. While metastatic lung cancer cells are frequently devoid of WWOX and p53, we provide new perspectives regarding the role of TIAF1 in the pathogenesis of lung cancer development, and propose a therapeutic approach for targeting TIAF1.
Collapse
Affiliation(s)
- Qunying Hong
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, Peoples' Republic China
| | - Li-Jin Hsu
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University College of Medicine, Tainan, Taiwan
| | - Pei-Yi Chou
- Institute of Molecular Medicine, National Cheng Kung University College of Medicine, Tainan, Taiwan
| | - Ying-Tsen Chou
- Institute of Basic Medical Science, National Cheng Kung University College of Medicine, Tainan, Taiwan
| | - Chen-Yu Lu
- Institute of Molecular Medicine, National Cheng Kung University College of Medicine, Tainan, Taiwan
| | - Yu-An Chen
- Institute of Molecular Medicine, National Cheng Kung University College of Medicine, Tainan, Taiwan
| | - Nan-Shan Chang
- Institute of Molecular Medicine, National Cheng Kung University College of Medicine, Tainan, Taiwan. .,Advanced Optoelectronic Technology Center, National Cheng Kung University, Tainan, Taiwan. .,Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, NY, USA. .,Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA.
| |
Collapse
|
33
|
Singh M. Dysregulated A to I RNA editing and non-coding RNAs in neurodegeneration. Front Genet 2013; 3:326. [PMID: 23346095 PMCID: PMC3551214 DOI: 10.3389/fgene.2012.00326] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 12/28/2012] [Indexed: 12/14/2022] Open
Abstract
RNA editing is an alteration in the primary nucleotide sequences resulting from a chemical change in the base. RNA editing is observed in eukaryotic mRNA, transfer RNA, ribosomal RNA, and non-coding RNAs (ncRNA). The most common RNA editing in the mammalian central nervous system is a base modification, where the adenosine residue is base-modified to inosine (A to I). Studies from ADAR (adenosine deaminase that act on RNA) mutants in Caenorhabditis elegans, Drosophila, and mice clearly show that the RNA editing process is an absolute requirement for nervous system homeostasis and normal physiology of the animal. Understanding the mechanisms of editing and findings of edited substrates has provided a better knowledge of the phenotype due to defective and hyperactive RNA editing. A to I RNA editing is catalyzed by a family of enzymes knows as ADARs. ADARs modify duplex RNAs and editing of duplex RNAs formed by ncRNAs can impact RNA functions, leading to an altered regulatory gene network. Such altered functions by A to I editing is observed in mRNAs, microRNAs (miRNA) but other editing of small and long ncRNAs (lncRNAs) has yet to be identified. Thus, ncRNA and RNA editing may provide key links between neural development, nervous system function, and neurological diseases. This review includes a summary of seminal findings regarding the impact of ncRNAs on biological and pathological processes, which may be further modified by RNA editing. NcRNAs are non-translated RNAs classified by size and function. Known ncRNAs like miRNAs, smallRNAs (smRNAs), PIWI-interacting RNAs (piRNAs), and lncRNAs play important roles in splicing, DNA methylation, imprinting, and RNA interference. Of note, miRNAs are involved in development and function of the nervous system that is heavily dependent on both RNA editing and the intricate spatiotemporal expression of ncRNAs. This review focuses on the impact of dysregulated A to I editing and ncRNAs in neurodegeneration.
Collapse
Affiliation(s)
- Minati Singh
- Department of Internal Medicine, University of Iowa Iowa City, IA, USA
| |
Collapse
|
34
|
Abstract
Cancer has been considered a genetic disease with a wide array of well-characterized gene mutations and chromosomal abnormalities. Of late, aberrant epigenetic modifications have been elucidated in cancer, and together with genetic alterations, they have been helpful in understanding the complex traits observed in neoplasia. "Cancer Epigenetics" therefore has contributed substantially towards understanding the complexity and diversity of various cancers. However, the positioning of epigenetic events during cancer progression is still not clear, though there are some reports implicating aberrant epigenetic modifications in very early stages of cancer. Amongst the most studied aberrant epigenetic modifications are the DNA methylation differences at the promoter regions of genes affecting their expression. Hypomethylation mediated increased expression of oncogenes and hypermethylation mediated silencing of tumor suppressor genes are well known examples. This chapter also explores the correlation of DNA methylation and demethylation enzymes with cancer.
