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Christoph S, Alicia S, Fritz T, Vanessa T, Ralf K, Jin KY, Stefan L, Joachim O. The intra-tumoral heterogeneity in glioblastoma - a limitation for prognostic value of epigenetic markers? Acta Neurochir (Wien) 2023; 165:1635-1644. [PMID: 37083881 DOI: 10.1007/s00701-023-05594-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/10/2023] [Indexed: 04/22/2023]
Abstract
OBJECTIVE Epigenetic tumor features are getting into focus as prognostic markers in glioblastoma. Whether intra-tumoral heterogeneity in these epigenetic characteristics may influence prognostic value remains unclear. METHODS Of 154 patients suffering from glioblastoma, 120 patients served as reference collective, while 34 patients were compiled as test collective. MGMT, p15, and p16 promoter methylation and miRNA expression levels (miRNA-21, miRNA-24, miRNA-26a, and miRNA-181d) were measured in each tumor specimen. Serving as a statistical baseline, epigenetic heterogeneity between tumors (inter-tumoral) was estimated within a triplet of three tumor specimens from three different reference patients. For estimation of epigenetic heterogeneity within a tumor (intra-tumoral), previous results were compared to three tumor specimens within one glioblastoma of patients of the test collective. Resulting levels of heterogeneity were then correlated with survival and validated by an external TCGA data set. RESULTS Heterogeneity in MGMT promoter methylation occurred less likely in the test group compared to the reference group. No difference in heterogeneity was observed between test and reference group regarding p15 and p16 methylation. Intra-tumoral heterogeneity within the test group regarding miRNA-21, miRNA-24, miRNA-26a, and miRNA-181d expression was not distinguishable from inter-tumoral heterogeneity. A homogenously increased miRNA-21 expression was associated with reduced overall survival in the test collective. The findings could be validated by comparison with TCGA datasets. CONCLUSION Heterogeneity of epigenetic characteristics in one glioblastoma may be of the same magnitude as heterogeneity between different patients. Not only the extent of epigenetic characteristics but also the extent of intra-tumoral heterogeneity may influence survival in glioblastoma.
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Affiliation(s)
- Sippl Christoph
- Department of Neurosurgery, Faculty of Medicine, University of Saarland, Homburg/Saar, Germany.
| | - Saenz Alicia
- Department of Neurosurgery, Faculty of Medicine, University of Saarland, Homburg/Saar, Germany
| | - Teping Fritz
- Department of Neurosurgery, Faculty of Medicine, University of Saarland, Homburg/Saar, Germany
| | - Trenkpohl Vanessa
- Department of Neurosurgery, Faculty of Medicine, University of Saarland, Homburg/Saar, Germany
| | - Ketter Ralf
- Department of Neurosurgery, Faculty of Medicine, University of Saarland, Homburg/Saar, Germany
| | - Kim Yoo Jin
- Institute of Pathology, Faculty of Medicine, University of Saarland, Glockenstraße 54, Kaiserslautern, Germany
| | - Linsler Stefan
- Department of Neurosurgery, Faculty of Medicine, University of Saarland, Homburg/Saar, Germany
| | - Oertel Joachim
- Department of Neurosurgery, Faculty of Medicine, University of Saarland, Homburg/Saar, Germany
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2
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Bauman MMJ, Harrison DJ, Giesken MB, Daniels DJ. The evolving landscape of pilocytic astrocytoma: a bibliometric analysis of the top-100 most cited publications. Childs Nerv Syst 2022; 38:1271-1280. [PMID: 35352179 DOI: 10.1007/s00381-022-05503-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Pilocytic astrocytomas are the most common low-grade glioma of the central nervous system that typically occurs in children, and much research has been dedicated to characterizing their molecular features and clinical courses. We provide an overview of the current literature through the use of a bibliometric analysis of the top 100 most cited publications discussing pilocytic astrocytomas. METHODS We identified the top 100 most cited publications discussing pilocytic astrocytomas. Articles were ranked based on the number of citations. Descriptive statistics and univariate analysis were used to determine any trends or significant differences in the data. RESULTS Of the top 100 articles, 50 were basic science (50%), 34 were clinical (34%), and 16 were review (16%). The number of citations ranged from 79 to 921, with 123 being the median. The US had the most first authors and principal authors (n = 53 and n = 54, respectively). Years of publication had a left-skewed distribution and peaked during 2011 with 12 articles published in that year. Sixty percent of basic science articles investigated BRAF/MAPK pathways, while 67.6% of clinical articles focused on evaluating treatment options for pilocytic astrocytomas. Compared to basic science and clinical articles, review articles were published more recently (p < 0.001), had fewer authors (p = 0.025) and were published in journals with higher impact factors (p = 0.022). CONCLUSION Research regarding pilocytic astrocytomas has increased over the past three decades. Future directions of research point towards employing targeted therapies and discovering additional cellular pathways contributing to disease pathogenesis.
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Affiliation(s)
| | | | - Max B Giesken
- Mayo Clinic Alix School of Medicine, Rochester, MN, USA
| | - David J Daniels
- Department of Neurological Surgery, Rochester, MN, USA.
- Department of Neurological Surgery, Mayo Clinic, 200 1st St. SW, Rochester, MN, 55905, USA.
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3
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Grabowicz IE, Wilczyński B, Kamińska B, Roura AJ, Wojtaś B, Dąbrowski MJ. The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes. Sci Rep 2021; 11:15668. [PMID: 34341417 PMCID: PMC8329071 DOI: 10.1038/s41598-021-95009-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-wide studies have uncovered specific genetic alterations, transcriptomic patterns and epigenetic profiles associated with different glioma types. We have recently created a unique atlas encompassing genome-wide profiles of open chromatin, histone H3K27ac and H3Kme3 modifications, DNA methylation and transcriptomes of 33 glioma samples of different grades. Here, we intersected genome-wide atlas data with topologically associating domains (TADs) and demonstrated that the chromatin organization and epigenetic landscape of enhancers have a strong impact on genes differentially expressed in WHO low grade versus high grade gliomas. We identified TADs enriched in glioma grade-specific genes and/or epigenetic marks. We found the set of transcription factors, including REST, E2F1 and NFKB1, that are most likely to regulate gene expression in multiple TADs, containing specific glioma-related genes. Moreover, many genes associated with the cell-matrix adhesion Gene Ontology group, in particular 14 PROTOCADHERINs, were found to be regulated by long-range contacts with enhancers. Presented results demonstrate the existence of epigenetic differences associated with chromatin organization driving differential gene expression in gliomas of different malignancy.
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Affiliation(s)
- Ilona E Grabowicz
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
| | - Bartek Wilczyński
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Bożena Kamińska
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Adria-Jaume Roura
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtaś
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Michał J Dąbrowski
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
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4
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Scholz N, Kurian KM, Siebzehnrubl FA, Licchesi JDF. Targeting the Ubiquitin System in Glioblastoma. Front Oncol 2020; 10:574011. [PMID: 33324551 PMCID: PMC7724090 DOI: 10.3389/fonc.2020.574011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma is the most common primary brain tumor in adults with poor overall outcome and 5-year survival of less than 5%. Treatment has not changed much in the last decade or so, with surgical resection and radio/chemotherapy being the main options. Glioblastoma is highly heterogeneous and frequently becomes treatment-resistant due to the ability of glioblastoma cells to adopt stem cell states facilitating tumor recurrence. Therefore, there is an urgent need for novel therapeutic strategies. The ubiquitin system, in particular E3 ubiquitin ligases and deubiquitinating enzymes, have emerged as a promising source of novel drug targets. In addition to conventional small molecule drug discovery approaches aimed at modulating enzyme activity, several new and exciting strategies are also being explored. Among these, PROteolysis TArgeting Chimeras (PROTACs) aim to harness the endogenous protein turnover machinery to direct therapeutically relevant targets, including previously considered "undruggable" ones, for proteasomal degradation. PROTAC and other strategies targeting the ubiquitin proteasome system offer new therapeutic avenues which will expand the drug development toolboxes for glioblastoma. This review will provide a comprehensive overview of E3 ubiquitin ligases and deubiquitinating enzymes in the context of glioblastoma and their involvement in core signaling pathways including EGFR, TGF-β, p53 and stemness-related pathways. Finally, we offer new insights into how these ubiquitin-dependent mechanisms could be exploited therapeutically for glioblastoma.
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Affiliation(s)
- Nico Scholz
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Kathreena M. Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, United Kingdom
| | - Florian A. Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
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5
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Arthur-Farraj P, Moyon S. DNA methylation in Schwann cells and in oligodendrocytes. Glia 2020; 68:1568-1583. [PMID: 31958184 DOI: 10.1002/glia.23784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/17/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022]
Abstract
DNA methylation is one of many epigenetic marks, which directly modifies base residues, usually cytosines, in a multiple-step cycle. It has been linked to the regulation of gene expression and alternative splicing in several cell types, including during cell lineage specification and differentiation processes. DNA methylation changes have also been observed during aging, and aberrant methylation patterns have been reported in several neurological diseases. We here review the role of DNA methylation in Schwann cells and oligodendrocytes, the myelin-forming glia of the peripheral and central nervous systems, respectively. We first address how methylation and demethylation are regulating myelinating cells' differentiation during development and repair. We then mention how DNA methylation dysregulation in diseases and cancers could explain their pathogenesis by directly influencing myelinating cells' proliferation and differentiation capacities.
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Affiliation(s)
- Peter Arthur-Farraj
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sarah Moyon
- Neuroscience Initiative Advanced Science Research Center, CUNY, New York, New York
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6
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Zhao T, Afrifa J, Wang D, Yu J. Association between HIC1 promoter methylation and solid tumor: A meta-analysis. EXCLI JOURNAL 2020; 19:476-489. [PMID: 32398971 PMCID: PMC7214777 DOI: 10.17179/excli2020-1102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/27/2020] [Indexed: 01/11/2023]
Abstract
The epigenetic silencing of tumor suppressor genes by promoter methylation plays an increasingly important role in cancer research. A number of studies have reported the contribution of HIC1 promoter methylation towards the occurrence and development of solid tumors, even though HIC1 promoter methylation has also been found in normal and benign tissue samples. We sought to perform a more accurate and comprehensive meta-analysis to assess the association between HIC1 promoter methylation and cancer risk. We searched and retrieved all published studies on HIC1 promoter methylation in PubMed, Google Scholar, Embase, Cochrane Library, and Web of Science databases. After two reviewers checked the studies and extracted the necessary data independently, the meta-analysis was performed using STATA 12.0 software. A total of 14 case-control studies (949 cancer patients, 282 benign, and 371 normal controls) were included in our study. We report a significantly elevated HIC1 promoter methylation in tumor samples compared to normal (OR = 7.02, 95 % CI 3.12-15.78, P < 0.001) and benign controls (OR = 2.69, 95 % CI 1.13-6.42, P = 0.025). Subgroup analysis stratified by ethnicity showed a significantly reduced heterogeneity among North American (I2 = 0.0 %, P = 0.502) and European (I2 = 33.7 %, P = 0.183) samples. In addition, heterogeneity was significantly reduced among MSP based detection method (I2 = 36.4 %, P = 0.139) when samples were stratified based on the methylation detection methods. The overall outcome demonstrated that HIC1 promoter methylation may be involved in the occurrence and development of solid tumors and has the potential to serve as an epigenetic maker in various specific tumors.
