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medip-seq cancer

Wenji Li, Ying Huang, Davit Sargsyan, Tin Oo Khor, Yue Guo, Limin Shu, Anne Yuqing Yang, Chengyue Zhang, Ximena Paredes-Gonzalez, Michael Verzi, Ronald P Hart, Ah-Ng Kong
Purpose: We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods: Prostate DNA samples from 24-week-old TRAMP and C57BL/6 male mice were isolated. The DNA methylation profiles were analyzed by methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (MeDIP-seq)...
2018: Cell & Bioscience
Takeshi Otsubo, Kazuhiko Yamada, Teruki Hagiwara, Kenshiro Oshima, Kei Iida, Koro Nishikata, Tetsuro Toyoda, Toru Igari, Kyoko Nohara, Satoshi Yamashita, Masahira Hattori, Taeko Dohi, Yuki I Kawamura
Esophageal squamous cell carcinoma (ESCC) is associated with the accumulation of genetic and epigenetic changes in the background mucosa. Dysregulated DNA methylation is known to lead to the inactivation of tumor suppressor genes and the activation of oncogenes. To identify the genes whose expression is perturbed by abnormal DNA methylation in ESCC, integrative transcriptomics by serial analysis of gene expression (SAGE) and methylome sequencing by methyl-DNA immunoprecipitation (MeDIP) analysis were performed...
October 13, 2017: Oncotarget
Tsung-Han Hsieh, Yun-Ru Liu, Ting-Yu Chang, Muh-Lii Liang, Hsin-Hung Chen, Hsei-Wei Wang, Yun Yen, Tai-Tong Wong
Background: Pediatric central nervous system germ cell tumors (CNSGCTs) are rare and heterogeneous neoplasms, and they can be divided into germinomas and nongerminomatous GCTs (NGGCTs). NGGCTs are further subdivided into mature teratomas and nongerminomatous malignant GCTs (NGMGCTs). Clinical outcomes suggest that NGMGCTs have poor prognosis and survival, and that they require more extensive radiotherapy and adjuvant chemotherapy. However, the mechanisms underlying this difference are still unclear...
October 3, 2017: Neuro-oncology
Jun Ding, Ziv Bar-Joseph
Motivation: Profiling of genome wide DNA methylation is now routinely performed when studying development, cancer and several other biological processes. Although Whole genome Bisulfite Sequencing provides high-quality methylation measurements at the resolution of nucleotides, it is relatively costly and so several studies have used alternative methods for such profiling. One of the most widely used low cost alternatives is MeDIP-Seq. However, MeDIP-Seq is biased for CpG enriched regions and thus its results need to be corrected in order to determine accurate methylation levels...
November 1, 2017: Bioinformatics
Matthias Lienhard, Sabrina Grasse, Jana Rolff, Steffen Frese, Uwe Schirmer, Michael Becker, Stefan Börno, Bernd Timmermann, Lukas Chavez, Holger Sültmann, Gunda Leschber, Iduna Fichtner, Michal R Schweiger, Ralf Herwig
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data...
April 7, 2017: Nucleic Acids Research
Myung-Chul Kim, Na-Yon Kim, Yu-Ri Seo, Yongbaek Kim
Intratumoral heterogeneity is a hallmark of all cancers and functions as the major barrier against effective cancer therapy. In contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous cancer cells remains largely undetermined. This study was performed to evaluate the epigenetic mechanisms involved in the tumor cell heterogeneity using side population (SP) and non-SP cells isolated from a human malignant mesothelioma (HMM) cell line. The subpopulations of cancer cells were analyzed by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) and RNA-seq methodology...
2016: Journal of Cancer
Chul H Kim, Eun K Lee, Yoen J Choi, Hye J An, Hyung O Chung, Dae E Park, Byung C Ghim, Byung P Yu, Jong Bhak, Hae Y Chung
DNA methylation plays major roles in many biological processes, including aging, carcinogenesis, and development. Analyses of DNA methylation using next-generation sequencing offer a new way to profile and compare methylomes across the genome in the context of aging. We explored genomewide DNA methylation and the effects of short-term calorie restriction (CR) on the methylome of aged rat kidney. Whole-genome methylation of kidney in young (6 months old), old (25 months old), and OCR (old with 4-week, short-term CR) rats was analyzed by methylated DNA immunoprecipitation and next-generation sequencing (MeDIP-Seq)...
August 25, 2016: Aging Cell
Yuanhang Liu, Desiree Wilson, Robin J Leach, Yidong Chen
BACKGROUND: Since its initial discovery in 1975, DNA methylation has been intensively studied and shown to be involved in various biological processes, such as development, aging and tumor progression. Many experimental techniques have been developed to measure the level of DNA methylation. Methyl-CpG binding domain-based capture followed by high-throughput sequencing (MBDCap-seq) is a widely used method for characterizing DNA methylation patterns in a genome-wide manner. However, current methods for processing MBDCap-seq datasets does not take into account of the region-specific genomic characteristics that might have an impact on the measurements of the amount of methylated DNA (signal) and background fluctuation (noise)...