Collapse
Affiliation(s)
- Gopinathan Gokul
- Laboratory of Mammalian Genetics, CDFD, Hyderabad, 500001, India
| | | |
Collapse
|
35
|
Ross JP, Shaw JM, Molloy PL. Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing. Epigenetics 2012; 8:113-27. [PMID: 23257838 PMCID: PMC3549874 DOI: 10.4161/epi.23330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specific labeling (using a biotin-labeled nucleotide ligand) of methylated cytosines in bisulfite-converted DNA. This step is then followed by affinity capture, using streptavidin-coupled magnetic beads. SuBLiME is highly adaptable and can be combined with deep sequencing library generation and/or genomic complexity-reduction. In this pilot study, we enriched methylated DNA from Csp6I-cut complexity-reduced genomes of colorectal cancer cell lines (HCT-116, HT-29 and SW-480) and normal blood leukocytes with the aim of discovering colorectal cancer biomarkers. Enriched libraries were sequenced with SOLiD-3 technology. In pairwise comparisons, we scored a total of 1,769 gene loci and 33 miRNA loci as differentially methylated between the cell lines and leukocytes. Of these, 516 loci were differently methylated in at least two promoter-proximal CpG sites over two discrete Csp6I fragments. Identified methylated gene loci were associated with anatomical development, differentiation and cell signaling. The data correlated with good agreement to a number of published colorectal cancer DNA methylation biomarkers and genomic data sets. SuBLiME is effective in the enrichment of methylated nucleic acid and in the detection of known and novel biomarkers.
Collapse
Affiliation(s)
- Jason P Ross
- Preventative Health National Research Flagship, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, NSW, Australia.
| | | | | |
Collapse
|
36
|
Severson PL, Tokar EJ, Vrba L, Waalkes MP, Futscher BW. Agglomerates of aberrant DNA methylation are associated with toxicant-induced malignant transformation. Epigenetics 2012; 7:1238-48. [PMID: 22976526 PMCID: PMC3499325 DOI: 10.4161/epi.22163] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epigenetic dysfunction is a known contributor in carcinogenesis, and is emerging as a mechanism involved in toxicant-induced malignant transformation for environmental carcinogens such as arsenicals or cadmium. In addition to aberrant DNA methylation of single genes, another manifestation of epigenetic dysfunction in cancer is agglomerative DNA methylation, which can participate in long-range epigenetic silencing that targets many neighboring genes and has been shown to occur in several types of clinical cancers. Using in vitro model systems of toxicant-induced malignant transformation, we found hundreds of aberrant DNA methylation events that emerge during malignant transformation, some of which occur in an agglomerative fashion. In an arsenite-transformed prostate epithelial cell line, the protocadherin (PCDH), HOXC and HOXD gene family clusters are targeted for agglomerative DNA methylation. The agglomerative DNA methylation changes induced by arsenicals appear to be common and clinically relevant events, since they occur in other human cancer cell lines and models of malignant transformation, as well as clinical cancer specimens. Aberrant DNA methylation in general occurred more often within histone H3 lysine-27 trimethylation stem cell domains. We found a striking association between enrichment of histone H3 lysine-9 trimethylation stem cell domains and toxicant-induced agglomerative DNA methylation, suggesting these epigenetic modifications may become aberrantly linked during malignant transformation. In summary, we found an association between toxicant-induced malignant transformation and agglomerative DNA methylation, which lends further support to the hypothesis that epigenetic dysfunction plays an important role in toxicant-induced malignant transformation.
Collapse
Affiliation(s)
- Paul L Severson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | | | | | | | | |
Collapse
|
37
|
Labrie V, Pai S, Petronis A. Epigenetics of major psychosis: progress, problems and perspectives. Trends Genet 2012; 28:427-35. [PMID: 22622229 PMCID: PMC3422438 DOI: 10.1016/j.tig.2012.04.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/03/2012] [Accepted: 04/23/2012] [Indexed: 01/26/2023]
Abstract
Understanding the origins of normal and pathological behavior is one of the most exciting opportunities in contemporary biomedical research. There is increasing evidence that, in addition to DNA sequence and the environment, epigenetic modifications of DNA and histone proteins may contribute to complex phenotypes. Inherited and/or acquired epigenetic factors are partially stable and have regulatory roles in numerous genomic activities, thus making epigenetics a promising research path in etiological studies of psychiatric disease. In this article, we review recent epigenetic studies examining the brain and other tissues, including those from individuals with schizophrenia (SCZ) and bipolar disorder (BPD). We also highlight heuristic aspects of the epigenetic theory of psychiatric disease and discuss the future directions of psychiatric epigenetics.
