1
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5-Azacytidine-Mediated Modulation of the Immune Microenvironment in Murine Acute Myeloid Leukemia. Cancers (Basel) 2022; 15:cancers15010118. [PMID: 36612115 PMCID: PMC9817798 DOI: 10.3390/cancers15010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Cancer cells accumulate epigenetic modifications that allow escape from intrinsic and extrinsic surveillance mechanisms. In the case of acute myeloid leukemias (AML) and myelodysplastic syndromes, agents that disrupt chromatin structure, namely hypomethylating agents (HMAs), have shown tremendous promise as an alternate, milder treatment option for older, clinically non-fit patients. HMAs reprogram the epigenetic landscape in tumor cells through the reversal of DNA hypermethylation. Therapeutic effects resulting from these epigenetic changes are incredibly effective, sometimes resulting in complete remissions, but are frequently lost due to primary or acquired resistance. In this study, we describe syngeneic murine leukemias that are responsive to the HMA 5-azacytidine (5-Aza), as determined by augmented expression of a transduced luciferase reporter. We also found that 5-Aza treatment re-established immune-related transcript expression, suppressed leukemic burden and extended survival in leukemia-challenged mice. The effects of 5-Aza treatment were short-lived, and analysis of the immune microenvironment reveals possible mechanisms of resistance, such as simultaneous increase in immune checkpoint protein expression. This represents a model system that is highly responsive to HMAs and recapitulates major therapeutic outcomes observed in human leukemia (relapse) and may serve as a pre-clinical tool for studying acquired resistance and novel treatment combinations.
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2
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Varier KM, Dhandapani H, Liu W, Song J, Wang C, Hu A, Ben-David Y, Shen X, Li Y, Gajendran B. An immunotherapeutic approach to decipher the role of long non-coding RNAs in cancer progression, resistance and epigenetic regulation of immune cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:242. [PMID: 34303380 PMCID: PMC8305593 DOI: 10.1186/s13046-021-01997-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Immunotherapeutic treatments are gaining attention due to their effective anti-tumor response. Particularly, the revolution of immune checkpoint inhibitors (ICIs) produces promising outcomes for various cancer types. However, the usage of immunotherapy is limited due to its low response rate, suggesting that tumor cells escape the immune surveillance. Rapid advances in transcriptomic profiling have led to recognize immune-related long non-coding RNAs (LncRNAs), as regulators of immune cell-specific gene expression that mediates immune stimulatory as well as suppression of immune response, indicating LncRNAs as targets to improve the efficacy of immunotherapy against tumours. Moreover, the immune-related LncRNAs acting as epigenetic modifiers are also under deep investigation. Thus, herein, is a summarised knowledge of LncRNAs and their regulation in the adaptive and innate immune system, considering their importance in autophagy and predicting putative immunotherapeutic responses.
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Affiliation(s)
- Krishnapriya M Varier
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hemavathi Dhandapani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India.,Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Wuling Liu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Jialei Song
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Anling Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Xiangchun Shen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
| | - Yanmei Li
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
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3
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Lohse I, Statz-Geary K, Brothers SP, Wahlestedt C. Precision medicine in the treatment stratification of AML patients: challenges and progress. Oncotarget 2018; 9:37790-37797. [PMID: 30701032 PMCID: PMC6340870 DOI: 10.18632/oncotarget.26492] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/10/2018] [Indexed: 01/04/2023] Open
Abstract
Recent advances in high throughput technologies have led to the generation of vast amounts of clinical data and the development of personalized medicine approaches in acute myeloid leukemia (AML). The ability to treat cancer patients based upon their individual molecular characteristics or drug sensitivity profiles is expected to significantly advance cancer treatment and improve the long-term survival of patients with refractory AML, for whom current treatment options are restricted to palliative approaches. The clinical development of omics-based and phenotypic screens, however, is limited by a number of bottlenecks including the generation of cost-effective high-throughput data, data interpretation and integration of multiple approaches, sample availability, clinically relevant timelines, and the development and education of multidisciplinary teams. Recently, a number of small clinical trials have shown survival benefits in patients treated based on personalized medicine approaches. While these preliminary studies are encouraging, larger trials are needed to evaluate the utility of these technologies in routine clinical settings.
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Affiliation(s)
- Ines Lohse
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, FL, USA.,Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA.,Molecular Therapeutics Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami, FL, USA
| | - Kurt Statz-Geary
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Shaun P Brothers
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, FL, USA.,Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA.,Molecular Therapeutics Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, FL, USA.,Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
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4
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Shen N, Yan F, Pang J, Zhao N, Gangat N, Wu L, Bode AM, Al-Kali A, Litzow MR, Liu S. Inactivation of Receptor Tyrosine Kinases Reverts Aberrant DNA Methylation in Acute Myeloid Leukemia. Clin Cancer Res 2017; 23:6254-6266. [PMID: 28720666 DOI: 10.1158/1078-0432.ccr-17-0235] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 06/18/2017] [Accepted: 07/12/2017] [Indexed: 01/05/2023]
Abstract
Purpose: Receptor tyrosine kinases (RTKs) are frequently deregulated in leukemia, yet the biological consequences of this deregulation remain elusive. The mechanisms underlying aberrant methylation, a hallmark of leukemia, are not fully understood. Here we investigated the role of RTKs in methylation abnormalities and characterized the hypomethylating activities of RTK inhibitors.Experimental Design: Whether and how RTKs regulate expression of DNA methyltransferases (DNMTs), tumor suppressor genes (TSGs) as well as global and gene-specific DNA methylation were examined. The pharmacologic activities and mechanisms of actions of RTK inhibitors in vitro, ex vivo, in mice, and in nilotinib-treated leukemia patients were determined.Results: Upregulation of RTKs paralleled DNMT overexpression in leukemia cell lines and patient blasts. Knockdown of RTKs disrupted, whereas enforced expression increased DNMT expression and DNA methylation. Treatment with the RTK inhibitor, nilotinib, resulted in a reduction of Sp1-dependent DNMT1 expression, the diminution of global DNA methylation, and the upregulation of the p15INK4B gene through promoter hypomethylation in AML cell lines and patient blasts. This led to disruption of AML cell clonogenicity and promotion of cellular apoptosis without obvious changes in cell cycle. Importantly, nilotinib administration in mice and human patients with AML impaired expression of DNMTs followed by DNA hypomethylation, TSG re-expression, and leukemia regression.Conclusions: Our findings demonstrate RTKs as novel regulators of DNMT-dependent DNA methylation and define DNA methylation status in AML cells as a pharmacodynamic marker for their response to RTK-based therapy, providing new therapeutic avenues for RTK inhibitors in overcoming epigenetic abnormalities in leukemia. Clin Cancer Res; 23(20); 6254-66. ©2017 AACR.
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Affiliation(s)
- Na Shen
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Fei Yan
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Jiuxia Pang
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Na Zhao
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Naseema Gangat
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Laichu Wu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Mark R Litzow
- Division of Hematology, Mayo Clinic, Rochester, Minnesota.
| | - Shujun Liu
- The Hormel Institute, University of Minnesota, Austin, Minnesota.