August 18, 2016: BMC Genomics
Pedro Castelo-Branco, Ricardo Leão, Tatiana Lipman, Brittany Campbell, Donghyun Lee, Aryeh Price, Cindy Zhang, Abolfazl Heidari, Derek Stephens, Stefan Boerno, Hugo Coelho, Ana Gomes, Celia Domingos, Joana D Apolonio, Georg Schäfer, Robert G Bristow, Michal R Schweiger, Robert Hamilton, Alexandre Zlotta, Arnaldo Figueiredo, Helmut Klocker, Holger Sültmann, Uri Tabori
The identification of new biomarkers to differentiate between indolent and aggressive prostate tumors is an important unmet need. We examined the role of THOR (TERT Hypermethylated Oncological Region) as a diagnostic and prognostic biomarker in prostate cancer (PCa).We analyzed THOR in common cancers using genome-wide methylation arrays. Methylation status of the whole TERT gene in benign and malignant prostate samples was determined by MeDIP-Seq. The prognostic role of THOR in PCa was assessed by pyrosequencing on discovery and validation cohorts from patients who underwent radical prostatectomy with long-term follow-up data...
September 6, 2016: Oncotarget
Chao Ye, Ran Tao, Qingyi Cao, Danhua Zhu, Yini Wang, Jie Wang, Juan Lu, Ermei Chen, Lanjuan Li
Hepatocellular carcinoma (HCC) is a common solid tumor worldwide with a poor prognosis. Accumulating evidence has implicated important regulatory roles of epigenetic modifications in the occurrence and progression of HCC. In the present study, we analyzed 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels in the tumor tissues and paired adjacent peritumor tissues (APTs) from four individual HCC patients using a (hydroxy)methylated DNA immunoprecipitation approach combined with deep sequencing [(h)MeDIP-Seq]...
August 2016: International Journal of Oncology
Kun Tan, Zhenni Zhang, Kai Miao, Yong Yu, Linlin Sui, Jianhui Tian, Lei An
STUDY HYPOTHESIS: How does in vitro fertilization (IVF) alter promoter DNA methylation patterns and its subsequent effects on gene expression profiles during placentation in mice? STUDY FINDING: IVF-induced alterations in promoter DNA methylation might have functional consequences in a number of biological processes and functions during IVF placentation, including actin cytoskeleton organization, hematopoiesis, vasculogenesis, energy metabolism and nutrient transport...
July 2016: Molecular Human Reproduction
Lien Spans, Thomas Van den Broeck, Elien Smeets, Stefan Prekovic, Bernard Thienpont, Diether Lambrechts, R Jeffrey Karnes, Nicholas Erho, Mohammed Alshalalfa, Elai Davicioni, Christine Helsen, Thomas Gevaert, Lorenzo Tosco, Karin Haustermans, Evelyne Lerut, Steven Joniau, Frank Claessens
The clinical heterogeneity of prostate cancer (PCa) makes it difficult to identify those patients that could benefit from more aggressive treatments. As a contribution to a better understanding of the genomic changes in the primary tumor that are associated with the development of high-risk disease, we performed exome sequencing and copy number determination of a clinically homogeneous cohort of 47 high-risk PCas. We confirmed recurrent mutations in SPOP, PTEN and TP53 among the 850 point mutations we detected...
April 26, 2016: Oncotarget
Chen Chen, Hao Peng, Xiaojie Huang, Ming Zhao, Zhi Li, Ni Yin, Xiang Wang, Fenglei Yu, Bangliang Yin, Yunchang Yuan, Qianjin Lu
Esophageal squamous cell carcinoma (ESCC) is the leading cause of cancer-related death worldwide. Previous studies have suggested that DNA methylation involved in the development of ESCC. However, the precise mechanisms underlying the regulation and maintenance of the methylome as well as their relationship with ESCC remain poorly understood. Herein, we used methylated DNA immunoprecipitation sequencing (MeDIP-Seq) and RNA-Seq to investigate whole-genome DNA methylation patterns and the genome expression profiles in ESCC samples...
January 26, 2016: Oncotarget
Jeffrey M Bhasin, Bo Hu, Angela H Ting
DNA methylation differences capture substantial information about the molecular and gene-regulatory states among biological subtypes. Enrichment-based next generation sequencing methods such as MBD-isolated genome sequencing (MiGS) and MeDIP-seq are appealing for studying DNA methylation genome-wide in order to distinguish between biological subtypes. However, current analytic tools do not provide optimal features for analyzing three-group or larger study designs. MethylAction addresses this need by detecting all possible patterns of statistically significant hyper- and hypo- methylation in comparisons involving any number of groups...