Collapse
Affiliation(s)
- Viviane Labrie
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, ONT, M5T 1R8, Canada
| | | | | |
Collapse
|
38
|
DNA Hypomethylation and Hemimethylation in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 754:31-56. [DOI: 10.1007/978-1-4419-9967-2_2] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
39
|
Carvalho RH, Haberle V, Hou J, van Gent T, Thongjuea S, van Ijcken W, Kockx C, Brouwer R, Rijkers E, Sieuwerts A, Foekens J, van Vroonhoven M, Aerts J, Grosveld F, Lenhard B, Philipsen S. Genome-wide DNA methylation profiling of non-small cell lung carcinomas. Epigenetics Chromatin 2012; 5:9. [PMID: 22726460 PMCID: PMC3407794 DOI: 10.1186/1756-8935-5-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 06/22/2012] [Indexed: 12/15/2022] Open
Abstract
Background Non-small cell lung carcinoma (NSCLC) is a complex malignancy that owing to its heterogeneity and poor prognosis poses many challenges to diagnosis, prognosis and patient treatment. DNA methylation is an important mechanism of epigenetic regulation involved in normal development and cancer. It is a very stable and specific modification and therefore in principle a very suitable marker for epigenetic phenotyping of tumors. Here we present a genome-wide DNA methylation analysis of NSCLC samples and paired lung tissues, where we combine MethylCap and next generation sequencing (MethylCap-seq) to provide comprehensive DNA methylation maps of the tumor and paired lung samples. The MethylCap-seq data were validated by bisulfite sequencing and methyl-specific polymerase chain reaction of selected regions. Results Analysis of the MethylCap-seq data revealed a strong positive correlation between replicate experiments and between paired tumor/lung samples. We identified 57 differentially methylated regions (DMRs) present in all NSCLC tumors analyzed by MethylCap-seq. While hypomethylated DMRs did not correlate to any particular functional category of genes, the hypermethylated DMRs were strongly associated with genes encoding transcriptional regulators. Furthermore, subtelomeric regions and satellite repeats were hypomethylated in the NSCLC samples. We also identified DMRs that were specific to two of the major subtypes of NSCLC, adenocarcinomas and squamous cell carcinomas. Conclusions Collectively, we provide a resource containing genome-wide DNA methylation maps of NSCLC and their paired lung tissues, and comprehensive lists of known and novel DMRs and associated genes in NSCLC.
Collapse
Affiliation(s)
- Rejane Hughes Carvalho
- Department of Cell Biology, ErasmusMC, PO Box 2040, Rotterdam, CA, 3000, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Kloth M, Goering W, Ribarska T, Arsov C, Sorensen KD, Schulz WA. The SNP rs6441224 influences transcriptional activity and prognostically relevant hypermethylation of RARRES1 in prostate cancer. Int J Cancer 2012; 131:E897-904. [PMID: 22573467 DOI: 10.1002/ijc.27628] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 04/23/2012] [Indexed: 02/03/2023]
Abstract
Epigenetic aberrations are frequent in prostate cancer and could be useful for detection and prognostication. However, the underlying mechanisms and the sequence of these changes remain to be fully elucidated. The tumor suppressor gene RARRES1 (TIG1) is frequently hypermethylated in several cancers. Having noted changes in the expression of its paralogous neighbor gene LXN at 3q25.32, we used pyrosequencing to quantify DNA methylation at both genes and determine its relationship with clinicopathological parameters in 86 prostate cancer tissues from radical prostatectomies. Methylation at LXN and RARRES1 was highly correlated. Increasing methylation was associated with worse clinical features, including biochemical recurrence, and decreased expression of both genes. However, expression of three neighboring genes was unaffected. Intriguingly, RARRES1 methylation was influenced by the genotype of the rs6441224 single-nucleotide polymorphism (SNP) in its promoter. We found that this SNP is located within an ETS-family-response element and that the more strongly methylated allele confers lower activity in reporter assays. Concomitant methylation of RARRES1 and LXN in cancerous tissues was also detected in prostate cancer cell lines and was shown to be associated with repressive histone modifications and transcriptional downregulation. In conclusion, we found that genotype-associated hypermethylation of the ETS-family target gene RARRES1 influences methylation at its neighbor gene LXN and could be useful as a prognostic biomarker.