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5
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Zou J, Zhou Z, Wan L, Tong Y, Qin Y, Wang C, Zhou K. Targeting the Sonic Hedgehog-Gli1 Pathway as a Potential New Therapeutic Strategy for Myelodysplastic Syndromes. PLoS One 2015; 10:e0136843. [PMID: 26317501 PMCID: PMC4552723 DOI: 10.1371/journal.pone.0136843] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/10/2015] [Indexed: 12/31/2022] Open
Abstract
The complex mechanistic array underlying the pathogenesis of myelodysplastic syndrome (MDS) is still unclear. Although dysregulations of different signaling pathways involved in MDS have been described, the identification of specific biomarkers and therapy targets remains an important task in order to establish novel therapeutic approaches. Here, we demonstrated that the Shh signaling pathway is active in MDS and correlated it with disease progression. Additionally, the knockdown of Gli1 significantly inhibited cell proliferation in vitro and in vivo. Gli1 silencing also induced apoptosis and G0/G1 phase arrest. Furthermore, Gli1 silencing enhanced the demethylating effect of 5-aza-2'-deoxycytidine on the p15 gene promoter and subsequently promoted its expression by inhibiting DNA methyltransferase 1(DNMT1). Our findings show that the Shh signaling pathway plays a role in the pathogenesis and disease progression of MDS, and proceeds by modulating DNA methylation. This pathway may prove to be a potential therapeutic target for enhancing the therapeutic effects of 5-azacytidine on malignant transformation of MDS.
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Affiliation(s)
- Jixue Zou
- Department of Hematology, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai, People’s Republic of China
| | - Zhigang Zhou
- Department of Intensive Care Unit, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai, People’s Republic of China
| | - Liping Wan
- Department of Hematology, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai, People’s Republic of China
| | - Yin Tong
- Department of Hematology, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai, People’s Republic of China
| | - Youwen Qin
- Department of Hematology, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai, People’s Republic of China
| | - Chun Wang
- Department of Hematology, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai, People’s Republic of China
- * E-mail: (KZ); (CW)
| | - Kun Zhou
- Department of Hematology, Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai, People’s Republic of China
- * E-mail: (KZ); (CW)
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6
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Eriksson A, Lennartsson A, Lehmann S. Epigenetic aberrations in acute myeloid leukemia: Early key events during leukemogenesis. Exp Hematol 2015; 43:609-24. [PMID: 26118500 DOI: 10.1016/j.exphem.2015.05.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 05/23/2015] [Indexed: 12/17/2022]
Abstract
As a result of the introduction of new sequencing technologies, the molecular landscape of acute myeloid leukemia (AML) is rapidly evolving. From karyotyping, which detects only large genomic aberrations of metaphase chromosomes, we have moved into an era when sequencing of each base pair allows us to define the AML genome at highest resolution. This has revealed a new complex landscape of genetic aberrations where addition of mutations in epigenetic regulators has been one of the most important contributions to the understanding of the pathogenesis of AML. These findings, together with new insights into epigenetic mechanisms, have placed dysregulated epigenetic mechanisms at the forefront of AML development. Not only have several new mutations in genes directly involved in epigenetic regulatory mechanisms been discovered, but also previously well-known gene fusions have been found to exert aberrant effects through epigenetic mechanisms. In addition, mutations in epigenetic regulators such as DNMT3A, TET2, and ASXL1 have recently been found to be the earliest known events during AML evolution and to be present as preleukemic lesions before the onset of AML. In this article, we review epigenetic changes in AML also in relation to what is known about their mechanism of action and their prognostic role.
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Affiliation(s)
- Anna Eriksson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Stockholm, Sweden
| | - Sören Lehmann
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Centre of Hematology, HERM, Department of Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.
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7
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Sonnet M, Claus R, Becker N, Zucknick M, Petersen J, Lipka DB, Oakes CC, Andrulis M, Lier A, Milsom MD, Witte T, Gu L, Kim-Wanner SZ, Schirmacher P, Wulfert M, Gattermann N, Lübbert M, Rosenbauer F, Rehli M, Bullinger L, Weichenhan D, Plass C. Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia. Genome Med 2014; 6:34. [PMID: 24944583 PMCID: PMC4062060 DOI: 10.1186/gm551] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/25/2014] [Indexed: 12/13/2022] Open
Abstract
Background Aberrant DNA methylation is frequently found in human malignancies including acute myeloid leukemia (AML). While most studies focus on later disease stages, the onset of aberrant DNA methylation events and their dynamics during leukemic progression are largely unknown. Methods We screened genome-wide for aberrant CpG island methylation in three disease stages of a murine AML model that is driven by hypomorphic expression of the hematopoietic transcription factor PU.1. DNA methylation levels of selected genes were correlated with methylation levels of CD34+ cells and lineage negative, CD127-, c-Kit+, Sca-1+ cells; common myeloid progenitors; granulocyte-macrophage progenitors; and megakaryocyte-erythroid progenitors. Results We identified 1,184 hypermethylated array probes covering 762 associated genes in the preleukemic stage. During disease progression, the number of hypermethylated genes increased to 5,465 in the late leukemic disease stage. Using publicly available data, we found a significant enrichment of PU.1 binding sites in the preleukemic hypermethylated genes, suggesting that shortage of PU.1 makes PU.1 binding sites in the DNA accessible for aberrant methylation. Many known AML associated genes such as RUNX1 and HIC1 were found among the preleukemic hypermethylated genes. Nine novel hypermethylated genes, FZD5, FZD8, PRDM16, ROBO3, CXCL14, BCOR, ITPKA, HES6 and TAL1, the latter four being potential PU.1 targets, were confirmed to be hypermethylated in human normal karyotype AML patients, underscoring the relevance of the mouse model for human AML. Conclusions Our study identified early aberrantly methylated genes as potential contributors to onset and progression of AML.
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Affiliation(s)
- Miriam Sonnet
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Rainer Claus
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany ; Department of Hematology/Oncology, University Medical Center, D-79106 Freiburg, Germany
| | - Natalia Becker
- Division of Biostatistics, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Manuela Zucknick
- Division of Biostatistics, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Jana Petersen
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Daniel B Lipka
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Christopher C Oakes
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Mindaugas Andrulis
- Department of General Pathology, Institute of Pathology, University Heidelberg, D-69120 Heidelberg, Germany
| | - Amelie Lier
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Michael D Milsom
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Tania Witte
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Lei Gu
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany ; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Soo-Zin Kim-Wanner
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Peter Schirmacher
- Department of General Pathology, Institute of Pathology, University Heidelberg, D-69120 Heidelberg, Germany
| | - Michael Wulfert
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine University, D-40225 Düsseldorf, Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine University, D-40225 Düsseldorf, Germany
| | - Michael Lübbert
- Department of Hematology/Oncology, University Medical Center, D-79106 Freiburg, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, Westfälische Wilhelms Universität, D-48149 Münster, Germany
| | - Michael Rehli
- Department of Hematology and Oncology, University Hospital Regensburg, D-93042 Regensburg, Germany
| | - Lars Bullinger
- Department of Internal Medicine III, University of Ulm, D-89081 Ulm, Germany
| | - Dieter Weichenhan
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Christoph Plass
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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8
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Plass C, Pfister SM, Lindroth AM, Bogatyrova O, Claus R, Lichter P. Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat Rev Genet 2013; 14:765-80. [DOI: 10.1038/nrg3554] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Florean C, Schnekenburger M, Grandjenette C, Dicato M, Diederich M. Epigenomics of leukemia: from mechanisms to therapeutic applications. Epigenomics 2012; 3:581-609. [PMID: 22126248 DOI: 10.2217/epi.11.73] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Leukemogenesis is a multistep process in which successive transformational events enhance the ability of a clonal population arising from hematopoietic progenitor cells to proliferate, differentiate and survive. Clinically and pathologically, leukemia is subdivided into four main categories: chronic lymphocytic leukemia, chronic myeloid leukemia, acute lymphocytic leukemia and acute myeloid leukemia. Leukemia has been previously considered only as a genetic disease. However, in recent years, significant advances have been made in the elucidation of the leukemogenesis-associated processes. Thus, we have come to understand that epigenetic alterations including DNA methylation, histone modifications and miRNA are involved in the permanent changes of gene expression controlling the leukemia phenotype. In this article, we will focus on the epigenetic defects associated with leukemia and their implications as biomarkers for diagnostic, prognostic and therapeutic applications.