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Affiliation(s)
- Tie Zhao
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Justice Afrifa
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China.,Department of Medical Laboratory Science, University of Cape Coast, Cape Coast, Ghana
| | - Dong Wang
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Jingcui Yu
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
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7
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Pan X, Zeng T, Yuan F, Zhang YH, Chen L, Zhu L, Wan S, Huang T, Cai YD. Screening of Methylation Signature and Gene Functions Associated With the Subtypes of Isocitrate Dehydrogenase-Mutation Gliomas. Front Bioeng Biotechnol 2019; 7:339. [PMID: 31803734 PMCID: PMC6871504 DOI: 10.3389/fbioe.2019.00339] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/30/2019] [Indexed: 02/05/2023] Open
Abstract
Isocitrate dehydrogenase (IDH) is an oncogene, and the expression of a mutated IDH promotes cell proliferation and inhibits cell differentiation. IDH exists in three different isoforms, whose mutation can cause many solid tumors, especially gliomas in adults. No effective method for classifying gliomas on genetic signatures is currently available. DNA methylation may be applied to distinguish cancer cells from normal tissues. In this study, we focused on three subtypes of IDH-mutation gliomas by examining methylation data. Several advanced computational methods were used, such as Monte Carlo feature selection (MCFS), incremental feature selection (IFS), support machine vector (SVM), etc. The MCFS method was adopted to analyze methylation features, resulting in a feature list. Then, the IFS method incorporating SVM was applied to the list to extract important methylation features and construct an optimal SVM classifier. As a result, several methylation features (sites) were found to relate to glioma subclasses, which are annotated onto multiple genes, such as FLJ37543, LCE3D, FAM89A, ADCY5, ESR1, C2orf67, REST, EPHA7, etc. These genes are enriched in biological functions, including cellular developmental process, neuron differentiation, cellular component morphogenesis, and G-protein-coupled receptor signaling pathway. Our results, which are supported by literature reports and independent dataset validation, showed that our identified genes and functions contributed to the detailed glioma subtypes. This study provided a basic research on IDH-mutation gliomas.
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Affiliation(s)
- XiaoYong Pan
- School of Life Sciences, Shanghai University, Shanghai, China.,Key Laboratory of System Control and Information Processing, Ministry of Education of China, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China.,IDLab, Department for Electronics and Information Systems, Ghent University, Ghent, Belgium
| | - Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Fei Yuan
- Department of Science and Technology, Binzhou Medical University Hospital, Binzhou, China
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China.,Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai, China
| | - LiuCun Zhu
- School of Life Sciences, Shanghai University, Shanghai, China
| | - SiBao Wan
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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8
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Barthel FP, Johnson KC, Wesseling P, Verhaak RGW. Evolving Insights into the Molecular Neuropathology of Diffuse Gliomas in Adults. Neurol Clin 2019; 36:421-437. [PMID: 30072063 DOI: 10.1016/j.ncl.2018.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recent advances in molecular analysis and genome sequencing have prompted a paradigm shift in neuropathology. This article discusses the discovery and clinical relevance of molecular biomarkers in diffuse gliomas in adults and how these biomarkers led to revision of the World Health Organization classification of these tumors. We relate progress in clinical classification to an overview of studies using molecular profiling to study gene expression and DNA methylation to categorize diffuse gliomas in adults and issues dealing with intratumoral heterogeneity. These efforts will refine the taxonomy of diffuse gliomas, facilitate selection of appropriate treatment regimens, and ultimately improve patient's lives.
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Affiliation(s)
- Floris P Barthel
- Department of Pathology, VU University Medical Center, Brain Tumor Center Amsterdam, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands; The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Pieter Wesseling
- Department of Pathology, VU University Medical Center, Brain Tumor Center Amsterdam, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands; Department of Pathology, Princess Máxima Center for Pediatric Oncology and University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands.
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
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9
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Jenkinson G, Abante J, Koldobskiy MA, Feinberg AP, Goutsias J. Ranking genomic features using an information-theoretic measure of epigenetic discordance. BMC Bioinformatics 2019; 20:175. [PMID: 30961526 PMCID: PMC6454630 DOI: 10.1186/s12859-019-2777-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background Establishment and maintenance of DNA methylation throughout the genome is an important epigenetic mechanism that regulates gene expression whose disruption has been implicated in human diseases like cancer. It is therefore crucial to know which genes, or other genomic features of interest, exhibit significant discordance in DNA methylation between two phenotypes. We have previously proposed an approach for ranking genes based on methylation discordance within their promoter regions, determined by centering a window of fixed size at their transcription start sites. However, we cannot use this method to identify statistically significant genomic features and handle features of variable length and with missing data. Results We present a new approach for computing the statistical significance of methylation discordance within genomic features of interest in single and multiple test/reference studies. We base the proposed method on a well-articulated hypothesis testing problem that produces p- and q-values for each genomic feature, which we then use to identify and rank features based on the statistical significance of their epigenetic dysregulation. We employ the information-theoretic concept of mutual information to derive a novel test statistic, which we can evaluate by computing Jensen-Shannon distances between the probability distributions of methylation in a test and a reference sample. We design the proposed methodology to simultaneously handle biological, statistical, and technical variability in the data, as well as variable feature lengths and missing data, thus enabling its wide-spread use on any list of genomic features. This is accomplished by estimating, from reference data, the null distribution of the test statistic as a function of feature length using generalized additive regression models. Differential assessment, using normal/cancer data from healthy fetal tissue and pediatric high-grade glioma patients, illustrates the potential of our approach to greatly facilitate the exploratory phases of clinically and biologically relevant methylation studies. Conclusions The proposed approach provides the first computational tool for statistically testing and ranking genomic features of interest based on observed DNA methylation discordance in comparative studies that accounts, in a rigorous manner, for biological, statistical, and technical variability in methylation data, as well as for variability in feature length and for missing data. Electronic supplementary material The online version of this article (10.1186/s12859-019-2777-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Garrett Jenkinson
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Currently with Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
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10
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Hypermethylated gene ANKDD1A is a candidate tumor suppressor that interacts with FIH1 and decreases HIF1α stability to inhibit cell autophagy in the glioblastoma multiforme hypoxia microenvironment. Oncogene 2018; 38:103-119. [PMID: 30082910 PMCID: PMC6318269 DOI: 10.1038/s41388-018-0423-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 06/01/2018] [Accepted: 06/25/2018] [Indexed: 01/28/2023]
Abstract
Ectopic epigenetic mechanisms play important roles in facilitating tumorigenesis. Here, we first demonstrated that ANKDD1A is a functional tumor suppressor gene, especially in the hypoxia microenvironment. ANKDD1A directly interacts with FIH1 and inhibits the transcriptional activity of HIF1α by upregulating FIH1. In addition, ANKDD1A decreases the half-life of HIF1α by upregulating FIH1, decreases glucose uptake and lactate production, inhibits glioblastoma multiforme (GBM) autophagy, and induces apoptosis in GBM cells under hypoxia. Moreover, ANKDD1A is highly frequently methylated in GBM. The tumor-specific methylation of ANKDD1A indicates that it could be used as a potential epigenetic biomarker as well as a possible therapeutic target.
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11
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Sippl C, Urbschat S, Kim YJ, Senger S, Oertel J, Ketter R. Promoter methylation of RB1, P15, P16, and MGMT and their impact on the clinical course of pilocytic astrocytomas. Oncol Lett 2018; 15:1600-1606. [PMID: 29434855 PMCID: PMC5776924 DOI: 10.3892/ol.2017.7490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/05/2017] [Indexed: 01/11/2023] Open
Abstract
Promoter methylation of P15, P16, RB transcriptional corepressor 1 (RB1) and O-6-methylguanine-DNA methyltransferase (MGMT) impacts the prognosis of numerous glioma subtypes. However, whether promoter methylation of these genes also has an impact on the clinical course of pilocytic astrocytoma remains unclear. Using methylation-specific polymerase chain reaction, the methylation status of the tumor suppressor genes P15, P16, RB1, and MGMT in pilocytic astrocytomas (n=18) was analyzed. Immunohistochemical staining for the R132H mutation of the isocitrate dehydrogenase (NADP(+)) 1, cytosolic (IDH1) gene was performed. Clinical data including age, gender, localization of tumor, extent of resection, treatment modality, progression-free survival and overall survival were collected. The methylation index for P15, P16, RB1 and MGMT was 0.0, 0.0, 5.6% (1/18) and 44.5% (8/18), respectively. If the MGMT promoter was methylated, the probability of relapse and second subsequent therapy was significantly increased (P=0.019). The one patient with methylation of P15 demonstrated a poor clinical course. The pilocytic astrocytomas of all 18 patients revealed wild-type IDH1. Clinically, there was a significant correlation of subtotal resection with the occurrence of relapse (P=0.005) and of the localization of the tumor with the extent of resection (P=0.031). Gross total resection was achieved significantly more often in pediatric patients than in adult patients (P=0.003). Adult patients demonstrated more relapses following the first tumor resection (P=0.001). The present study indicates that methylation of MGMT is associated with a poor clinical course and represents an age-independent risk factor for an unfavorable outcome. Other influential factors of outcome were the age of the patient and extent of resection.
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Affiliation(s)
- Christoph Sippl
- Department of Neurosurgery, University of Saarland, Faculty of Medicine, Homburg/Saar, D-66424 Homburg, Germany
| | - Steffi Urbschat
- Department of Neurosurgery, University of Saarland, Faculty of Medicine, Homburg/Saar, D-66424 Homburg, Germany
| | - Yoo Jin Kim
- Institute of Neuropathology, University of Saarland, Faculty of Medicine, Homburg/Saar, D-66424 Homburg, Germany
| | - Sebastian Senger
- Department of Neurosurgery, University of Saarland, Faculty of Medicine, Homburg/Saar, D-66424 Homburg, Germany
| | - Joachim Oertel
- Department of Neurosurgery, University of Saarland, Faculty of Medicine, Homburg/Saar, D-66424 Homburg, Germany
| | - Ralf Ketter
- Department of Neurosurgery, University of Saarland, Faculty of Medicine, Homburg/Saar, D-66424 Homburg, Germany
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12
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Saffari A, Silver MJ, Zavattari P, Moi L, Columbano A, Meaburn EL, Dudbridge F. Estimation of a significance threshold for epigenome-wide association studies. Genet Epidemiol 2018; 42:20-33. [PMID: 29034560 PMCID: PMC5813244 DOI: 10.1002/gepi.22086] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 05/30/2017] [Accepted: 07/24/2017] [Indexed: 12/17/2022]
Abstract
Epigenome-wide association studies (EWAS) are designed to characterise population-level epigenetic differences across the genome and link them to disease. Most commonly, they assess DNA-methylation status at cytosine-guanine dinucleotide (CpG) sites, using platforms such as the Illumina 450k array that profile a subset of CpGs genome wide. An important challenge in the context of EWAS is determining a significance threshold for declaring a CpG site as differentially methylated, taking multiple testing into account. We used a permutation method to estimate a significance threshold specifically for the 450k array and a simulation extrapolation approach to estimate a genome-wide threshold. These methods were applied to five different EWAS datasets derived from a variety of populations and tissue types. We obtained an estimate of α=2.4×10-7 for the 450k array, and a genome-wide estimate of α=3.6×10-8. We further demonstrate the importance of these results by showing that previously recommended sample sizes for EWAS should be adjusted upwards, requiring samples between ∼10% and ∼20% larger in order to maintain type-1 errors at the desired level.