Collapse
Affiliation(s)
- Michael Kloth
- Department of Urology, Heinrich Heine University, Duesseldorf, Germany
| | | | | | | | | | | |
Collapse
|
41
|
Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res 2012; 22:1197-211. [PMID: 22613842 PMCID: PMC3396362 DOI: 10.1101/gr.132662.111] [Citation(s) in RCA: 395] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide, and adenocarcinoma is its most common histological subtype. Clinical and molecular evidence indicates that lung adenocarcinoma is a heterogeneous disease, which has important implications for treatment. Here we performed genome-scale DNA methylation profiling using the Illumina Infinium HumanMethylation27 platform on 59 matched lung adenocarcinoma/non-tumor lung pairs, with genome-scale verification on an independent set of tissues. We identified 766 genes showing altered DNA methylation between tumors and non-tumor lung. By integrating DNA methylation and mRNA expression data, we identified 164 hypermethylated genes showing concurrent down-regulation, and 57 hypomethylated genes showing increased expression. Integrated pathways analysis indicates that these genes are involved in cell differentiation, epithelial to mesenchymal transition, RAS and WNT signaling pathways, and cell cycle regulation, among others. Comparison of DNA methylation profiles between lung adenocarcinomas of current and never-smokers showed modest differences, identifying only LGALS4 as significantly hypermethylated and down-regulated in smokers. LGALS4, encoding a galactoside-binding protein involved in cell–cell and cell–matrix interactions, was recently shown to be a tumor suppressor in colorectal cancer. Unsupervised analysis of the DNA methylation data identified two tumor subgroups, one of which showed increased DNA methylation and was significantly associated with KRAS mutation and to a lesser extent, with smoking. Our analysis lays the groundwork for further molecular studies of lung adenocarcinoma by identifying novel epigenetically deregulated genes potentially involved in lung adenocarcinoma development/progression, and by describing an epigenetic subgroup of lung adenocarcinoma associated with characteristic molecular alterations.
Collapse
|
42
|
Abstract
DNA hypomethylation was the initial epigenetic abnormality recognized in human tumors. However, for several decades after its independent discovery by two laboratories in 1983, it was often ignored as an unwelcome complication, with almost all of the attention on the hypermethylation of promoters of genes that are silenced in cancers (e.g., tumor-suppressor genes). Because it was subsequently shown that global hypomethylation of DNA in cancer was most closely associated with repeated DNA elements, cancer linked-DNA hypomethylation continued to receive rather little attention. DNA hypomethylation in cancer can no longer be considered an oddity, because recent high-resolution genome-wide studies confirm that DNA hypomethylation is the almost constant companion to hypermethylation of the genome in cancer, just usually (but not always) in different sequences. Methylation changes at individual CpG dyads in cancer can have a high degree of dependence not only on the regional context, but also on neighboring sites. DNA demethylation during carcinogenesis may involve hemimethylated dyads as intermediates, followed by spreading of the loss of methylation on both strands. In this review, active demethylation of DNA and the relationship of cancer-associated DNA hypomethylation to cancer stem cells are discussed. Evidence is accumulating for the biological significance and clinical relevance of DNA hypomethylation in cancer, and for cancer-linked demethylation and de novo methylation being highly dynamic processes.
Collapse
Affiliation(s)
- Melanie Ehrlich
- Hayward Genetics Program, Department of Biochemistry, Tulane Cancer Center, Tulane Medical School, 1430 TulaneAvenue, New Orleans, LA 70112, USA.
| |
Collapse
|
43
|
Arai E, Kanai Y. DNA methylation profiles in precancerous tissue and cancers: carcinogenetic risk estimation and prognostication based on DNA methylation status. Epigenomics 2012; 2:467-81. [PMID: 22121905 DOI: 10.2217/epi.10.16] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Alterations in DNA methylation, which are associated with DNA methyltransferase abnormalities and result in silencing of tumor-related genes and chromosomal instability, are involved even in precancerous changes in various organs. DNA methylation alterations also account for the histological heterogeneity and clinicopathological diversity of human cancers. Therefore, we have analyzed DNA methylation on a genome-wide scale in clinical tissue samples. Our approach using the bacterial artificial chromosome array-based methylated CpG island amplification method has revealed that DNA methylation alterations correlated with the future development of more malignant cancers are already accumulated at the precancerous stage in the kidney, liver and urinary tract. DNA methylation profiles at precancerous stages are basically inherited by the corresponding cancers developing in individual patients. Such DNA methylation alterations may confer vulnerability to further genetic and epigenetic alterations, generate more malignant cancers, and thus determine patient outcome. On the basis of bacterial artificial chromosome array-based methylated CpG island amplification data, indicators for carcinogenetic risk estimation have been established using liver tissue specimens from patients with hepatitis virus infection, chronic hepatitis and liver cirrhosis or histologically normal urothelia, and for prognostication using biopsy or surgically resected specimens from patients with renal cell carcinoma, hepatocellular carcinoma and urothelial carcinoma. Such genome-wide DNA methylation profiling has now firmly established the clinical relevance of translational epigenetics.