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Affiliation(s)
- Cristina Florean
- Laboratoire de Biologie Moléculaire et Cellulaire de Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg
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10
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Claus R, Hackanson B, Poetsch AR, Zucknick M, Sonnet M, Blagitko-Dorfs N, Hiller J, Wilop S, Brümmendorf TH, Galm O, Platzbecker U, Byrd JC, Döhner K, Döhner H, Lübbert M, Plass C. Quantitative analyses of DAPK1 methylation in AML and MDS. Int J Cancer 2011; 131:E138-42. [PMID: 21918973 DOI: 10.1002/ijc.26429] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 09/05/2011] [Indexed: 12/25/2022]
Abstract
Aberrant DNA methylation and concomitant transcriptional silencing of death-associated protein kinase 1 (DAPK1) have been demonstrated to be key pathogenic events in chronic lymphocytic leukemia (CLL). In acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), however, the presence of elevated DNA methylation levels has been a matter of continued controversy. Several studies demonstrated highly variable frequencies of DAPK1 promoter methylation by the use of methylation-specific PCR (MSP). By quantitative high-resolution assessment, we demonstrate that aberrant DNA methylation is an extremely rare event in this region. We observed elevated levels just in one out of 246 (0.4%) AML patients, all 42 MDS patients were unmethylated. In conclusion, we present a refined DAPK1 methylation analysis in a large representative patient cohort of AML and MDS patients proofing almost complete absence of elevated DNA methylation. Our results highlight the importance of quantitative measurements for translational research questions on primary patient specimens, particularly.
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Affiliation(s)
- Rainer Claus
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center, DKFZ, Heidelberg, Germany
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11
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Claus R, Plass C, Armstrong SA, Bullinger L. DNA methylation profiling in acute myeloid leukemia: from recent technological advances to biological and clinical insights. Future Oncol 2011; 6:1415-31. [PMID: 20919827 DOI: 10.2217/fon.10.110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia represents a heterogeneous malignant hematological disease with a complex underlying biology suggesting multiple patterns of genetic and epigenetic alterations. Recent evidence suggests that epigenetic mechanisms, especially deregulation of DNA methylation, play an important pathogenic role in leukemogenesis and the first epigenetic drugs have entered the clinic. Therefore, an improved understanding of the impact of altered epigenetic patterns on leukemogenesis represents a pre-requisite for improved patient management and outcome. Here, we provide an overview of current advances in deciphering the leukemic epigenome and its clinical relevance. Recent high-throughput analyses and genome-wide studies provide an optimal starting point for future epigenetic and integrative analyses that will further the development and use of predictive and prognostic epigenetic markers in acute myeloid leukemia.
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Affiliation(s)
- Rainer Claus
- Department of Epigenomics & Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
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12
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Abstract
There is growing evidence that aberrant gene expression in cancer is linked to epigenetic deregulation like promoter cytosine methylation in CpG-islands. In this issue of Cancer Cell, Figueroa et al. show that genome-wide promoter DNA methylation profiling reveals unique AML subgroups and methylation patterns that are associated with clinical outcome.
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Affiliation(s)
- Lars Bullinger
- Department of Internal Medicine III, University of Ulm, 89081 Ulm, Germany
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13
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Abstract
Epigenetics refers to a stable, mitotically perpetuated regulatory mechanism of gene expression without an alteration of the coding sequence. Epigenetic mechanism include DNA methylation and histone tail modifications. Epigenetic regulation is part of physiologic development and becomes abnormal in neoplasia, where silencing of critical genes by DNA methylation or histone deacetylation can contribute to leukemogenesis as an alternative to deletion or loss-of-function mutation. In acute myelogenous leukemia (AML), aberrant DNA methylation can be observed in multiple functionally relevant genes such as p15, p 73, E-cadherin, ID 4, RARbeta2. Abnormal activities of histone tail-modifying enzymes have also been seen in AML, frequently as a direct result of chromosomal translocations. It is now clear that these epigenetic changes play a significant role in development and progression of AML, and thus constitute important targets of therapy. The aim of targeting epigenetic effector protein or "epigenetic therapy" is to reverse epigenetic silencing and reactive various genes to induce a therapeutic effect such as differentiation, growth arrest, or apoptosis. Recent clinical studies have shown the relative safety and efficacy of such epigenetic therapies.
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Affiliation(s)
- Yasuhiro Oki
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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14
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Brown KW, Power F, Moore B, Charles AK, Malik KTA. Frequency and timing of loss of imprinting at 11p13 and 11p15 in Wilms' tumor development. Mol Cancer Res 2008; 6:1114-23. [PMID: 18644976 DOI: 10.1158/1541-7786.mcr-08-0002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epigenetic changes occur frequently in Wilms' tumor (WT), especially loss of imprinting (LOI) of IGF2/H19 at 11p15. Our previous results have identified imprinted transcripts (WT1-AS and AWT1) from the WT1 locus at 11p13 and showed LOI of these in some WTs. In this article, we set out to test the relationship between LOI at 11p13 and 11p15 and their timing in WT progression relative to other genetic changes. We found a higher level (83%) of 11p13 LOI in WT than of 11p15 LOI (71%). There was no correlation between methylation levels at the 11p13 and 11p15 differentially methylated regions or between allelic expression of WT1-AS/AWT1 and IGF2. Interestingly, retention of normal imprinting at 11p13 was associated with a small group of relatively late-onset, high-stage WTs. An examination of genetic and epigenetic alterations in nephrogenic rests, which are premalignant WT precursors, showed that LOI at both 11p13 and 11p15 occurred before either 16q loss of heterozygosity (LOH) or 7p LOH. This suggests that these LOH events are very unlikely to be a cause of LOI but that LOH may act by potentiating the effects of overexpression of IGF2 and/or WT1-AS/AWT1 that result from LOI.
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Affiliation(s)
- Keith W Brown
- Department of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom.