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Affiliation(s)
- Ayden Saffari
- Department of Non‐Communicable Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
- MRC Unit, The Gambia and MRC International Nutrition GroupLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
- Department of Psychological Sciences, BirkbeckUniversity of LondonLondonUnited Kingdom
| | - Matt J. Silver
- MRC Unit, The Gambia and MRC International Nutrition GroupLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Patrizia Zavattari
- Department of Biomedical SciencesUniversity of CagliariCagliariSardiniaItaly
| | - Loredana Moi
- Department of Biomedical SciencesUniversity of CagliariCagliariSardiniaItaly
| | - Amedeo Columbano
- Department of Biomedical SciencesUniversity of CagliariCagliariSardiniaItaly
| | - Emma L. Meaburn
- Department of Psychological Sciences, BirkbeckUniversity of LondonLondonUnited Kingdom
| | - Frank Dudbridge
- Department of Non‐Communicable Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
- Department of Health SciencesUniversity of LeicesterLeicesterUnited Kingdom
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13
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Saunderson EA, Stepper P, Gomm JJ, Hoa L, Morgan A, Allen MD, Jones JL, Gribben JG, Jurkowski TP, Ficz G. Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors. Nat Commun 2017; 8:1450. [PMID: 29133799 PMCID: PMC5684409 DOI: 10.1038/s41467-017-01078-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 08/16/2017] [Indexed: 12/19/2022] Open
Abstract
Aberrant promoter DNA hypermethylation is a hallmark of cancer; however, whether this is sufficient to drive cellular transformation is not clear. To investigate this question, we use a CRISPR-dCas9 epigenetic editing tool, where an inactive form of Cas9 is fused to DNA methyltransferase effectors. Using this system, here we show simultaneous de novo DNA methylation of genes commonly methylated in cancer, CDKN2A, RASSF1, HIC1 and PTEN in primary breast cells isolated from healthy human breast tissue. We find that promoter methylation is maintained in this system, even in the absence of the fusion construct, and this prevents cells from engaging senescence arrest. Our data show that the key driver of this phenotype is repression of CDKN2A transcript p16 where myoepithelial cells harbour cancer-like gene expression but do not exhibit anchorage-independent growth. This work demonstrates that hit-and-run epigenetic events can prevent senescence entry, which may facilitate tumour initiation. “Although aberrant promoter DNA hypermethylation is a hallmark of cancer, it is not clear whether it is sufficient to drive transformation. Here, the authors use CRISPR-dCas9 to perform hit-and-run epigenetic editing, which prevents senescence entry in primary breast cells from healthy donors.”
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Affiliation(s)
- Emily A Saunderson
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Peter Stepper
- Institute for Biochemistry and Technical Biochemistry, Department of Biochemistry, Faculty of Chemistry, University of Stuttgart, D-70569, Stuttgart, Germany
| | - Jennifer J Gomm
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Lily Hoa
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Adrienne Morgan
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael D Allen
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - J Louise Jones
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - John G Gribben
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Tomasz P Jurkowski
- Institute for Biochemistry and Technical Biochemistry, Department of Biochemistry, Faculty of Chemistry, University of Stuttgart, D-70569, Stuttgart, Germany.
| | - Gabriella Ficz
- Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK.
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14
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Moyon S, Casaccia P. DNA methylation in oligodendroglial cells during developmental myelination and in disease. NEUROGENESIS 2017; 4:e1270381. [PMID: 28203606 DOI: 10.1080/23262133.2016.1270381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/23/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
Oligodendrocyte progenitor cells (OPC) are the myelinating cells of the central nervous system (CNS). During development, they differentiate into mature oligodendrocytes (OL) and ensheath axons, providing trophic and functional support to the neurons. This process is regulated by the dynamic expression of specific transcription factors, which, in turn, is controlled by epigenetic marks such as DNA methylation. Here we discuss recent findings showing that DNA methylation levels are differentially regulated in the oligodendrocyte lineage during developmental myelination, affecting both genes expression and alternative splicing events. Based on the phenotypic characterization of mice with genetic ablation of DNA methyltransferase 1 (Dnmt1) we conclude that DNA methylation is critical for efficient OPC expansion and for developmental myelination. Previous work suggests that in the context of diseases such as multiple sclerosis (MS) or gliomas, DNA methylation is differentially regulated in the CNS of affected individuals compared with healthy controls. In this commentary, based on the results of previous work, we propose the potential role of DNA methylation in adult oligodendroglial lineage cells in physiologic and pathological conditions, and delineate potential research approaches to be undertaken to test this hypothesis. A better understanding of this epigenetic modification in adult oligodendrocyte progenitor cells is essential, as it can potentially result in the design of new therapeutic strategies to enhance remyelination in MS patients or reduce proliferation in glioma patients.
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Affiliation(s)
- Sarah Moyon
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai , New York, NY, USA
| | - Patrizia Casaccia
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Neuroscience Initiative Advanced Science Research Center, CUNY, New York, NY, USA
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15
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Jiao W, Xun X, Liu J, Yang J, Wang Q, Wang L, Chen C, Wang H, Dai P. Diagnostic significance of suppressor of cytokine signalling 3 (SOCS3) methylation and its correlation with IDH1 mutation in Chinese glioma patients. Biomarkers 2016; 21:686-691. [DOI: 10.3109/1354750x.2016.1139001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Weili Jiao
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
| | - Xiaojie Xun
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
| | - Jinhui Liu
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
| | - Jianhui Yang
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
| | - Qi Wang
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
| | - Lin Wang
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
| | - Chao Chen
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
| | - Huijuan Wang
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
| | - Penggao Dai
- The National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, PR China
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16
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Kuo LT, Lu HY, Lee CC, Tsai JC, Lai HS, Tseng HM, Kuo MF, Tu YK. Multiplexed methylation profiles of tumor suppressor genes and clinical outcome in oligodendroglial tumors. Cancer Med 2016; 5:1830-9. [PMID: 27367901 PMCID: PMC4971911 DOI: 10.1002/cam4.762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 04/07/2016] [Accepted: 04/15/2016] [Indexed: 01/03/2023] Open
Abstract
Aberrant methylation has been associated with transcriptional inactivation of tumor‐related genes in a wide spectrum of human neoplasms. The influence of DNA methylation in oligodendroglial tumors is not fully understood. Genomic DNA was isolated from 61 oligodendroglial tumors for analysis of methylation using methylation‐specific multiplex ligation‐dependent probe amplification assay (MS‐MLPA). We correlated methylation status with clinicopathological findings and outcome. The genes found to be most frequently methylated in oligodendroglial tumors were RASSF1A (80.3%), CASP8 (70.5%), and CDKN2A (52.5%). Kaplan–Meier survival curve analysis demonstrated longer duration of progression‐free survival in patients with 19q loss, aged less than 38 years, and with a proliferative index of less than 5%. Methylation of the ESR1 promoter is significantly associated with shorter duration of overall survival and progression‐free survival, and that methylation of IGSF4 and RASSF1A is significantly associated with shorter duration of progression‐free survival. However, none of the methylation status of ESR1, IGSF4, and RASSF1A was of prognostic value for survival in a multivariate Cox model. A number of novel and interesting epigenetic alterations were identified in this study. The findings highlight the importance of methylation profiles in oligodendroglial tumors and their possible involvement in tumorigenesis.
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Affiliation(s)
- Lu-Ting Kuo
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Hsueh-Yi Lu
- Department of Industrial Engineering and Management, National Yunlin University of Science and Technology, Douliu, Yunlin county, 640, Taiwan
| | - Chien-Chang Lee
- Department of Emergency Medicine, National Taiwan University Hospital, Yun-Lin branch, Yun-Lin county, 640, Taiwan
| | - Jui-Chang Tsai
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Hong-Shiee Lai
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Ham-Min Tseng
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Meng-Fai Kuo
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Yong-Kwang Tu
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
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17
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Moyon S, Liang J, Casaccia P. Epigenetics in NG2 glia cells. Brain Res 2016; 1638:183-198. [PMID: 26092401 PMCID: PMC4683112 DOI: 10.1016/j.brainres.2015.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/11/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022]
Abstract
The interplay of transcription and epigenetic marks is essential for oligodendrocyte progenitor cell (OPC) proliferation and differentiation during development. Here, we review the recent advances in this field and highlight mechanisms of transcriptional repression and activation involved in OPC proliferation, differentiation and plasticity. We also describe how dysregulation of these epigenetic events may affect demyelinating disorders, and consider potential ways to manipulate NG2 cell behavior through modulation of the epigenome. This article is part of a Special Issue entitled SI:NG2-glia(Invited only).
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Affiliation(s)
- Sarah Moyon
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jialiang Liang
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrizia Casaccia
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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18
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Janeckova L, Kolar M, Svec J, Lanikova L, Pospichalova V, Baloghova N, Vojtechova M, Sloncova E, Strnad H, Korinek V. HIC1 Expression Distinguishes Intestinal Carcinomas Sensitive to Chemotherapy. Transl Oncol 2016; 9:99-107. [PMID: 27084425 PMCID: PMC4833890 DOI: 10.1016/j.tranon.2016.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 12/13/2022] Open
Abstract
Neoplastic growth is frequently associated with genomic DNA methylation that causes transcriptional silencing of tumor suppressor genes. We used a collection of colorectal polyps and carcinomas in combination with bioinformatics analysis of large datasets to study the expression and methylation of Hypermethylated in cancer 1 (HIC1), a tumor suppressor gene inactivated in many neoplasms. In premalignant stages, HIC1 expression was decreased, and the decrease was linked to methylation of a specific region in the HIC1 locus. However, in carcinomas, the HIC1 expression was variable and, in some specimens, comparable to healthy tissue. Importantly, high HIC1 production distinguished a specific type of chemotherapy-responsive tumors.