Collapse
Affiliation(s)
- Eri Arai
- Pathology Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | | |
Collapse
|
44
|
da Costa Prando E, Cavalli LR, Rainho CA. Evidence of epigenetic regulation of the tumor suppressor gene cluster flanking RASSF1 in breast cancer cell lines. Epigenetics 2012; 6:1413-24. [PMID: 22139571 DOI: 10.4161/epi.6.12.18271] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Epigenetic mechanisms are frequently deregulated in cancer cells and can lead to the silencing of genes with tumor suppressor activities. The isoform A of the Ras-association domain family member 1 (RASSF1A) gene is one of the most frequently silenced transcripts in human tumors, however, few studies have simultaneously investigated epigenetic abnormalities associated with the 3p21.3 tumor suppressor gene cluster flanking RASSF1 (i.e., SEMA3B, HYAL3, HYAL2, HYAL1, TUSC2, RASSF1, ZMYND10, NPRL2, TMEM115, and CACNA2D2). This study aimed to investigate the role of epigenetic changes to these genes in seventeen breast cancer cell lines and in three non-tumorigenic epithelial breast cell lines (184A1, 184B5, and MCF 10A) and to evaluate the effect on gene expression of treatment with the demethylating agent 5-Aza-2'-deoxycytidine and/or Trichostatin A (TSA), a histone deacetylase inhibitor. We report that, although the RASSF1A isoform was determined to be epigenetically silenced in 15 of the 17 breast cancer cell lines, all the cell lines expressed the RASSF1C isoform. Five breast cancer cell lines overexpressed RASSF1C, when compared to the normal epithelial cell line 184A1. Furthermore, the genes HYAL1 and CACNA2D2 were significantly overexpressed after the treatments. After the combinated treatment, RASSF1A re-expression was accompanied by an increase in expression levels of the flanking genes. The Spearman's correlation coefficient indicated a positive co-regulation of the following gene pairs: RASSF1 and TUSC2 (r=0.64, p=0.002), RASSF1 and ZMYND10 (r=0.58, p=0.07), RASSF1 and NPRL2 (r=0.48, p=0.03), ZMYND10 and NPRL2 (r=0.71; p=0,0004), and NPRL2 and TMEM115 (r=0.66, p=0.001). Interestingly, the genes TUSC2, NPRL2 and TMEM115 were found to be unmethylated in each of the untreated cell lines. Chromatin immunoprecipitation using antibodies against the acetylated and trimethylated lysine 9 of histone H3 demonstrated low levels of histone methylation in these genes, which are located closest to RASSF1. These results provide evidence that epigenetic repression is involved in the down-regulation of multiple genes at 3p21.3 in breast cancer cells.