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Abstract
Acute myeloid leukemia (AML) is a disease characterized by uncontrolled proliferation of clonal neoplastic hematopoietic precursor cells. This leads to the disruption of normal hematopoiesis and bone marrow failure. Major breakthroughs in the past have contributed to our understanding of the genetic failures and the changed biology in AML cells that underlie the initiation and progression of the disease. It is now recognized that not only genetic but also epigenetic alterations are similarly important in this process. Since these alterations do not change the DNA sequences and are pharmacologically reversible, they have been regarded as optimal targets for what is now known as epigenetic therapy. In this review, we will discuss our current understanding of normal epigenetic processes, outline our knowledge of epigenetic alterations in AML, and discuss how this information is being used to improve current therapy of this disease.
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16
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DNA hypermethylation and epigenetic silencing of the tumor suppressor gene, SLC5A8, in acute myeloid leukemia with the MLL partial tandem duplication. Blood 2008; 112:2013-6. [PMID: 18566324 DOI: 10.1182/blood-2008-01-128595] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Posttranslationally modified histones and DNA hypermethylation frequently interplay to deregulate gene expression in cancer. We report that acute myeloid leukemia (AML) with an aberrant histone methyltransferase, the mixed lineage leukemia partial tandem duplication (MLL-PTD), exhibits increased global DNA methylation versus AML with MLL-wildtype (MLL-WT; P = .02). Among the differentially methylated genes, the SLC5A8 tumor suppressor gene (TSG) was more frequently hypermethylated (P = .003). In MLL-PTD(+) cell lines having SLC5A8 promoter hypermethylation, incubation with decitabine activated SLC5A8 expression. Ectopic SLC5A8 expression enhanced histones H3 and H4 acetylation in response to the histone deacetylase inhibitor, valproate, consistent with the encoded protein-SMCT1-short-chain fatty acid transport function. In addition, enhanced cell death was observed in SMCT1-expressing MLL-PTD(+) AML cells treated with valproate. Within the majority of MLL-PTD AML is a mechanism in which DNA hypermethylation silences a TSG that, together with MLL-PTD, can contribute further to aberrant chromatin remodeling and altered gene expression.
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17
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Klisovic RB, Stock W, Cataland S, Klisovic MI, Liu S, Blum W, Green M, Odenike O, Godley L, Burgt JV, Van Laar E, Cullen M, Macleod AR, Besterman JM, Reid GK, Byrd JC, Marcucci G. A phase I biological study of MG98, an oligodeoxynucleotide antisense to DNA methyltransferase 1, in patients with high-risk myelodysplasia and acute myeloid leukemia. Clin Cancer Res 2008; 14:2444-9. [PMID: 18413836 DOI: 10.1158/1078-0432.ccr-07-1320] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Epigenetic silencing via aberrant promoter DNA hypermethylation of normal genes has been described as a leukemogenic mechanism in myelodysplastic syndromes (MDS) and acute myeloid leukemias (AML). We hypothesized that MG98, an oligonucleotide antisense to DNA methyltransferase 1 (DNMT1), could reverse malignant phenotypes by down-regulating DNMT1 and inducing reexpression of hypermethylated genes. This phase I study was conducted to determine a biologically effective dose and describe the safety of MG98 in MDS/AML. EXPERIMENTAL DESIGN Twenty-three patients with MDS (n = 11) and AML (n = 12) were enrolled. Biologically effective dose was defined as the dose at which > or =50% of patients experienced >50% reduction in DNMT1 expression with acceptable toxicity. Escalating doses of MG98 were administered according to two schedules (2-hour i.v. bolus followed by 5-day continuous i.v. infusion every 14 days, or 14-day continuous i.v. infusion every 21 days). RESULTS DNMT1 down-regulation was observed in 8 patients. However, biologically effective dose was not reached. Reexpression of target genes (P15, WIT1, and ER) was observed in 12 patients but did not correlate with DNMT1 down-regulation. Escalation was stopped due to dose-limiting toxicities (bone pain, nausea, and fever). No objective clinical response was observed. Disease stabilization occurred in 6 (26%) patients. CONCLUSIONS No pharmacodynamic or clinical activity was observed at MG98 doses and schedules administered. Despite this, pursuing DNMT1 down-regulation remains a sound approach for targeting aberrant epigenetics in AML/MDS. Future studies with different formulation and/or doses and schedules will be required to ensure efficient MG98 intracellular uptake and fully evaluate its therapeutic potential.
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Affiliation(s)
- Rebecca B Klisovic
- Division of Hematology and Oncology, Department of Medicine, The Ohio State University, Columbus, OH 43210, USA
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18
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Dallosso AR, Hancock AL, Malik S, Salpekar A, King-Underwood L, Pritchard-Jones K, Peters J, Moorwood K, Ward A, Malik KTA, Brown KW. Alternately spliced WT1 antisense transcripts interact with WT1 sense RNA and show epigenetic and splicing defects in cancer. RNA (NEW YORK, N.Y.) 2007; 13:2287-99. [PMID: 17940140 PMCID: PMC2080606 DOI: 10.1261/rna.562907] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Many mammalian genes contain overlapping antisense RNAs, but the functions and mechanisms of action of these transcripts are mostly unknown. WT1 is a well-characterized developmental gene that is mutated in Wilms' tumor (WT) and acute myeloid leukaemia (AML) and has an antisense transcript (WT1-AS), which we have previously found to regulate WT1 protein levels. In this study, we show that WT1-AS is present in multiple spliceoforms that are usually expressed in parallel with WT1 RNA in human and mouse tissues. We demonstrate that the expression of WT1-AS correlates with methylation of the antisense regulatory region (ARR) in WT1 intron 1, displaying imprinted monoallelic expression in normal kidney and loss of imprinting in WT. However, we find no evidence for imprinting of mouse Wt1-as. WT1-AS transcripts are exported into the cytoplasm and form heteroduplexes with WT1 mRNA in the overlapping region in WT1 exon 1. In AML, there is often abnormal splicing of WT1-AS, which may play a role in the development of this malignancy. These results show that WT1 encodes conserved antisense RNAs that may have an important regulatory role in WT1 expression via RNA:RNA interactions, and which can become deregulated by a variety of mechanisms in cancer.
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Affiliation(s)
- Anthony R Dallosso
- CLIC Sargent Research Unit, Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
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19
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Plass C, Smiraglia DJ. Genome-wide Analysis of DNA Methylation Changes in Human Malignancies. Curr Top Microbiol Immunol 2006; 310:179-98. [PMID: 16909911 DOI: 10.1007/3-540-31181-5_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation is an epigenetic modification of the DNA sequence and thus does not change the genetic code but affects chromosomal stability and gene expression. DNA methylation patterns are heritable and can be passed on to the daughter cell. In this review, we briefly summarize our current knowledge on normal DNA methylation patterns and move on to discuss the current state of the field with respect to altered DNA methylation in cancer. We make a special attempt to address current questions relating to genome-wide DNA methylation patterns. Since DNA methylation is used as a therapeutic target in clinical studies, it is of utmost importance to define potential target sequences that could be used as diagnostic or prognostic markers. We conclude the review by outlining possible scenarios that may explain tumor type-specific DNA methylation patterns described by assays evaluating genome-wide levels of DNA methylation.