January 8, 2016: Nucleic Acids Research
Yue Guo, Jong Hun Lee, Limin Shu, Ying Huang, Wenji Li, Chengyue Zhang, Anne Yuqing Yang, Sarandeep Ss Boyanapalli, Ansu Perekatt, Ronald P Hart, Michael Verzi, Ah-Ng Tony Kong
BACKGROUND: Aberrant DNA methylation at the 5-carbon on cytosine residues (5mC) in CpG dinucleotides is probably the most extensively characterized epigenetic modification in colon cancer. It has been suggested that the loss of adenomatous polyposis coli (APC) function initiates tumorigenesis and that additional genetic and epigenetic events are involved in colon cancer progression. We aimed to study the genome-wide DNA methylation profiles of intestinal tumorigenesis in Apc(min/+) mice...
2015: Cell & Bioscience
Paul Guilhamon, Lee M Butcher, Nadege Presneau, Gareth A Wilson, Andrew Feber, Dirk S Paul, Moritz Schütte, Johannes Haybaeck, Ulrich Keilholz, Jens Hoffman, Mark T Ross, Adrienne M Flanagan, Stephan Beck
BACKGROUND: The use of tumour xenografts is a well-established research tool in cancer genomics but has not yet been comprehensively evaluated for cancer epigenomics. METHODS: In this study, we assessed the suitability of patient-derived tumour xenografts (PDXs) for methylome analysis using Infinium 450 K Beadchips and MeDIP-seq. RESULTS: Controlled for confounding host (mouse) sequences, comparison of primary PDXs and matching patient tumours in a rare (osteosarcoma) and common (colon) cancer revealed that an average 2...
2014: Genome Medicine
Barry I Milavetz, Lata Balakrishnan
DNA tumor viruses including members of the polyomavirus, adenovirus, papillomavirus, and herpes virus families are presently the subject of intense interest with respect to the role that epigenetics plays in control of the virus life cycle and the transformation of a normal cell to a cancer cell. To date, these studies have primarily focused on the role of histone modification, nucleosome location, and DNA methylation in regulating the biological consequences of infection. Using a wide variety of strategies and techniques ranging from simple ChIP to ChIP-chip and ChIP-seq to identify histone modifications, nuclease digestion to genome wide next generation sequencing to identify nucleosome location, and bisulfite treatment to MeDIP to identify DNA methylation sites, the epigenetic regulation of these viruses is slowly becoming better understood...
2015: Methods in Molecular Biology
Bo Zhang, XiaoYun Xing, Jing Li, Rebecca F Lowdon, Yan Zhou, Nan Lin, Baoxue Zhang, Vasavi Sundaram, Katherine B Chiappinelli, Ian S Hagemann, David G Mutch, Paul J Goodfellow, Ting Wang
BACKGROUND: Aberrant DNA methylation is a hallmark of many cancers. Classically there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I, and uterine papillary serous carcinoma (UPSC), or Type II. However, the whole genome DNA methylation changes in these two classical types of endometrial cancer is still unknown. RESULTS: Here we described complete genome-wide DNA methylome maps of EAC, UPSC, and normal endometrium by applying a combined strategy of methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme digestion sequencing (MRE-seq)...
October 6, 2014: BMC Genomics
Ming-Tao Zhao, Jeffrey J Whyte, Garrett M Hopkins, Mark D Kirk, Randall S Prather
DNA modifications, such as methylation and hydroxymethylation, are pivotal players in modulating gene expression, genomic imprinting, X-chromosome inactivation, and silencing repetitive sequences during embryonic development. Aberrant DNA modifications lead to embryonic and postnatal abnormalities and serious human diseases, such as cancer. Comprehensive genome-wide DNA methylation and hydroxymethylation studies provide a way to thoroughly understand normal development and to identify potential epigenetic mutations in human diseases...
June 2014: Cellular Reprogramming
Raman P Nagarajan, Bo Zhang, Robert J A Bell, Brett E Johnson, Adam B Olshen, Vasavi Sundaram, Daofeng Li, Ashley E Graham, Aaron Diaz, Shaun D Fouse, Ivan Smirnov, Jun Song, Pamela L Paris, Ting Wang, Joseph F Costello
Aberrant DNA hypomethylation may play an important role in the growth rate of glioblastoma (GBM), but the functional impact on transcription remains poorly understood. We assayed the GBM methylome with MeDIP-seq and MRE-seq, adjusting for copy number differences, in a small set of non-glioma CpG island methylator phenotype (non-G-CIMP) primary tumors. Recurrent hypomethylated loci were enriched within a region of chromosome 5p15 that is specified as a cancer amplicon and also encompasses TERT, encoding telomerase reverse transcriptase, which plays a critical role in tumorigenesis...
May 2014: Genome Research
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