Collapse
Affiliation(s)
- Erika da Costa Prando
- Department of Genetics, Biosciences Institute, Sao Paulo State University, Sao Paulo, Brazil
| | | | | |
Collapse
|
45
|
Siddiqi S, Terry M, Matushansky I. Hiwi mediated tumorigenesis is associated with DNA hypermethylation. PLoS One 2012; 7:e33711. [PMID: 22438986 PMCID: PMC3306289 DOI: 10.1371/journal.pone.0033711] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 02/15/2012] [Indexed: 02/07/2023] Open
Abstract
Expression of Piwi proteins is confined to early development and stem cells during which they suppress transposon migration via DNA methylation to ensure genomic stability. Piwi's genomic protective function conflicts with reports that its human ortholog, Hiwi, is expressed in numerous cancers and prognosticates shorter survival. However, the role of Hiwi in tumorigenesis has not been examined. Here we demonstrate that (1) over-expressing Hiwi in sarcoma precursors inhibits their differentiation in vitro and generates sarcomas in vivo; (2) transgenic mice expressing Hiwi (mesodermally restricted) develop sarcomas; and (3) inducible down-regulation of Hiwi in human sarcomas inhibits growth and re-establishes differentiation. Our data indicates that Hiwi is directly tumorigenic and Hiwi-expressing cancers may be addicted to Hiwi expression. We further show that Hiwi associated DNA methylation and cyclin-dependent kinase inhibitor (CDKI) silencing is reversible along with Hiwi-induced tumorigenesis, via DNA-methyltransferase inhibitors. Our studies reveal for the first time not only a novel oncogenic role for Hiwi as a driver of tumorigenesis, but also suggest that the use of epigenetic agents may be clinically beneficial for treatment of tumors that express Hiwi. Additionally, our data showing that Hiwi-associated DNA hyper-methylation with subsequent genetic and epigenetic changes favoring a tumorigenic state reconciles the conundrum of how Hiwi may act appropriately to promote genomic integrity during early development (via transposon silencing) and inappropriately in adult tissues with subsequent tumorigenesis.
Collapse
Affiliation(s)
- Sara Siddiqi
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, United States of America
| | - Melissa Terry
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, United States of America
| | - Igor Matushansky
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
46
|
Banelli B, Brigati C, Di Vinci A, Casciano I, Forlani A, Borzì L, Allemanni G, Romani M. A pyrosequencing assay for the quantitative methylation analysis of the PCDHB gene cluster, the major factor in neuroblastoma methylator phenotype. J Transl Med 2012; 92:458-65. [PMID: 22157715 DOI: 10.1038/labinvest.2011.169] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epigenetic alterations are hallmarks of cancer and powerful biomarkers, whose clinical utilization is made difficult by the absence of standardization and of common methods of data interpretation. The coordinate methylation of many loci in cancer is defined as 'CpG island methylator phenotype' (CIMP) and identifies clinically distinct groups of patients. In neuroblastoma (NB), CIMP is defined by a methylation signature, which includes different loci, but its predictive power on outcome is entirely recapitulated by the PCDHB cluster only. We have developed a robust and cost-effective pyrosequencing-based assay that could facilitate the clinical application of CIMP in NB. This assay permits the unbiased simultaneous amplification and sequencing of 17 out of 19 genes of the PCDHB cluster for quantitative methylation analysis, taking into account all the sequence variations. As some of these variations were at CpG doublets, we bypassed the data interpretation conducted by the methylation analysis software to assign the corrected methylation value at these sites. The final result of the assay is the mean methylation level of 17 gene fragments in the protocadherin B cluster (PCDHB) cluster. We have utilized this assay to compare the methylation levels of the PCDHB cluster between high-risk and very low-risk NB patients, confirming the predictive value of CIMP. Our results demonstrate that the pyrosequencing-based assay herein described is a powerful instrument for the analysis of this gene cluster that may simplify the data comparison between different laboratories and, in perspective, could facilitate its clinical application. Furthermore, our results demonstrate that, in principle, pyrosequencing can be efficiently utilized for the methylation analysis of gene clusters with high internal homologies.
Collapse
Affiliation(s)
- Barbara Banelli
- Laboratory of Tumor Genetics and Epigenetic, Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi, Genova, Italy.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Saunthararajah Y, Triozzi P, Rini B, Singh A, Radivoyevitch T, Sekeres M, Advani A, Tiu R, Reu F, Kalaycio M, Copelan E, Hsi E, Lichtin A, Bolwell B. p53-Independent, normal stem cell sparing epigenetic differentiation therapy for myeloid and other malignancies. Semin Oncol 2012; 39:97-108. [PMID: 22289496 PMCID: PMC3655437 DOI: 10.1053/j.seminoncol.2011.11.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cytotoxic chemotherapy for acute myeloid leukemia (AML) usually produces only temporary remissions, at the cost of significant toxicity and risk for death. One fundamental reason for treatment failure is that it is designed to activate apoptosis genes (eg, TP53) that may be unavailable because of mutation or deletion. Unlike deletion of apoptosis genes, genes that mediate cell cycle exit by differentiation are present in myelodysplastic syndrome (MDS) and AML cells but are epigenetically repressed: MDS/AML cells express high levels of key lineage-specifying transcription factors. Mutations in these transcription factors (eg, CEBPA) or their cofactors (eg., RUNX1) affect transactivation function and produce epigenetic repression of late-differentiation genes that antagonize MYC. Importantly, this aberrant epigenetic repression can be redressed clinically by depleting DNA methyltransferase 1 (DNMT1, a central component of the epigenetic network that mediates transcription repression) using the deoxycytidine analogue decitabine at non-cytotoxic concentrations. The DNMT1 depletion is sufficient to trigger upregulation of late-differentiation genes and irreversible cell cycle exit by p53-independent differentiation mechanisms. Fortuitously, the same treatment maintains or increases self-renewal of normal hematopoietic stem cells, which do not express high levels of lineage-specifying transcription factors. The biological rationale for this approach to therapy appears to apply to cancers other than MDS/AML also. Decitabine or 5-azacytidine dose and schedule can be rationalized to emphasize this mechanism of action, as an alternative or complement to conventional apoptosis-based oncotherapy.