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Affiliation(s)
- C Plass
- Division of Human Cancer Genetics, The Ohio State University, Tzagournis Medical Research Facility, Columbus 43210, USA.
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20
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Parcells BW, Ikeda AK, Simms-Waldrip T, Moore TB, Sakamoto KM. FMS-like tyrosine kinase 3 in normal hematopoiesis and acute myeloid leukemia. Stem Cells 2006; 24:1174-84. [PMID: 16410383 DOI: 10.1634/stemcells.2005-0519] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ligand-mediated activation of the FMS-like tyrosine kinase 3 (FLT3) receptor is important for normal proliferation of primitive hematopoietic cells. However, activating mutations in FLT3 induce ligand-independent downstream signaling that promotes oncogenesis through pathways involved in proliferation, differentiation, and survival. FLT3 mutations are identified as the most frequent genetic abnormality in acute myeloid leukemia and are also observed in other leukemias. Multiple small-molecule inhibitors are under development to target aberrant FLT3 activity that confers a poor prognosis in patients.
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Affiliation(s)
- Bertrand W Parcells
- Division of Hematology-Oncology, Department of Pediatrics, Mattel Children's Hospital, Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
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21
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Abstract
Epigenetic mechanisms including DNA and histone modifications result in silencing of genes without changing the coding sequence of the gene. Even though these events are heritable, they are potentially reversible, thus opening up opportunities for therapeutic intervention. The importance of epigenetic changes in human cancer is only now being recognized in the medical community. A series of discoveries over the last four decades has thrust epigenetics into the forefront of new drug discoveries. Three systems--DNA methylation, RNA-associated silencing, and histone modification--are used to initiate and sustain epigenetic silencing. Current knowledge suggests that agents that intervene in this process by "turning back on" silenced genes may represent a significant advancement in treating many forms of cancer. In addition, changed patterns of methylation can be detected with a high degree of sensitivity thus providing clinicians with prognostic information.
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Affiliation(s)
- Peter A Jones
- Department of Urology, University of Southern California/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA 90089-9181, USA.
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22
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Wang Y, Yu Q, Cho AH, Rondeau G, Welsh J, Adamson E, Mercola D, McClelland M. Survey of differentially methylated promoters in prostate cancer cell lines. Neoplasia 2005; 7:748-60. [PMID: 16207477 PMCID: PMC1501885 DOI: 10.1593/neo.05289] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 04/15/2005] [Accepted: 04/22/2005] [Indexed: 12/31/2022]
Abstract
DNA methylation and copy number in the genomes of three immortalized prostate epithelial and five cancer cell lines (LNCaP, PC3, PC3M, PC3M-Pro4, and PC3M-LN4) were compared using a microarray-based technique. Genomic DNA is cut with a methylation-sensitive enzyme HpaII, followed by linker ligation, polymerase chain reaction (PCR) amplification, labeling, and hybridization to an array of promoter sequences. Only those parts of the genomic DNA that have unmethylated restriction sites within a few hundred base pairs generate PCR products detectable on an array. Of 2732 promoter sequences on a test array, 504 (18.5%) showed differential hybridization between immortalized prostate epithelial and cancer cell lines. Among candidate hypermethylated genes in cancer-derived lines, there were eight (CD44, CDKN1A, ESR1, PLAU, RARB, SFN, TNFRSF6, and TSPY) previously observed in prostate cancer and 13 previously known methylation targets in other cancers (ARHI, bcl-2, BRCA1, CDKN2C, GADD45A, MTAP, PGR, SLC26A4, SPARC, SYK, TJP2, UCHL1, and WIT-1). The majority of genes that appear to be both differentially methylated and differentially regulated between prostate epithelial and cancer cell lines are novel methylation targets, including PAK6, RAD50, TLX3, PIR51, MAP2K5, INSR, FBN1, and GG2-1, representing a rich new source of candidate genes used to study the role of DNA methylation in prostate tumors.
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Affiliation(s)
- Yipeng Wang
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - Qiuju Yu
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - Ann H Cho
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - Gaelle Rondeau
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - John Welsh
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - Eileen Adamson
- The Burnham Institute, Cancer Research Center, La Jolla, CA, USA
| | - Dan Mercola
- Department of Pathology, University of California at Irvine, Irvine, CA 92697, USA
| | - Michael McClelland
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
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23
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Hackanson B, Guo Y, Lübbert M. The silence of the genes: epigenetic disturbances in haematopoietic malignancies. Expert Opin Ther Targets 2005; 9:45-61. [PMID: 15757481 DOI: 10.1517/14728222.9.1.45] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cancer-associated disturbances of regulated DNA methylation include both global hypomethylation and gene-specific (often even cancer-specific) hypermethylation. Both coexist and have become the subject of intense investigation. In haematological neoplasias, distinct sets of genes, including the p15/INK4b cell cycle inhibitor (mostly in myeloid malignancies) as well as p16/INK4a (only very infrequently in myeloid neoplasia), have been well characterised as to incidence of hypermethylation, concurrent gene inactivation and their re-expression following treatment with DNA methylation inhibitors. Several genes frequently methylated in haematological neoplasias have been studied with respect to their prognostic value. With the advance of low-dose schedules of demethylating agents (explored particularly in the elderly patient population) the rationale for reverting the 'hyper-methylator phenotype' has also prompted in vivo studies of gene reactivation following this type of treatment. However, ubiquitous surrogate markers for the efficacy of this type of treatment need to be developed. These may include reactivated haemoglobin F (HbF), as demethylating agents can result in clinically meaningful induction of HbF in patients with haemoglobinopathies. Because 'cancer testis antigens', which provide powerful signals for T cell cytotoxic activity on solid tumour cells, are usually silenced in leukaemia but can be reactivated in vitro and in vivo, they provide a rationale for an immuno-modulatory effect of demethylating therapy.
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Affiliation(s)
- Björn Hackanson
- University of Freiburg Medical Center, Department of Hematology/Oncology, 79106 Freiburg, Germany
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24
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Chen CY, Tsay W, Tang JL, Shen HL, Lin SW, Huang SY, Yao M, Chen YC, Shen MC, Wang CH, Tien HF. SOCS1 methylation in patients with newly diagnosed acute myeloid leukemia. Genes Chromosomes Cancer 2003; 37:300-5. [PMID: 12759928 DOI: 10.1002/gcc.10222] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The proliferation and differentiation of hematopoietic precursor cells depend on various cytokines. The suppressor of cytokine signaling-1 (SOCS1) down-regulates Janus kinases/signal transducers and activators of transcription (JAK/STAT) pathway activity and inhibits the biological effects of cytokines. SOCS1 has been shown to have tumor-suppressor activity, and methylation of this gene, resulting in transcriptional silencing, has been found in 65% of hepatocellular carcinoma and has been suggested to play an important role in the development of the cancer. The methylation status of the SOCS1 gene in acute myeloid leukemia (AML) has not been reported before. In this study, we analyzed SOCS1 methylation in 89 patients with newly diagnosed AML and correlated the result with immunophenotypes, cytogenetics, clinical features, and treatment outcome. SOCS1 methylation was found in the leukemic cells from 53 patients (60%). Thirteen (76%) of the 17 patients with t(15;17) had SOCS1 methylation, whereas this gene was methylated in only one (11%) of the nine patients with t(8;21). The frequencies of SOCS1 methylation among various cytogenetic subgroups differed significantly (P = 0.014). Other clinical and laboratory parameters and the disease-free survival and overall survival were similar between patients with and without SOCS1 methylation. In conclusion, SOCS1 methylation occurs in more than half of AML cases, correlates with cytogenetic abnormalities, and may play an important role in the development of subsets of AML.