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Affiliation(s)
- Lucie Janeckova
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Michal Kolar
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Jiri Svec
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic; Department of Radiotherapy and Oncology, Third Faculty of Medicine, Charles University, Prague, Srobarova 50, 100 34 Prague 4, Czech Republic
| | - Lucie Lanikova
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Vendula Pospichalova
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Nikol Baloghova
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Martina Vojtechova
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Eva Sloncova
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Hynek Strnad
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Vladimir Korinek
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic; Division BIOCEV, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
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19
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Abstract
Sorting and grading of glial tumors by the WHO classification provide clinicians with guidance as to the predicted course of the disease and choice of treatment. Nonetheless, histologically identical tumors may have very different outcome and response to treatment. Molecular markers that carry both diagnostic and prognostic information add useful tools to traditional classification by redefining tumor subtypes within each WHO category. Therefore, molecular markers have become an integral part of tumor assessment in modern neuro-oncology and biomarker status now guides clinical decisions in some subtypes of gliomas. The routine assessment of IDH status improves histological diagnostic accuracy by differentiating diffuse glioma from reactive gliosis. It carries a favorable prognostic implication for all glial tumors and it is predictive for chemotherapeutic response in anaplastic oligodendrogliomas with codeletion of 1p/19q chromosomes. Glial tumors that contain chromosomal codeletion of 1p/19q are defined as tumors of oligodendroglial lineage and have favorable prognosis. MGMT promoter methylation is a favorable prognostic marker in astrocytic high-grade gliomas and it is predictive for chemotherapeutic response in anaplastic gliomas with wild-type IDH1/2 and in glioblastoma of the elderly. The clinical implication of other molecular markers of gliomas like mutations of EGFR and ATRX genes and BRAF fusion or point mutation is highlighted. The potential of molecular biomarker-based classification to guide future therapeutic approach is discussed and accentuated.
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20
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Lee EJ, Rath P, Liu J, Ryu D, Pei L, Noonepalle SK, Shull AY, Feng Q, Litofsky NS, Miller DC, Anthony DC, Kirk MD, Laterra J, Deng L, Xin HB, Wang X, Choi JH, Shi H. Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells. J Genet Genomics 2015; 42:355-71. [PMID: 26233891 DOI: 10.1016/j.jgg.2015.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 12/15/2022]
Abstract
Glioblastoma (GBM) is the most common and most aggressive primary brain tumor in adults. The existence of a small population of stem-like tumor cells that efficiently propagate tumors and resist cytotoxic therapy is one proposed mechanism leading to the resilient behavior of tumor cells and poor prognosis. In this study, we performed an in-depth analysis of the DNA methylation landscape in GBM-derived cancer stem cells (GSCs). Parallel comparisons of primary tumors and GSC lines derived from these tumors with normal controls (a neural stem cell (NSC) line and normal brain tissue) identified groups of hyper- and hypomethylated genes that display a trend of either increasing or decreasing methylation levels in the order of controls, primary GBMs, and their counterpart GSC lines, respectively. Interestingly, concurrent promoter hypermethylation and gene body hypomethylation were observed in a subset of genes including MGMT, AJAP1 and PTPRN2. These unique DNA methylation signatures were also found in primary GBM-derived xenograft tumors indicating that they are not tissue culture-related epigenetic changes. Integration of GSC-specific epigenetic signatures with gene expression analysis further identified candidate tumor suppressor genes that are frequently down-regulated in GBMs such as SPINT2, NEFM and PENK. Forced re-expression of SPINT2 reduced glioma cell proliferative capacity, anchorage independent growth, cell motility, and tumor sphere formation in vitro. The results from this study demonstrate that GSCs possess unique epigenetic signatures that may play important roles in the pathogenesis of GBM.
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Affiliation(s)
- Eun-Joon Lee
- GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA
| | - Prakash Rath
- Department of Biology, College of Art and Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jimei Liu
- GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA
| | - Dungsung Ryu
- GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA
| | - Lirong Pei
- GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA
| | - Satish K Noonepalle
- GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Georgia Regents University, Augusta, GA 30912, USA
| | - Austin Y Shull
- GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Georgia Regents University, Augusta, GA 30912, USA
| | - Qi Feng
- Division of Neurological Surgery, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - N Scott Litofsky
- Division of Neurological Surgery, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Douglas C Miller
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Douglas C Anthony
- Department of Pathology and Laboratory Medicine, Brown University and Lifespan Academic Medical Center, Providence, RI 02903, USA
| | - Mark D Kirk
- Department of Biology, College of Art and Sciences, University of Missouri, Columbia, MO 65211, USA
| | - John Laterra
- Department of Neurology, The Hugo W. Moser Research Institute at Kennedy Krieger Inc. and The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Libin Deng
- Institute of Translational Medicine, Nanchang University, Nanchang 330031, China
| | - Hong-Bo Xin
- Institute of Translational Medicine, Nanchang University, Nanchang 330031, China
| | - Xinguo Wang
- David H. Murdock Research Institute, Kannapolis, NC 28081, USA
| | - Jeong-Hyeon Choi
- GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA; Department of Biostatistics and Epidemiology, Georgia Regents University, Augusta, GA 30912, USA.
| | - Huidong Shi
- GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Georgia Regents University, Augusta, GA 30912, USA.
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21
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Alexanian AR, Huang YW. Specific combinations of the chromatin-modifying enzyme modulators significantly attenuate glioblastoma cell proliferation and viability while exerting minimal effect on normal adult stem cells growth. Tumour Biol 2015; 36:9067-72. [PMID: 26084611 DOI: 10.1007/s13277-015-3654-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/09/2015] [Indexed: 02/06/2023] Open
Abstract
The discoveries of recent decade showed that all critical changes in cancer cells, such as silencing of tumor-suppressor genes and activation of oncogenes, are caused not only by genetic but also by epigenetic mechanisms. Although epigenetic changes are somatically heritable, in contrast to genetic changes, they are potentially reversible, making them good targets for therapeutic intervention. Covalent modifications of chromatin such as methylation and acetylation of histones and methylation of DNA are the important components of epigenetic machinery. In this study, we investigated the effect of different modulators of DNA and histone covalent-modifying enzymes on the proliferation and viability of normal adult stem cells, such as human bone marrow mesenchymal stem cells (hMSCs), and on malignant tumor cells, such as glioblastoma (GB) D54 cells. Results demonstrated that specific combinations of histone methyltransferases and deacetylases inhibitors significantly attenuated D54 cells viability but having only a small effect on hMSCs growth. Taken together, these studies suggest that specific combinations of histone covalent modifiers could be an effective treatment option for the most aggressive type of primary brain tumors such as glioblastoma multiforme.
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Affiliation(s)
- Arshak R Alexanian
- Cell Reprogramming & Therapeutics LLC, W229 N1870 Westwood Drive, Waukesha, WI, 53186, USA.
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 9200 West Wisconsin Ave., Milwaukee, WI, 53226-3522, USA.
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 9200 West Wisconsin Ave., Milwaukee, WI, 53226-3522, USA.
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22
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Ping Y, Deng Y, Wang L, Zhang H, Zhang Y, Xu C, Zhao H, Fan H, Yu F, Xiao Y, Li X. Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data. Nucleic Acids Res 2015; 43:1997-2007. [PMID: 25653168 PMCID: PMC4344511 DOI: 10.1093/nar/gkv074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The driver genetic aberrations collectively regulate core cellular processes underlying cancer development. However, identifying the modules of driver genetic alterations and characterizing their functional mechanisms are still major challenges for cancer studies. Here, we developed an integrative multi-omics method CMDD to identify the driver modules and their affecting dysregulated genes through characterizing genetic alteration-induced dysregulated networks. Applied to glioblastoma (GBM), the CMDD identified a core gene module of 17 genes, including seven known GBM drivers, and their dysregulated genes. The module showed significant association with shorter survival of GBM. When classifying driver genes in the module into two gene sets according to their genetic alteration patterns, we found that one gene set directly participated in the glioma pathway, while the other indirectly regulated the glioma pathway, mostly, via their dysregulated genes. Both of the two gene sets were significant contributors to survival and helpful for classifying GBM subtypes, suggesting their critical roles in GBM pathogenesis. Also, by applying the CMDD to other six cancers, we identified some novel core modules associated with overall survival of patients. Together, these results demonstrate integrative multi-omics data can identify driver modules and uncover their dysregulated genes, which is useful for interpreting cancer genome.
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Affiliation(s)
- Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yulan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hongyi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Huihui Fan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Fulong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
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23
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Siegal T. Clinical impact of molecular biomarkers in gliomas. J Clin Neurosci 2014; 22:437-44. [PMID: 25533211 DOI: 10.1016/j.jocn.2014.10.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 10/01/2014] [Indexed: 12/21/2022]
Abstract
The World Health Organization (WHO) classification system for glial tumors provides guidance as to the predicted course of the disease and choice of treatment. However, histologically identical tumors may have a very different outcome and response to treatment. Molecular markers that carry both diagnostic and prognostic information add valuable tools by redefining tumor subtypes within each WHO category. Therefore, molecular biomarkers have become an integral part of tumor assessment in modern neuro-oncology and biomarker status now guides clinical decisions in some subtypes of gliomas, including anaplastic oligodendroglioma and glioblastoma in the elderly. This review discusses the prognostic and predictive impact of molecular markers that have undergone extensive study in recent years. The clinical relevance of contemporary molecular classification of gliomas using the routine assessment of IDH mutations, promoter methylation of MGMT, chromosomal deletion of 1p/19q, mutations of EGFR and ATRX genes, and BRAF fusion or point mutation is highlighted. The potential of molecular biomarker-based classification to guide future therapeutic approach is discussed and accentuated.
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Affiliation(s)
- Tali Siegal
- Center for Neuro-Oncology, Davidoff Institute of Oncology, Rabin Medical Center, Campus Beilinson, 49100 Petach Tikva, Israel.
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24
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Zhao H, Cai W, Su S, Zhi D, Lu J, Liu S. Screening genes crucial for pediatric pilocytic astrocytoma using weighted gene coexpression network analysis combined with methylation data analysis. Cancer Gene Ther 2014; 21:448-55. [PMID: 25257306 DOI: 10.1038/cgt.2014.49] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 12/25/2022]
Abstract
To identify novel genes associated with pediatric pilocytic astrocytoma (PA) for better understanding the molecular mechanism underlying the pediatric PA pathogenesis. Gene expression profile data of GSE50161 and GSE44971 and the methylation data of GSE44684 were downloaded from Gene Expression Omnibus. The differentially expressed genes (DEGs) between PA and normal control samples were screened using the limma package in R, and then used to construct weighted gene coexpression network (WGCN) using the WGCN analysis (WGCNA) package in R. Significant modules of DEGs were selected using the clustering analysis. Function enrichment analysis of the DEGs in significant modules were performed using the WGCNA package and clusterprofiler package in R. Correlation between methylation sites of DEGs and PA was analyzed using the CpGassoc package in R. Totally, 3479 DEGs were screened in PA samples. Thereinto, 3424 DEGs were used to construct the WGCN. Several significant modules of DEGs were selected based on the WGCN, in which the turquoise module was positively related to PA, whereas blue module was negatively related to PA. DEGs (for example, DOCK2 (dedicator of cytokinesis 2), DOCK8 and FCGR2A (Fc fragment of IgG, low affinity IIa)) in blue module were mainly involved in Fc gamma R-mediated phagocytosis pathway and natural killer cell-mediated cytotoxicity pathway. Methylations of 14 DEGs among the top 30 genes in blue module were related to PA. Our data suggest that DOCK2, DOCK8 and FCGR2A may represent potential therapeutic targets in PA that merits further investigation.