Collapse
Affiliation(s)
- Yogen Saunthararajah
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
The whole-genome sequencing of mosquitoes has facilitated our understanding of fundamental biological processes at their basic molecular levels and holds potential for application to mosquito control and prevention of mosquito-borne disease transmission. Draft genome sequences are available for Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus. Collectively, these represent the major vectors of African malaria, dengue fever and yellow fever viruses, and lymphatic filariasis, respectively. Rapid advances in genome technologies have revealed detailed information on genome architecture as well as phenotype-specific transcriptomics and proteomics. These resources allow for detailed comparative analyses within and across populations as well as species. Next-generation sequencing technologies will likely promote a proliferation of genome sequences for additional mosquito species as well as for individual insects. Here we review the current status of genome research in mosquitoes and identify potential areas for further investigations.
Collapse
Affiliation(s)
- David W Severson
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA.
| | | |
Collapse
|
49
|
Javierre BM, Rodriguez-Ubreva J, Al-Shahrour F, Corominas M, Graña O, Ciudad L, Agirre X, Pisano DG, Valencia A, Roman-Gomez J, Calasanz MJ, Prosper F, Esteller M, Gonzalez-Sarmiento R, Ballestar E. Long-range epigenetic silencing associates with deregulation of Ikaros targets in colorectal cancer cells. Mol Cancer Res 2011; 9:1139-51. [PMID: 21737484 DOI: 10.1158/1541-7786.mcr-10-0515] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Transcription factors are common targets of epigenetic inactivation in human cancer. Promoter hypermethylation and subsequent silencing of transcription factors can lead to further deregulation of their targets. In this study, we explored the potential epigenetic deregulation in cancer of Ikaros family genes, which code for essential transcription factors in cell differentiation and exhibit genetic defects in hematologic neoplasias. Unexpectedly, our analysis revealed that Ikaros undergoes very specific promoter hypermethylation in colorectal cancer, including in all the cell lines studied and around 64% of primary colorectal adenocarcinomas, with increasing proportions in advanced Duke's stages. Ikaros hypermethylation occurred in the context of a novel long-range epigenetic silencing (LRES) region. Reintroduction of Ikaros in colorectal cancer cells, ChIP-chip analysis, and validation in primary samples led us to identify a number of direct targets that are possibly related with colorectal cancer progression. Our results not only provide the first evidence that LRES can have functional specific effects in cancer but also identify several deregulated Ikaros targets that may contribute to progression in colorectal adenocarcinoma.
Collapse
Affiliation(s)
- Biola M Javierre
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011; 43:768-75. [PMID: 21706001 PMCID: PMC3145050 DOI: 10.1038/ng.865] [Citation(s) in RCA: 763] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 05/25/2011] [Indexed: 02/07/2023]
Abstract
Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other, suggesting that these cDMRs might be generalized across cancer types. Here we show stochastic methylation variation of the same cDMRs, distinguishing cancer from normal, in colon, lung, breast, thyroid, and Wilms tumors, with intermediate variation in adenomas. Whole genome bisulfite sequencing shows these variable cDMRs are related to loss of sharply delimited methylation boundaries at CpG islands. Furthermore, we find hypomethylation of discrete blocks encompassing half the genome, with extreme gene expression variability. Genes associated with the cDMRs and large blocks are involved in mitosis and matrix remodeling, respectively. These data suggest a model for cancer involving loss of epigenetic stability of well-defined genomic domains that underlies increased methylation variability in cancer and could contribute to tumor heterogeneity.
Collapse
|