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Affiliation(s)
- Chien-Yuan Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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25
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Abstract
The DNA methylation profile of cancer cells is frequently characterized by global hypomethylation and simultaneous hypermethylation of selected CpG island gene promoters. In recent years, the epigenetic phenomenon of DNA promoter methylation has gained increasing recognition as an important mechanism for transcriptional inactivation of cancer related genes. Studies on both liquid and solid tumors have revealed myriad aberrant methylation events, some of which may provide important clues to the pathogenesis of these tumors. The identification of these methylation alterations and elucidation of the mechanistic events surrounding them are of prime importance, as the methylation status of cancer cells can now be manipulated in vivo with demethylating chemotherapeutics.
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Affiliation(s)
- Laura J Rush
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA.
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26
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Rush LJ, Plass C. Restriction landmark genomic scanning for DNA methylation in cancer: past, present, and future applications. Anal Biochem 2002; 307:191-201. [PMID: 12202234 DOI: 10.1016/s0003-2697(02)00033-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The field of molecular biology was revolutionized by the advent of gel electrophoresis. Restriction landmark genomic scanning (RLGS) is a type of two-dimensional electrophoresis employed in the genome-wide assessment of genomic alterations. RLGS has been used to study genetic and epigenetic changes in normal tissues, primary tumors, cancer cell lines, and various organisms such as mice, rats, hamsters, bacteria, and plants. An RLGS profile displays over 2000 radiolabeled restriction landmark sites in a single assay. When conducted with methylation-sensitive restriction enzymes whose sites are preferentially located in CpG island regulatory regions, RLGS becomes a very versatile tool for the investigation of both normal and aberrant methylation patterns. Early studies performed on tumor DNA were mainly descriptive in nature, essentially a catalogue of loci that were changed to varying degrees in different tumor types. Over time, as investigators have become more proficient with RLGS and have undertaken high-throughput studies, the need for efficient cloning, imaging, and analysis systems has become paramount. Current studies focus on identifying specific genes and pathways involved in deregulated methylation in cancer. As such, RLGS analysis of tumor samples has made tremendous contributions to our understanding of the role of DNA methylation in cancer. Future directions will take advantage of the abundant genomic sequence data available to link all of the RLGS loci to genes and create biologically relevant methylation profiles of cancer. This review discusses practical considerations of using RLGS as a genome scanning tool and the past, present, and future applications in cancer biology.
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Affiliation(s)
- Laura J Rush
- Department of Veterinary Biosciences, Division of Human Cancer Genetics, The Ohio State University, Columbus, OH 43210, USA.
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27
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Smiraglia DJ, Plass C. The study of aberrant methylation in cancer via restriction landmark genomic scanning. Oncogene 2002; 21:5414-26. [PMID: 12154404 DOI: 10.1038/sj.onc.1205608] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Restriction landmark genomic scanning (RLGS) has been used to study DNA methylation in cancer for nearly a decade. The strong bias of RLGS for assessing the methylation state of CpG islands genome wide makes this an attractive technique to study both hypo- and hypermethylation of regions of the genome likely to harbor genes. RLGS has been used successfully to identify regions of hypomethylation, candidate tumor suppressor genes, correlations between hypermethylation events and clinical factors, and quantification of hypermethylation in a multitude of malignancies. This review will examine the major uses of RLGS in the study of aberrant methylation in cancer and discuss the significance of some of the findings.
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Affiliation(s)
- Dominic J Smiraglia
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, OH 43210, USA.
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28
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French SW, Dawson DW, Miner MD, Doerr JR, Malone CS, Wall R, Teitell MA. DNA methylation profiling: a new tool for evaluating hematologic malignancies. Clin Immunol 2002; 103:217-30. [PMID: 12173296 DOI: 10.1006/clim.2002.5186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Samuel W French
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, 675 Charles E. Young Dr. South, MRL 4-760, Los Angeles, CA 90095-1732, USA
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29
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Majumder S, Ghoshal K, Datta J, Bai S, Dong X, Quan N, Plass C, Jacob ST. Role of de novo DNA methyltransferases and methyl CpG-binding proteins in gene silencing in a rat hepatoma. J Biol Chem 2002; 277:16048-58. [PMID: 11844796 PMCID: PMC2241740 DOI: 10.1074/jbc.m111662200] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The expression of metallothionein-I (MT-I), a known antioxidant, was suppressed in a transplanted rat hepatoma because of promoter methylation and was induced by heavy metals only after demethylation by 5-azacytidine (5-AzaC). Treatment of the tumor-bearing rats with 5-AzaC resulted in significant regression of the hepatoma. When the inhibitor-treated tumor was allowed to grow in a new host, MT-I promoter was remethylated, which suggested de novo methylation. The activities of both de novo (3-fold) and maintenance DNA methyltransferases (DNMT) (5-fold) were higher in the hepatoma than in the host liver. The mRNA levels of the de novo methyltransferases DNMT3a and DNMT3b were 3- and 6-fold higher, respectively, in the tumor implicating transcriptional up-regulation of these two genes in this tissue. Immunohistochemical analysis showed exclusive localization of DNMT3a in the nuclei of both the liver and hepatoma, whereas DNMT3b was detected in the nuclei as well as the cytoplasm. Immunoblot assay showed that the levels of DNMT1, DNMT3a, and DNMT3b proteins in the hepatoma were 5-, 10-, and 4-fold higher, respectively, than in the liver. The mRNA level of the major methyl CpG-binding protein (MeCP2) was 8-fold higher in the tumor compared with the liver. Immunohistochemical studies showed that MeCP2 is localized exclusively in the nuclei of both tissues. A chromatin immunoprecipitation assay demonstrated that MeCP2 was associated with the MT-I promoter in the hepatoma implicating its involvement in repressing the methylated promoter. Analysis of the DNA isolated from the liver and hepatoma by RLGS-M (restriction landmark genomic scanning with methylation-sensitive enzyme) (NotI) showed that many genes in addition to MT-I were methylated in the hepatoma. These data demonstrate suppression of the MT-I gene and probably other genes in a solid tumor by promoter methylation and have provided potential molecular mechanisms for the altered methylation profile of the genes in this tumor.