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Affiliation(s)
- H Zhao
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - W Cai
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - S Su
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - D Zhi
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - J Lu
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - S Liu
- Department of Neurosurgery, Shengjing Hospital, China Medical University, Shenyang, China
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25
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Jha P, Pia Patric IR, Shukla S, Pathak P, Pal J, Sharma V, Thinagararanjan S, Santosh V, Suri V, Sharma MC, Arivazhagan A, Suri A, Gupta D, Somasundaram K, Sarkar C. Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation. Neuro Oncol 2014; 16:1607-17. [PMID: 24997139 DOI: 10.1093/neuonc/nou113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Pediatric glioblastoma multiforme (GBM) is rare, and there is a single study, a seminal discovery showing association of histone H3.3 and isocitrate dehydrogenase (IDH)1 mutation with a DNA methylation signature. The present study aims to validate these findings in an independent cohort of pediatric GBM, compare it with adult GBM, and evaluate the involvement of important functionally altered pathways. METHODS Genome-wide methylation profiling of 21 pediatric GBM cases was done and compared with adult GBM data (GSE22867). We performed gene mutation analysis of IDH1 and H3 histone family 3A (H3F3A), status evaluation of glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP), and Gene Ontology analysis. Experimental evaluation of reactive oxygen species (ROS) association was also done. RESULTS Distinct differences were noted between methylomes of pediatric and adult GBM. Pediatric GBM was characterized by 94 hypermethylated and 1206 hypomethylated cytosine-phosphate-guanine (CpG) islands, with 3 distinct clusters, having a trend to prognostic correlation. Interestingly, none of the pediatric GBM cases showed G-CIMP/IDH1 mutation. Gene Ontology analysis identified ROS association in pediatric GBM, which was experimentally validated. H3F3A mutants (36.4%; all K27M) harbored distinct methylomes and showed enrichment of processes related to neuronal development, differentiation, and cell-fate commitment. CONCLUSIONS Our study confirms that pediatric GBM has a distinct methylome compared with that of adults. Presence of distinct clusters and an H3F3A mutation-specific methylome indicate existence of epigenetic subgroups within pediatric GBM. Absence of IDH1/G-CIMP status further indicates that findings in adult GBM cannot be simply extrapolated to pediatric GBM and that there is a strong need for identification of separate prognostic markers. A possible role of ROS in pediatric GBM pathogenesis is demonstrated for the first time and needs further evaluation.
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Affiliation(s)
- Prerana Jha
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Irene Rosita Pia Patric
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Sudhanshu Shukla
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Jagriti Pal
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Sivaarumugam Thinagararanjan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Vani Santosh
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Arimappamagan Arivazhagan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Ashish Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Deepak Gupta
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Kumaravel Somasundaram
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
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26
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Martínez R, Carmona FJ, Vizoso M, Rohde V, Kirsch M, Schackert G, Ropero S, Paulus W, Barrantes A, Gomez A, Esteller M. DNA methylation alterations in grade II- and anaplastic pleomorphic xanthoastrocytoma. BMC Cancer 2014; 14:213. [PMID: 24650279 PMCID: PMC4000050 DOI: 10.1186/1471-2407-14-213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/13/2014] [Indexed: 12/31/2022] Open
Abstract
Background Pleomorphic xanthoastrocytoma (PXA) is a rare WHO grade II tumor accounting for less than 1% of all astrocytomas. Malignant transformation into PXA with anaplastic features, is unusual and correlates with poorer outcome of the patients. Methods Using a DNA methylation custom array, we have quantified the DNA methylation level on the promoter sequence of 807 cancer-related genes of WHO grade II (n = 11) and III PXA (n = 2) and compared to normal brain tissue (n = 10) and glioblastoma (n = 87) samples. DNA methylation levels were further confirmed on independent samples by pyrosequencing of the promoter sequences. Results Increasing DNA promoter hypermethylation events were observed in anaplastic PXA as compared with grade II samples. We further validated differential hypermethylation of CD81, HCK, HOXA5, ASCL2 and TES on anaplastic PXA and grade II tumors. Moreover, these epigenetic alterations overlap those described in glioblastoma patients, suggesting common mechanisms of tumorigenesis. Conclusions Even taking into consideration the small size of our patient populations, our data strongly suggest that epigenome-wide profiling of PXA is a valuable tool to identify methylated genes, which may play a role in the malignant progression of PXA. These methylation alterations may provide useful biomarkers for decision-making in those patients with low-grade PXA displaying a high risk of malignant transformation.
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Affiliation(s)
- Ramón Martínez
- Department of Neurosurgery, University of Goettingen, Robert Koch, Str, 40, 37075 Goettingen, Germany.
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27
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Liu Q, Zhang C, Ma G, Zhang Q. Expression of SPRR3 is associated with tumor cell proliferation and invasion in glioblastoma multiforme. Oncol Lett 2013; 7:427-432. [PMID: 24396461 PMCID: PMC3881942 DOI: 10.3892/ol.2013.1736] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 11/28/2013] [Indexed: 12/02/2022] Open
Abstract
Esophagin, also known as small proline-rich protein 3 (SPRR3), has been demonstrated to be important in the initiation and progression of numerous types of tumor, including colorectal and breast cancer. However, studies concerning the biological functions of SPRR3 in glioblastoma multiforme (GBM) are limited. Therefore, we aimed to identify the functions and molecular mechanisms underlying the role of SPRR3 in GBM. Hypomethylation of SPRR3 was observed and associated with a poor clinical outcome in GBM patients compared with healthy individuals by using gene methylation profiling. The present study was performed to investigate the expression status and effects of SPRR3 in GBM. The U251 cell line was used in the functional analyses. Cell growth was examined by MTT and colony formation assay. Cell invasion was measured using the Transwell invasion assay. The expression of SPRR3 in tissue samples was examined by immunohistochemistry. The results revealed that the overexpression of SPRR3 accelerates U251 cell proliferation and invasion. It was also observed that SPRR3 was markedly upregulated in 72.7% of GBM samples (24/33) compared with the normal tissue. These results suggest that an increased expression of SPRR3 is involved in tumorigenesis.
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Affiliation(s)
- Qingyang Liu
- Department of Immunology, Institute of Basic Medical Sciences, Capital Medical University, Beijing 100069, P.R. China
| | - Chuanbao Zhang
- Department of Neurosurgery, Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Guofo Ma
- Department of Neurosurgery, Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Quangeng Zhang
- Department of Immunology, Institute of Basic Medical Sciences, Capital Medical University, Beijing 100069, P.R. China
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28
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Thon N, Kreth S, Kreth FW. Personalized treatment strategies in glioblastoma: MGMT promoter methylation status. Onco Targets Ther 2013; 6:1363-72. [PMID: 24109190 PMCID: PMC3792931 DOI: 10.2147/ott.s50208] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The identification of molecular genetic biomarkers considerably increased our current understanding of glioma genesis, prognostic evaluation, and treatment planning. In glioblastoma, the most malignant intrinsic brain tumor entity in adults, the promoter methylation status of the gene encoding for the repair enzyme O6-methylguanine-DNA methyltransferase (MGMT) indicates increased efficacy of current standard of care, which is concomitant and adjuvant chemoradiotherapy with the alkylating agent temozolomide. In the elderly, MGMT promoter methylation status has recently been introduced to be a predictive biomarker that can be used for stratification of treatment regimes. This review gives a short summery of epidemiological, clinical, diagnostic, and treatment aspects of patients who are currently diagnosed with glioblastoma. The most important molecular genetic markers and epigenetic alterations in glioblastoma are summarized. Special focus is given to the physiological function of DNA methylation-in particular, of the MGMT gene promoter, its clinical relevance, technical aspects of status assessment, its correlation with MGMT mRNA and protein expressions, and its place within the management cascade of glioblastoma patients.
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Affiliation(s)
- Niklas Thon
- Department of Neurosurgery, Hospital of the University of Munich, Campus Grosshadern, Munich, Germany
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29
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Spyropoulou A, Piperi C, Adamopoulos C, Papavassiliou AG. Deregulated chromatin remodeling in the pathobiology of brain tumors. Neuromolecular Med 2013; 15:1-24. [PMID: 23114751 DOI: 10.1007/s12017-012-8205-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Brain tumors encompass a heterogeneous group of malignant tumors with variable histopathology, aggressiveness, clinical outcome and prognosis. Current gene expression profiling studies indicate interplay of genetic and epigenetic alterations in their pathobiology. A central molecular event underlying epigenetics is the alteration of chromatin structure by post-translational modifications of DNA and histones as well as nucleosome repositioning. Dynamic remodeling of the fundamental nucleosomal structure of chromatin or covalent histone marks located in core histones regulate main cellular processes including DNA methylation, replication, DNA-damage repair as well as gene expression. Deregulation of these processes has been linked to tumor suppressor gene silencing, cancer initiation and progression. The reversible nature of deregulated chromatin structure by DNA methylation and histone deacetylation inhibitors, leading to re-expression of tumor suppressor genes, makes chromatin-remodeling pathways as promising therapeutic targets. In fact, a considerable number of these inhibitors are being tested today either alone or in combination with other agents or conventional treatments in the management of brain tumors with considerable success. In this review, we focus on the mechanisms underpinning deregulated chromatin remodeling in brain tumors, discuss their potential clinical implications and highlight the advances toward new therapeutic strategies.
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Affiliation(s)
- Anastasia Spyropoulou
- Department of Biological Chemistry, Medical School, University of Athens, 75, M. Asias Street, 11527, Athens, Greece
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30
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DNA methylation and cancer diagnosis. Int J Mol Sci 2013; 14:15029-58. [PMID: 23873296 PMCID: PMC3742286 DOI: 10.3390/ijms140715029] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/28/2013] [Accepted: 07/04/2013] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a major epigenetic modification that is strongly involved in the physiological control of genome expression. DNA methylation patterns are largely modified in cancer cells and can therefore be used to distinguish cancer cells from normal tissues. This review describes the main technologies available for the detection and the discovery of aberrantly methylated DNA patterns. It also presents the different sources of biological samples suitable for DNA methylation studies. We discuss the interest and perspectives on the use of DNA methylation measurements for cancer diagnosis through examples of methylated genes commonly documented in the literature. The discussion leads to our consideration for why DNA methylation is not commonly used in clinical practice through an examination of the main requirements that constitute a reliable biomarker. Finally, we describe the main DNA methylation inhibitors currently used in clinical trials and those that exhibit promising results.