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Affiliation(s)
- Sarmila Majumder
- Department of Molecular and Cellular Biochemistry, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
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30
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Frühwald MC, Plass C. Global and gene-specific methylation patterns in cancer: aspects of tumor biology and clinical potential. Mol Genet Metab 2002; 75:1-16. [PMID: 11825059 DOI: 10.1006/mgme.2001.3265] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Heritable alterations of DNA that do not affect the base pair sequence itself but nevertheless regulate the predetermined activity of genes are referred to as epigenetic. Epigenetic mechanisms comprise diverse phenomena including stable feedback loops, nuclear compartmentalization, differential replication timing, heritable chromatin structures, and, foremost, DNA cytosine methylation (1-3). DNA cytosine methylation has recently gained major attention in the field of basic molecular biology as well as in studies of human diseases including cancer. Changes in DNA methylation patterns in human malignancies have been shown to contribute to carcinogenesis in multiple ways. Both hypo- and hypermethylation events have been described in various neoplasias leading to chromosomal instability and transcriptional gene silencing. DNA methylation research has entered the clinical arena and methylation patterns have become a major focus of clinicians seeking novel prognostic factors and therapeutic targets. The following minireview covers aspects of the basic molecular biology of DNA methylation and summarizes its importance in human cancers.
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Affiliation(s)
- Michael C Frühwald
- Klinik und Poliklinik für Kinderheilkunde, Universitätsklinikum Münster, Albert-Schweitzer-Strasse 33, 48149 Münster, Germany.
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31
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Plass C, Soloway PD. DNA methylation, imprinting and cancer. Eur J Hum Genet 2002; 10:6-16. [PMID: 11896451 DOI: 10.1038/sj.ejhg.5200768] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2001] [Revised: 12/05/2001] [Accepted: 12/06/2001] [Indexed: 11/09/2022] Open
Abstract
It is well known that a variety of genetic changes influence the development and progression of cancer. These changes may result from inherited or spontaneous mutations that are not corrected by repair mechanisms prior to DNA replication. It is increasingly clear that so called epigenetic effects that do not affect the primary sequence of the genome also play an important role in tumorigenesis. This was supported initially by observations that cancer genomes undergo changes in their methylation state and that control of parental allele-specific methylation and expression of imprinted loci is lost in several cancers. Many loci acquiring aberrant methylation in cancers have since been identified and shown to be silenced by DNA methylation. In many cases, this mechanism of silencing inactivates tumour suppressors as effectively as frank mutation and is one of the cancer-predisposing hits described in Knudson's two hit hypothesis. In contrast to mutations which are essentially irreversible, methylation changes are reversible, raising the possibility of developing therapeutics based on restoring the normal methylation state to cancer-associated genes. Development of such therapeutics will require identifying loci undergoing methylation changes in cancer, understanding how their methylation influences tumorigenesis and identifying the mechanisms regulating the methylation state of the genome. The purpose of this review is to summarise what is known about these issues.
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Affiliation(s)
- Christoph Plass
- Division of Human Cancer Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA.
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Dai Z, Lakshmanan RR, Zhu WG, Smiraglia DJ, Rush LJ, Frühwald MC, Brena RM, Li B, Wright FA, Ross P, Otterson GA, Plass C. Global methylation profiling of lung cancer identifies novel methylated genes. Neoplasia 2001; 3:314-23. [PMID: 11571631 PMCID: PMC1505864 DOI: 10.1038/sj.neo.7900162] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2001] [Accepted: 04/26/2001] [Indexed: 12/25/2022] Open
Abstract
Epigenetic changes, including DNA methylation, are a common finding in cancer. In lung cancers methylation of cytosine residues may affect tumor initiation and progression in several ways, including the silencing of tumor suppressor genes through promoter methylation and by providing the targets for adduct formation of polycyclic aromatic hydrocarbons present in combustion products of cigarette smoke. Although the importance of aberrant DNA methylation is well established, the extent of DNA methylation in lung cancers has never been determined. Restriction landmark genomic scanning (RLGS) is a highly reproducible two-dimensional gel electrophoresis that allows the determination of the methylation status of up to 2000 promoter sequences in a single gel. We selected 1184 CpG islands for RLGS analysis and determined their methylation status in 16 primary non-small cell lung cancers. Some tumors did not show methylation whereas others showed up to 5.3% methylation in all CpG islands of the profile. Cloning of 21 methylated loci identified 11 genes and 6 ESTs. We demonstrate that methylation is part of the silencing process of BMP3B in primary tumors and lung cancer cell lines.
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Affiliation(s)
- Zunyan Dai
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH
- Department of Pathology, The Ohio State University, Columbus, OH
| | - Romola R Lakshmanan
- Division of Hematology/Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Wei-Guo Zhu
- Division of Hematology/Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Dominic J Smiraglia
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH
| | - Laura J Rush
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
| | - Michael C Frühwald
- Westfälische Wilhelms-Universität Münster, Klinik und Poliklinik für Kinderheilkunde-Pädiatrische Hämatologie/Onkologie, Münster, Germany
| | - Romulo M Brena
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH
- Department of Molecular Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Bin Li
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH
| | - Fred A Wright
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH
| | - Patrick Ross
- Department of Clinical Surgery, The Ohio State University, Columbus, OH
| | - Gregory A Otterson
- Division of Hematology/Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Christoph Plass
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH
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Abstract
DNA methylation is not just for basic scientists any more. There is a growing awareness in the medical field that having the correct pattern of genomic methylation is essential for healthy cells and organs. If methylation patterns are not properly established or maintained, disorders as diverse as mental retardation, immune deficiency, and sporadic or inherited cancers may follow. Through inappropriate silencing of growth regulating genes and simultaneous destabilisation of whole chromosomes, methylation defects help create a chaotic state from which cancer cells evolve. Methylation defects are present in cells before the onset of obvious malignancy and therefore cannot be explained simply as a consequence of a deregulated cancer cell. Researchers are now able to detect with exquisite sensitivity the cells harbouring methylation defects, sometimes months or years before the time when cancer is clinically detectable. Furthermore, aberrant methylation of specific genes has been directly linked with the tumour response to chemotherapy and patient survival. Advances in our ability to observe the methylation status of the entire cancer cell genome have led us to the unmistakable conclusion that methylation abnormalities are far more prevalent than expected. This methylomics approach permits the integration of an ever growing repertoire of methylation defects with the genetic alterations catalogued from tumours over the past two decades. Here we discuss the current knowledge of DNA methylation in normal cells and disease states, and how this relates directly to our current understanding of the mechanisms by which tumours arise.
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Affiliation(s)
- J F Costello
- The Brain Tumor Research Center and the Department of Neurological Surgery, University of California, 2340 Sutter, Room N261, San Francisco, San Francisco, CA 94143-0875, USA.
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Costello JF, Plass C, Cavenee WK. Aberrant methylation of genes in low-grade astrocytomas. Brain Tumor Pathol 2001; 17:49-56. [PMID: 11210171 DOI: 10.1007/bf02482735] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The underlying basis of the malignant progression of astrocytomas is a specific and cumulative series of genetic alterations, most of which are confined to high-grade tumors. In contrast, a proportion of low-grade astrocytomas have a relatively normal-appearing genome when examined with standard genetic screening methods. These methods do not detect epigenetic events such as aberrant methylation of CpG island, which result in transcriptional silencing of important cancer genes. To determine if aberrant methylation is involved in the early stages of astrocytoma development, we assessed the methylation status of 1,184 genes in each of 14 low-grade astrocytomas using restriction landmark genome scanning (RLGS). The results showed nonrandom and astrocytoma-specific patterns of aberrantly methylated genes. We estimate that an average of 1,544 CpG island-associated genes (range, 38 to 3,731) of the approximately 45,000 in the genome are aberrantly methylated in each tumor. Expression of a significant proportion of the genes could be reactivated by 5-aza-2-deoxycytidine-induced demethylation in cultured glioma cell lines. The data suggest that aberrant methylation of genes is more prevalent than genetic alterations and may have consequences for the development of low-grade astrocytomas.