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31
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Carén H, Pollard SM, Beck S. The good, the bad and the ugly: epigenetic mechanisms in glioblastoma. Mol Aspects Med 2013; 34:849-62. [PMID: 22771539 PMCID: PMC3714597 DOI: 10.1016/j.mam.2012.06.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 06/27/2012] [Indexed: 12/31/2022]
Abstract
Cell type-specific patterns of gene expression reflect epigenetic changes imposed through a particular developmental lineage as well as those triggered by environmental cues within adult tissues. There is great interest in elucidating the molecular basis and functional importance of epigenetic mechanisms in both normal physiology and disease - particularly in cancer, where abnormal '-omic' states are often observed. In this article we review recent progress in studies of epigenetic mechanisms in the most common primary adult brain cancer, glioblastoma multiforme. Three distinct areas are discussed. First, the evidence in support of ongoing 'normal' epigenetic processes associated with differentiation - as predicted by 'cancer stem cell' models of the disease. Second, identification of site-specific and global epigenetic abnormalities. Third, genetic disruptions directly within the core epigenetic machinery, exemplified by the recently identified mutations within isocitrate dehydrogenase genes IDH1/2 and variant histone genes H3.3/H3F3A. These constitute the 'good, the bad and the ugly' of epigenetic mechanisms in cancer.
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Affiliation(s)
- Helena Carén
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
| | - Steven M. Pollard
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
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32
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Hughes LAE, Melotte V, de Schrijver J, de Maat M, Smit VTHBM, Bovée JVMG, French PJ, van den Brandt PA, Schouten LJ, de Meyer T, van Criekinge W, Ahuja N, Herman JG, Weijenberg MP, van Engeland M. The CpG island methylator phenotype: what's in a name? Cancer Res 2013; 73:5858-68. [PMID: 23801749 DOI: 10.1158/0008-5472.can-12-4306] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Although the CpG island methylator phenotype (CIMP) was first identified and has been most extensively studied in colorectal cancer, the term "CIMP" has been repeatedly used over the past decade to describe CpG island promoter methylation in other tumor types, including bladder, breast, endometrial, gastric, glioblastoma (gliomas), hepatocellular, lung, ovarian, pancreatic, renal cell, and prostate cancers, as well as for leukemia, melanoma, duodenal adenocarninomas, adrenocortical carcinomas, and neuroblastomas. CIMP has been reported to be useful for predicting prognosis and response to treatment in a variety of tumor types, but it remains unclear whether or not CIMP is a universal phenomenon across human neoplasia or if there should be cancer-specific definitions of the phenotype. Recently, it was shown that somatic isocitrate dehydrogenase-1 (IDH1) mutations, frequently observed in gliomas, establish CIMP in primary human astrocytes by remodeling the methylome. Interestingly, somatic IDH1 and IDH2 mutations, and loss-of-function mutations in ten-eleven translocation (TET) methylcytosine dioxygenase-2 (TET2) associated with a hypermethylation phenotype, are also found in multiple enchondromas of patients with Ollier disease and Mafucci syndrome, and leukemia, respectively. These data provide the first clues for the elucidation of a molecular basis for CIMP. Although CIMP appears as a phenomenon that occurs in various cancer types, the definition is poorly defined and differs for each tumor. The current perspective discusses the use of the term CIMP in cancer, its significance in clinical practice, and future directions that may aid in identifying the true cause and definition of CIMP in different forms of human neoplasia.
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Affiliation(s)
- Laura A E Hughes
- Authors' Affiliations: Departments of Epidemiology and Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht; Department of Surgery, Orbis Medical Center, Sittard-Geleen; Department of Pathology, Leiden University Medical Center, Leiden; Department of Neurology, Erasmus University Medical Center, Erasmus University, Rotterdam, the Netherlands; Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium; and The Johns Hopkins University School of Medicine, Baltimore, Maryland
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Zhang Z, Zhao Z, Liu B, Li D, Zhang D, Chen H, Liu D. Systems biomedicine: It’s your turn—Recent progress in systems biomedicine. QUANTITATIVE BIOLOGY 2013. [DOI: 10.1007/s40484-013-0009-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Abstract
World Health Organization (WHO) grade I astrocytomas include pilocytic astrocytoma (PA) and subependymal giant cell astrocytoma (SEGA). As technologies in pharmacologic neo-adjuvant therapy continue to progress and as molecular characteristics are progressively recognized as potential markers of both clinically significant tumor subtypes and response to therapy, interest in the biology of these tumors has surged. An updated review of the current knowledge of the molecular biology of these tumors is needed. We conducted a Medline search to identify published literature discussing the molecular biology of grade I astrocytomas. We then summarized this literature and discuss it in a logical framework through which the complex biology of these tumors can be clearly understood. A comprehensive review of the molecular biology of WHO grade I astrocytomas is presented. The past several years have seen rapid progress in the level of understanding of PA in particular, but the molecular literature regarding both PA and SEGA remains nebulous, ambiguous, and occasionally contradictory. In this review we provide a comprehensive discussion of the current understanding of the chromosomal, genomic, and epigenomic features of both PA and SEGA and provide a logical framework in which these data can be more readily understood.
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Affiliation(s)
- Nicholas F Marko
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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35
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Zheng J, Xiong D, Sun X, Wang J, Hao M, Ding T, Xiao G, Wang X, Mao Y, Fu Y, Shen K, Wang J. Signification of Hypermethylated in Cancer 1 (HIC1) as Tumor Suppressor Gene in Tumor Progression. CANCER MICROENVIRONMENT : OFFICIAL JOURNAL OF THE INTERNATIONAL CANCER MICROENVIRONMENT SOCIETY 2012; 5:285-93. [PMID: 22528874 PMCID: PMC3460058 DOI: 10.1007/s12307-012-0103-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 03/28/2012] [Indexed: 12/30/2022]
Abstract
Hypermethylated in cancer 1(HIC1) was identified as a strong suppressor gene in chromosome region 17p13.3 telomeric to TP53. This gene encodes a transcriptional repressor and is ubiquitously expressed in normal tissues but downexpressed in different tumor tissues where it is hypermethylated. The hypermethylation of this chromosomal region leads to epigenetic inactivation of HIC1, which would prompt cancer cells to alter survival and signaling pathways or specific transcription factors during the period of tumorigenesis. In vitro, HIC1 function is mainly a sequence-specific transcriptional repressor interacting with a still growing range of histone deacetylase(HDAC)-dependent and HDAC-independent corepressor complexes. Furthermore, a role for HIC1 in tumor development is firmly supported by Hic1 deficient mouse model and two double heterozygote models cooperate with p53 and Ptch1. Notably, our findings suggest that potential factors derived from tumor microenviroment may play a role in modulating HIC1 expression in tumor cells by epigenetic modification, which is responsible for tumor progression. In this review, we will describe genomic and proteinic structure of HIC1, and summary the potential role of HIC1 in human various solid tumors and leukemia, and explore the influence of tumor microenviroment on inducing HIC1 expression in tumor cells.
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Affiliation(s)
- Jianghua Zheng
- Department of Biochemistry and Molecular & Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Dan Xiong
- Department of Biochemistry and Molecular & Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Xueqing Sun
- Department of Biochemistry and Molecular & Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Jinglong Wang
- Department of Biochemistry and Molecular & Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Mingang Hao
- Department of Biochemistry and Molecular & Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Tao Ding
- Department of Urological Surgery, Shanghai the Tenth People’s Hospital of Tong Ji University, Shanghai, 200072 China
| | - Gang Xiao
- Department of Biochemistry and Molecular & Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Xiumin Wang
- Department of Biochemistry and Molecular & Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yan Mao
- Shanghai Ruijin Hospital, Comprehensive Breast Health Center, Shanghai, 200025 China
| | - Yuejie Fu
- Department of Thoracic Surgery, RenJi Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Kunwei Shen
- Shanghai Ruijin Hospital, Comprehensive Breast Health Center, Shanghai, 200025 China
| | - Jianhua Wang
- Department of Biochemistry and Molecular & Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
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36
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Genetics and pharmacogenomics of diffuse gliomas. Pharmacol Ther 2012; 137:78-88. [PMID: 22985521 DOI: 10.1016/j.pharmthera.2012.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 08/31/2012] [Indexed: 12/18/2022]
Abstract
Rapidly evolving techniques for analysis of the genome provide new opportunities for cancer therapy. For diffuse gliomas this has resulted in molecular markers with potential for personalized therapy. Some drugs that utilize pharmacogenomics are currently being tested in clinical trials. In melanoma, lung-, breast-, gastric- and colorectal carcinoma several molecular markers are already being clinically implemented for diagnosis and treatment. These insights can serve as a background for the promise and limitations that pharmacogenomics has for diffuse gliomas. Better molecular characterization of diffuse gliomas, including analysis of the molecular underpinnings of drug efficacy in clinical trials, is urgently needed. We foresee exciting developments in the upcoming years with clinical benefit for the patients.
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Beyond Genetics in Glioma Pathways: The Ever-Increasing Crosstalk between Epigenomic and Genomic Events. JOURNAL OF SIGNAL TRANSDUCTION 2012; 2012:519807. [PMID: 22778947 PMCID: PMC3385669 DOI: 10.1155/2012/519807] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 04/10/2012] [Indexed: 12/12/2022]
Abstract
Diffuse gliomas are the most frequent brain tumor in adults. This group of brain neoplasms, ranging from histologically benign to aggressive malignant forms, represents a challenge in modern neurooncology because of the diffuse infiltrative growth pattern and the inherent tendency to relapse as a more malignant tumor. Once the disease achieves the stage of glioblastoma multiforme (GBM), the prognosis of patients is dismal and the median survival time is 15 months. Exhaustive genetic analyses have revealed a variety of deregulated genetic pathways involved in DNA repair, apoptosis, cell migration/adhesion, and cell cycle. Recently, investigation of epigenetic alterations in gliomas has contributed to depict the complexity of the molecular lesions leading to these malignancies. Even though, the efficacy of the state-of-the-art form of chemotherapy in malignant gliomas with temozolomide is based on the methylation-associated silencing of the DNA repair gene MGMT. Nevertheless, the whole scenario including global DNA hypomethylation, aberrant promoter hypermethylation, histone modification, chromatin states, and the role of noncoding RNAs in gliomas has only been partially revealed. We discuss the repercussion of epigenetic alterations underlying deregulated molecular pathways in the pathogenesis and evolution of gliomas and their impact on management of patients.
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Epigenetics in human gliomas. Cancer Lett 2012; 342:185-92. [PMID: 22531315 DOI: 10.1016/j.canlet.2012.04.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 04/03/2012] [Accepted: 04/15/2012] [Indexed: 12/30/2022]
Abstract
Aberrant epigenetic landscapes and their involvement in genesis and progression of tumors, as well as in treatment responses and prognosis, indicate one of the most emerging fields in cancer research. In gliomas, the most common human primary brain tumors, and in particular in glioblastoma, the most malignant and devastating brain tumor entity in adults, the elucidation of distinct patterns of aberrant DNA methylation, histone modification, and miRNA expression and their interrelationship has fundamentally changed our point of view on these highly heterogeneous tumors. In the current review article, we address the basic principles of epigenetic control in gliomas, their current and putative future role in prognostic and predictive models and possible interactions within the epigenetic network. We discuss diagnostic and therapeutic opportunities appearing at horizon of epigenetic research. Moreover, we present current and propose future clinical workflow models for molecular characterization of malignant gliomas.
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39
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Hamid A. Folate malabsorption and its influence on DNA methylation during cancer development. DNA Cell Biol 2012. [PMID: 22468673 DOI: 10.1089/dna.2011.1576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The folate transport across the epithelial of the intestine, colon, kidney, and liver is essential for folate homeostasis. The relative localization of transporters in membranes is an important determinant for the vectorial flow of substrates across the epithelia. Folate deficiency is a highly prevalent vitamin deficiency in the world, and alcohol ingestion has been the major contributor. It can develop because of folate malabsorption in tissues, increased renal excretion dietary inadequacy, and altered hepatobiliary metabolism. Additionally, folate-mediated one-carbon metabolism is important for various cellular processes, including DNA synthesis and methylation. In this regard, the contribution of alcohol-associated and dietary folate deficiency to methylation patterns is under intense investigation, especially in cancer. The epigenetic events have increasing relevance in the development of strategies for early diagnosis, prevention, and treatment of cancer.
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Affiliation(s)
- Abid Hamid
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine, CSIR, Jammu, India
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40
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Malzkorn B, Wolter M, Riemenschneider MJ, Reifenberger G. Unraveling the glioma epigenome: from molecular mechanisms to novel biomarkers and therapeutic targets. Brain Pathol 2012; 21:619-32. [PMID: 21939466 DOI: 10.1111/j.1750-3639.2011.00536.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Epigenetic regulation of gene expression by DNA methylation and histone modification is frequently altered in human cancers including gliomas, the most common primary brain tumors. In diffuse astrocytic and oligodendroglial gliomas, epigenetic changes often present as aberrant hypermethylation of 5'-cytosine-guanine (CpG)-rich regulatory sequences in a large variety of genes, a phenomenon referred to as glioma CpG island methylator phenotype (G-CIMP). G-CIMP is particularly common but not restricted to gliomas with isocitrate dehydrogenase 1 (IDH1) or 2 (IDH2) mutation. Recent studies provided a mechanistic link between these genetic mutations and the associated widespread epigenetic modifications. Specifically, 2-hydroxyglutarate, the oncometabolite produced by mutant IDH1 and IDH2 proteins, has been shown to function as a competitive inhibitor of various α-ketoglutarate (α-KG)-dependent dioxygenases, including histone demethylases and members of the ten-eleven-translocation (TET) family of 5-methylcytosine (5mC) hydroxylases. In this review article, we briefly address (i) the basic principles of epigenetic control of gene expression; (ii) the most important methods to analyze focal and global epigenetic alterations in cells and tissues; and (iii) the involvement of epigenetic alterations in the molecular pathogenesis of gliomas. Moreover, we discuss the promising roles of epigenetic alterations as molecular diagnostic markers and novel therapeutic targets, and highlight future perspectives toward unraveling the "glioma epigenome."
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Affiliation(s)
- Bastian Malzkorn
- Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany
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41
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Muñoz J, Inda MDM, Lázcoz P, Zazpe I, Fan X, Alfaro J, Tuñón T, Rey JA, Castresana JS. Promoter Methylation of RASSF1A Associates to Adult Secondary Glioblastomas and Pediatric Glioblastomas. ISRN NEUROLOGY 2012; 2012:576578. [PMID: 22389839 PMCID: PMC3263565 DOI: 10.5402/2012/576578] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 09/29/2011] [Indexed: 11/29/2022]
Abstract
While allelic losses and mutations of tumor suppressor genes implicated in the etiology of astrocytoma have been widely assessed, the role of epigenetics is still a matter of study. We analyzed the frequency of promoter hypermethylation by methylation-specific PCR (MSP) in five tumor suppressor genes (PTEN, MGMT, RASSF1A, p14ARF, and p16INK4A), in astrocytoma samples and cell lines. RASSF1A was the most frequently hypermethylated gene in all grades of astrocytoma samples, in cell lines, and in adult secondary GBM. It was followed by MGMT. PTEN showed a slight methylation signal in only one GBM and one pilocytic astrocytoma, and in two cell lines; while p14ARF and p16INK4A did not show any evidence of methylation in primary tumors or cell lines. In pediatric GBM, RASSF1A was again the most frequently altered gene, followed by MGMT; PTEN, p14 and p16 showed no alterations. Lack or reduced expression of RASSF1A in cell lines was correlated with the presence of methylation. RASSF1A promoter hypermethylation might be used as a diagnostic marker for secondary GBM and pediatric GBM. Promoter hypermethylation might not be an important inactivation mechanism in other genes like PTEN, p14ARF and p16INK4A, in which other alterations (mutations, homozygous deletions) are prevalent.
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Affiliation(s)
- Jorge Muñoz
- Unidad de Biología de Tumores Cerebrales, Universidad de Navarra, 31008 Pamplona, Spain
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42
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Liu X, Tang H, Wang Z, Huang C, Zhang Z, She X, Wu M, Li G. F10 gene hypomethylation, a putative biomarker for glioma prognosis. J Neurooncol 2011; 107:479-85. [PMID: 22160665 DOI: 10.1007/s11060-011-0775-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 11/29/2011] [Indexed: 12/26/2022]
Abstract
Tumors are usually characterized by an imbalance in cytosine methylation, including hypomethylation of CpG islands. In this study, bisulfite sequencing PCR was used to assess the promoter methylation status of coagulation factor X (F10) gene in tumors of 96 glioma patients and in glioma cells U251, SF767, and SF126, and the effect of promoter hypomethylation on protein expression was evaluated immunohistochemically. The study showed that the demethylation ratio of F10 in SF126, SF767, and U251 cells was 38.6, 26.4, and 24.3% respectively. Hypomethylation of F10 was detected in 82.3% of glioma specimens and in no normal brain tissues, with significant correlation with its protein expression. However there was no remarkable relationship between F10 hypomethylation and sex, age, and advanced tumor grade. The correlation between F10 hypomethylation, protein expression, and overall survival (OS) was statistically significant. Hypomethylation of F10 promoter in gliomas accounted for F10 encoding protein FX overexpression and aggressive biological behavior in a subset of patients. Furthermore, in the F10 hypomethylation group, OS was shorter for patients with F10 overexpression than for those without. Detection of these epigenetic changes in tumors may provide important information regarding prognosis.
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Affiliation(s)
- Xiaoping Liu
- Cancer Research Institute, Central South University, 110# Xiangya Road, Changsha, Hunan Province, China
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43
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Zheng S, Houseman EA, Morrison Z, Wrensch MR, Patoka JS, Ramos C, Haas-Kogan DA, McBride S, Marsit CJ, Christensen BC, Nelson HH, Stokoe D, Wiemels JL, Chang SM, Prados MD, Tihan T, Vandenberg SR, Kelsey KT, Berger MS, Wiencke JK. DNA hypermethylation profiles associated with glioma subtypes and EZH2 and IGFBP2 mRNA expression. Neuro Oncol 2011; 13:280-9. [PMID: 21339190 DOI: 10.1093/neuonc/noq190] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We explored the associations of aberrant DNA methylation patterns in 12 candidate genes with adult glioma subtype, patient survival, and gene expression of enhancer of zeste human homolog 2 (EZH2) and insulin-like growth factor-binding protein 2 (IGFBP2). We analyzed 154 primary glioma tumors (37 astrocytoma II and III, 52 primary glioblastoma multiforme (GBM), 11 secondary GBM, 54 oligodendroglioma/oligoastrocytoma II and III) and 13 nonmalignant brain tissues for aberrant methylation with quantitative methylation-specific PCR (qMS-PCR) and for EZH2 and IGFBP2 expression with quantitative reverse transcription PCR (qRT-PCR). Global methylation was assessed by measuring long interspersed nuclear element-1 (LINE1) methylation. Unsupervised clustering analyses yielded 3 methylation patterns (classes). Class 1 (MGMT, PTEN, RASSF1A, TMS1, ZNF342, EMP3, SOCS1, RFX1) was highly methylated in 82% (75/91) of lower-grade astrocytic and oligodendroglial tumors, 73% (8/11) of secondary GBMs, and 12% (6/52) of primary GBMs. The primary GBMs in this class were early onset (median age 37 years). Class 2 (HOXA9 and SLIT2) was highly methylated in 37% (19/52) of primary GBMs. None of the 10 genes for class 3 that were differentially methylated in classes 1 and 2 were hypermethylated in 92% (12/13) of nonmalignant brain tissues and 52% (27/52) of primary GBMs. Class 1 tumors had elevated EZH2 expression but not elevated IGFBP2; class 2 tumors had both high IGFBP2 and high EZH2 expressions. The gene-specific hypermethylation class correlated with higher levels of global LINE1 methylation and longer patient survival times. These findings indicate a generalized hypermethylation phenotype in glioma linked to improved survival and low IGFBP2. DNA methylation markers are useful in characterizing distinct glioma subtypes and may hold promise for clinical applications.
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Affiliation(s)
- Shichun Zheng
- Department of Neurological Surgery, University of California-San Francisco, Helen Diller Family Cancer Center, 1450 3rd Street, San Francisco, CA 94158, USA
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44
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Liu X, Tang H, Zhang Z, Li W, Wang Z, Zheng Y, Wu M, Li G. POTEH hypomethylation, a new epigenetic biomarker for glioma prognosis. Brain Res 2011; 1391:125-31. [PMID: 21439273 DOI: 10.1016/j.brainres.2011.03.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 03/12/2011] [Accepted: 03/16/2011] [Indexed: 10/18/2022]
Abstract
POTE ankyrin domain family, member H (POTEH) belongs to POTE family, which expresses in many cancers. In this study, methylation status of POTEH promoter and its correlation with clinicopathological parameters were evaluated in glioma tissues and cells. Bisulfite sequencing PCR was carried out to investigate the promoter methylation status of POTEH in tumor of 96 glioma patients and glioma cells U251, SF767, and SF126. The effect of promoter hypomethylation on protein expression was evaluated by immunohistochemistry. POTEH was hypomethylated in 81.3% gliomas and none in normal brain tissues, and correlated significantly with its protein expression. But there was no remarkable relationship between sex, age, advanced tumor grade and POTEH hypomethylation. With the grade progressing, POTEH protein expression was enhanced. The correlation between POTEH hypomethylation, protein expression and overall survival was statistically significant. In POTEH hypomethylation group, patients with POTEH high expression had shorter overall survival than those with low expression. Hypomethylation of POTEH promoter in gliomas accounted for POTEH protein overexpression and poor outcome in a subset of patients. Detection of these epigenetic changes in tumors may provide information regarding prognosis.