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Affiliation(s)
- J F Costello
- University of California-San Francisco, The Brain Tumor Research Center, USA.
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Frühwald MC, O'Dorisio MS, Rush LJ, Reiter JL, Smiraglia DJ, Wenger G, Costello JF, White PS, Krahe R, Brodeur GM, Plass C. Gene amplification in PNETs/medulloblastomas: mapping of a novel amplified gene within the MYCN amplicon. J Med Genet 2000; 37:501-9. [PMID: 10882752 PMCID: PMC1734623 DOI: 10.1136/jmg.37.7.501] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES The pathological entity of primitive neuroectodermal tumour/medulloblastoma (PNET/MB) comprises a very heterogeneous group of neoplasms on a clinical as well as on a molecular level. We evaluated the importance of DNA amplification in medulloblastomas and other primitive neuroectodermal tumours (PNETs) of the CNS. METHOD Restriction landmark genomic scanning (RLGS), a method that allows the detection of low level amplification, was used. RLGS provides direct access to DNA sequences circumventing positional cloning efforts. Furthermore, we analysed several samples by CGH. DESIGN Twenty primary medulloblastomas, five supratentorial PNETs, and five medulloblastoma cell lines were studied. RESULTS Although our analysis confirms that gene amplification is generally a rare event in childhood PNET/MB, we found a total of 17 DNA fragments that were amplified in seven different tumours. Cloning and sequencing of several of these fragments confirmed the previous finding of MYC amplification in the cell line D341 Med and identified novel DNA sequences amplified in PNET/MB. We describe for the first time amplification of the novel gene, NAG, in a subset of PNET/MB. Despite genomic amplification, NAG was not overexpressed in the tumours studied. We have determined that NAG maps less than 50 kb 5' of DDX1 and approximately 400 kb telomeric of MYCN on chromosome 2p24. CONCLUSION We found a similar but slightly higher frequency of amplification than previously reported. We present several DNA fragments that may belong to the CpG islands of novel genes amplified in a small subset of PNET/MB. As an example we describe for the first time the amplification of NAG in the MYCN amplicon in PNET/MB.
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MESH Headings
- Blotting, Northern
- Blotting, Southern
- Brain Neoplasms/genetics
- Brain Neoplasms/pathology
- Cerebellar Neoplasms/genetics
- Cerebellar Neoplasms/pathology
- Child
- Child, Preschool
- Chromosomes, Artificial, Yeast
- Contig Mapping
- CpG Islands
- DNA Mutational Analysis
- DNA, Neoplasm/analysis
- Expressed Sequence Tags
- Female
- Gene Amplification
- Genes, myc/genetics
- Humans
- Male
- Medulloblastoma/genetics
- Medulloblastoma/pathology
- Neoplasm Proteins/genetics
- Neuroectodermal Tumors, Primitive/genetics
- Organ Specificity
- Polymerase Chain Reaction
- Polymorphism, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- M C Frühwald
- Division of Pediatric Hematology and Oncology, The Ohio State University and the Comprehensive Cancer Center, Columbus 43210, USA.
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Costello JF, Frühwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X, Wright FA, Feramisco JD, Peltomäki P, Lang JC, Schuller DE, Yu L, Bloomfield CD, Caligiuri MA, Yates A, Nishikawa R, Su Huang H, Petrelli NJ, Zhang X, O'Dorisio MS, Held WA, Cavenee WK, Plass C. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet 2000; 24:132-8. [PMID: 10655057 DOI: 10.1038/72785] [Citation(s) in RCA: 933] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CpG islands frequently contain gene promoters or exons and are usually unmethylated in normal cells. Methylation of CpG islands is associated with delayed replication, condensed chromatin and inhibition of transcription initiation. The investigation of aberrant CpG-island methylation in human cancer has primarily taken a candidate gene approach, and has focused on less than 15 of the estimated 45,000 CpG islands in the genome. Here we report a global analysis of the methylation status of 1,184 unselected CpG islands in each of 98 primary human tumours using restriction landmark genomic scanning (RLGS). We estimate that an average of 600 CpG islands (range of 0 to 4,500) of the 45,000 in the genome were aberrantly methylated in the tumours, including early stage tumours. We identified patterns of CpG-island methylation that were shared within each tumour type, together with patterns and targets that displayed distinct tumour-type specificity. The expression of many of these genes was reactivated by experimental demethylation in cultured tumour cells. Thus, the methylation of particular subsets of CpG islands may have consequences for specific tumour types.
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Affiliation(s)
- J F Costello
- [1] Ludwig Institute for Cancer Research, University of California-San Diego, La Jolla, California, USA.
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Abstract
Restriction landmark genomic scanning applied to a broad variety of cancer types can disclose tumour-specific and tumour-type-specific global methylation profiles. This and other genome-scanning approaches allows the rapid analysis of methylation profiles of thousands of genes in parallel-and promises to identify new genes critical to carcinogenesis and other biological processes.
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Smiraglia DJ, Frühwald MC, Costello JF, McCormick SP, Dai Z, Peltomäki P, O'Dorisio MS, Cavenee WK, Plass C. A new tool for the rapid cloning of amplified and hypermethylated human DNA sequences from restriction landmark genome scanning gels. Genomics 1999; 58:254-62. [PMID: 10373323 DOI: 10.1006/geno.1999.5840] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Restriction landmark genome scanning (RLGS) is an effective genome-scanning technique capable of identifying DNA amplification and aberrant DNA methylation. Previously published methods for the cloning of human DNA fragments from RLGS gels have been successful only for high-copy-number fragments (repetitive elements or DNA amplifications). We present here the first technique capable of efficiently cloning single-copy human DNA fragments ("spots") identified in RLGS profiles. This technique takes advantage of a plasmid-based, human genomic DNA, NotI/EcoRV boundary library. The library is arrayed in microtiter plates. When clones from a single plate are pooled and mixed with genomic DNA, the resultant RLGS gel is a normal profile with a defined set of spots showing enhanced intensity for that particular plate. This was performed for a set of 32 plates as well as their pooled rows and columns. Thus, we have mapped individual RLGS spots to exact plate, row, and column addresses in the library and have thereby obtained immediate access to these clones. The feasibility of the technique is demonstrated in examples of cloning methylated DNA fragments identified in human breast tumor and testicular tumor RLGS profiles and in the cloning of an amplified DNA fragment identified in a human medulloblastoma RLGS profile.
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Affiliation(s)
- D J Smiraglia
- Department of Medical Microbiology and Immunology, The Ohio State University, Columbus, Ohio 43210, USA.
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