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Affiliation(s)
- Xiaoping Liu
- Cancer Research Institute, Central South University, 110(#) Xiangya Road, Changsha, Hunan Province, China
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45
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Haque A, Banik NL, Ray SK. Molecular alterations in glioblastoma: potential targets for immunotherapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 98:187-234. [PMID: 21199773 DOI: 10.1016/b978-0-12-385506-0.00005-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glioblastoma is the most common and deadly brain tumor, possibly arising from genetic and epigenetic alterations in normal astroglial cells. Multiple cytogenetic, chromosomal, and genetic alterations have been identified in glioblastoma, with distinct expression of antigens (Ags) and biomarkers that may alter therapeutic potential of this aggressive cancer. Current therapy consists of surgical resection, followed by radiation therapy and chemotherapy. In spite of these treatments, the prognosis for glioblastoma patients is poor. Although recent studies have focused on the development of novel immunotherapeutics against glioblastoma, little is known about glioblastoma-specific immune responses. A better understanding of the molecular interactions among glioblastoma tumors, host immune cells, and the tumor microenvironment may give rise to novel integrated approaches for the simultaneous control of tumor escape pathways and the activation of antitumor immune responses. This review provides a detailed overview concerning genetic alterations in glioblastoma, their effects on Ag and biomarker expression, and the future design of chemoimmunotherapeutics against glioblastoma.
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Affiliation(s)
- Azizul Haque
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
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46
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Laffaire J, Everhard S, Idbaih A, Crinière E, Marie Y, de Reyniès A, Schiappa R, Mokhtari K, Hoang-Xuan K, Sanson M, Delattre JY, Thillet J, Ducray F. Methylation profiling identifies 2 groups of gliomas according to their tumorigenesis. Neuro Oncol 2010; 13:84-98. [PMID: 20926426 DOI: 10.1093/neuonc/noq110] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Extensive genomic and gene expression studies have been performed in gliomas, but the epigenetic alterations that characterize different subtypes of gliomas remain largely unknown. Here, we analyzed the methylation patterns of 807 genes (1536 CpGs) in a series of 33 low-grade gliomas (LGGs), 36 glioblastomas (GBMs), 8 paired initial and recurrent gliomas, and 9 controls. This analysis was performed with Illumina's Golden Gate Bead methylation arrays and was correlated with clinical, histological, genomic, gene expression, and genotyping data, including IDH1 mutations. Unsupervised hierarchical clustering resulted in 2 groups of gliomas: a group corresponding to de novo GBMs and a group consisting of LGGs, recurrent anaplastic gliomas, and secondary GBMs. When compared with de novo GBMs and controls, this latter group was characterized by a very high frequency of IDH1 mutations and by a hypermethylated profile similar to the recently described glioma CpG island methylator phenotype. MGMT methylation was more frequent in this group. Among the LGG cluster, 1p19q codeleted LGG displayed a distinct methylation profile. A study of paired initial and recurrent gliomas demonstrated that methylation profiles were remarkably stable across glioma evolution, even during anaplastic transformation, suggesting that epigenetic alterations occur early during gliomagenesis. Using the Cancer Genome Atlas data set, we demonstrated that GBM samples that had an LGG-like hypermethylated profile had a high rate of IDH1 mutations and a better outcome. Finally, we identified several hypermethylated and downregulated genes that may be associated with LGG and GBM oncogenesis, LGG oncogenesis, 1p19q codeleted LGG oncogenesis, and GBM oncogenesis.
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Affiliation(s)
- Julien Laffaire
- Université Pierre et Marie Curie-Paris 6, Centre de Recherche de l'Institut du Cerveau et de la Moëlle épinière (CRICM) UMR-S975, 75013 Paris, France.
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47
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Martinez R, Esteller M. The DNA methylome of glioblastoma multiforme. Neurobiol Dis 2010; 39:40-6. [DOI: 10.1016/j.nbd.2009.12.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 12/21/2009] [Accepted: 12/30/2009] [Indexed: 12/14/2022] Open
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48
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Wu AH, Siegmund KD, Long TI, Cozen W, Wan P, Tseng CC, Shibata D, Laird PW. Hormone therapy, DNA methylation and colon cancer. Carcinogenesis 2010; 31:1060-7. [PMID: 20064828 PMCID: PMC2878358 DOI: 10.1093/carcin/bgq009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 12/29/2009] [Accepted: 01/06/2010] [Indexed: 02/07/2023] Open
Abstract
Observational epidemiological studies and randomized trials have reported a protective effect of estrogen and progestin therapy (EPT) on the risk of colorectal cancer but the findings on estrogen-alone therapy (ET) are less consistent. The mechanism by which menopausal hormones influence risk of colorectal cancer has not been well studied. To further investigate the relationship between menopausal hormones and risk of colon cancer, we conducted a population-based case-control study in Los Angeles County involving 831 women with newly diagnosed colon cancer and 755 population-based control women. Risk of colon cancer decreased significantly with increasing duration of current use of ET and EPT; the adjusted relative risk was 0.83 [95% confidence interval (95% CI) = 0.76-0.99)] per 5 years of ET use and 0.88 (95% CI = 0.78-0.99) per 5 years of EPT use. Risk of colon cancer was unrelated to past ET or EPT use. We explored if current use of menopausal hormones is associated with DNA methylation of estrogen receptor (ESR1 and ESR2), progesterone receptor and other genes in the colonic tissues of a subset of colon cancer patients (n = 280) we interviewed. Our results suggest that current menopausal hormone users compared with non-current users displayed increased DNA methylation of progesterone receptor in the 'normal' colonic tissues (P = 0.055) and increased DNA methylation of ESR1 in the 'tumorous' colonic tissues (P = 0.056). These findings on DNA methylation and hormone therapy use need confirmation in larger studies.
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Affiliation(s)
- Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA, USA.
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49
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Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW, Aldape K. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 2010; 17:510-22. [PMID: 20399149 PMCID: PMC2872684 DOI: 10.1016/j.ccr.2010.03.017] [Citation(s) in RCA: 1759] [Impact Index Per Article: 125.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 02/18/2010] [Accepted: 03/30/2010] [Indexed: 12/14/2022]
Abstract
We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA). We found that a distinct subset of samples displays concerted hypermethylation at a large number of loci, indicating the existence of a glioma-CpG island methylator phenotype (G-CIMP). We validated G-CIMP in a set of non-TCGA glioblastomas and low-grade gliomas. G-CIMP tumors belong to the proneural subgroup, are more prevalent among lower-grade gliomas, display distinct copy-number alterations, and are tightly associated with IDH1 somatic mutations. Patients with G-CIMP tumors are younger at the time of diagnosis and experience significantly improved outcome. These findings identify G-CIMP as a distinct subset of human gliomas on molecular and clinical grounds.
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Affiliation(s)
- Houtan Noushmehr
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | | | - Kristin Diefes
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Heidi S. Phillips
- Department of Tumor Biology and Angiogenesis, Genentech, Inc., South San Francisco, California 94080, USA
| | - Kanan Pujara
- Department of Tumor Biology and Angiogenesis, Genentech, Inc., South San Francisco, California 94080, USA
| | - Benjamin P. Berman
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | - Fei Pan
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | - Christopher E. Pelloski
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik P. Sulman
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Krishna P. Bhat
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roel G.W. Verhaak
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Katherine A. Hoadley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - D. Neil Hayes
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles M. Perou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Heather K. Schmidt
- The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Li Ding
- The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K. Wilson
- The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - David Van Den Berg
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | - Hui Shen
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
| | - Henrik Bengtsson
- Department of Statistics, University of California, Berkeley, California, USA
| | - Pierre Neuvial
- Department of Statistics, University of California, Berkeley, California, USA
| | - Leslie M. Cope
- Department on Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Jonathan Buckley
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - James G. Herman
- Department on Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Stephen B. Baylin
- Department on Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Peter W. Laird
- USC Epigenome Center, University of Southern California, Los Angeles, CA, 90033 USA
- To whom correspondence should be addressed. , FAX: (323) 442-7880
| | - Kenneth Aldape
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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50
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Yu J, Bulk E, Ji P, Hascher A, Tang M, Metzger R, Marra A, Serve H, Berdel WE, Wiewroth R, Koschmieder S, Müller-Tidow C. The EPHB6 receptor tyrosine kinase is a metastasis suppressor that is frequently silenced by promoter DNA hypermethylation in non-small cell lung cancer. Clin Cancer Res 2010; 16:2275-83. [PMID: 20371680 DOI: 10.1158/1078-0432.ccr-09-2000] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Loss of EPHB6 receptor tyrosine kinase expression in early-stage non-small cell lung carcinoma (NSCLC) is associated with the subsequent development of distant metastasis. Here, we analyzed the regulation and function of EPHB6 in lung cancer metastasis. EXPERIMENTAL DESIGN The expression levels of EPHB6 were compared among normal lung tissue (n = 9), NSCLC without metastasis (n = 39), and NSCLC with metastasis (n = 39) according to the history of the patients. In addition, EPHB6 expression levels of matched tumor-normal pairs from 24 NSCLC patients were analyzed. The promoter DNA methylation status and its association with the expression levels of EPHB6 were determined among 14 pairs of tumor-normal samples. Metastatic potential of EPHB6 was assessed in vitro and in vivo in a metastasis mouse model. Overexpression and RNA interference (RNAi) approaches were used for analysis of the biological functions of EPHB6. RESULTS EPHB6 mRNA and protein levels were significantly reduced in NSCLC tumors compared with matched normal lung tissue. Decreased EPHB6 expression levels were associated with an increased risk for metastasis development in NSCLC patients. Loss of expression correlated with EPHB6 hypermethylation. EPHB6 expression was induced by 5-aza-2'-deoxycytidine treatment in an NSCLC cell line. Restoration of EPHB6 expression in lung adenocarcinoma cells increased adhesion and decreased migration. Reexpression of EPHB6 in lung cancer cells almost entirely abolished metastasis formation in non obese diabetic (NOD)/severe combined immunodeficient mice. CONCLUSIONS Taken together, these analyses show that EPHB6 is a metastasis inhibitory gene that is frequently silenced by hypermethylation of its promoter in NSCLC.
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Affiliation(s)
- Jun Yu
- Department of Medicine A--Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
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