Genome-wide methylation profiling identifies novel methylated genes in neuroblastoma tumors

Epigenetics : Official Journal of the DNA Methylation Society
Maja OlssonHelena Carén

Abstract

Neuroblastoma is a very heterogeneous tumor of childhood. The clinical spectra range from very aggressive metastatic disease to spontaneous regression, even without therapy. Aberrant DNA methylation pattern is a common feature of most cancers. For neuroblastoma, it has been demonstrated both for single genes as well as genome-wide, where a so-called methylator phenotype has been described. Here, we present a study using Illumina 450K methylation arrays on 60 neuroblastoma tumors. We show that aggressive tumors, characterized by International Neuroblastoma Risk Group (INRG) as stage M, are hypermethylated compared to low-grade tumors. On the contrary, INRG stage L tumors display more non-CpG methylation. The genes with the highest number of hypermethylated CpG sites in INRG M tumors are TERT, PCDHGA4, DLX5, and DLX6-AS1. Gene ontology analysis showed a representation of neuronal tumor relevant gene functions among the differentially methylated genes. For validation, we used a set of independent tumors previously analyzed with the Illumina 27K methylation arrays, which confirmed the differentially methylated sites. Top candidate genes with aberrant methylation were analyzed for altered gene expression through the R2 platform ( ht...Continue Reading

References

Jun 5, 2002·Genome Research·W James KentDavid Haussler
Aug 19, 2004·Journal of the National Cancer Institute·Miguel AlaminosManel Esteller
Oct 18, 2007·British Journal of Cancer·H CarénT Martinsson
Sep 30, 2008·Cancer Letters·Jasmien HoebeeckJo Vandesompele
Oct 17, 2008·Nature·Isabelle Janoueix-LeroseyOlivier Delattre
Oct 17, 2008·Nature·Yuyan ChenSeishi Ogawa
Dec 3, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Tom MonclairUNKNOWN INRG Task Force
Dec 3, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Susan L CohnUNKNOWN INRG Task Force
Feb 24, 2009·Biochemical and Biophysical Research Communications·Naoto MiyajimaShigetsugu Hatakeyama
Aug 5, 2009·Neurochemistry International·Johanna El Andaloussi-LiljaAnna Forsby
Feb 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Helena CarénTommy Martinsson
Aug 16, 2011·Genomics·Marina BibikovaRichard Shen
Dec 18, 2013·Bioinformatics·Tiffany J MorrisStephan Beck
Oct 31, 2015·Seminars in Cell & Developmental Biology·Cristina Tocchini, Rafal Ciosk

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Citations

Dec 31, 2016·International Journal of Molecular Sciences·Brittany M SalazarShizhen Zhu
Jan 20, 2018·Cell and Tissue Research·Kaat Durinck, Frank Speleman
Nov 24, 2019·International Journal of Molecular Sciences·Sandra Ackermann, Matthias Fischer
Jun 9, 2020·Clinical and Translational Medicine·Ting-Juan ZhangJing-Dong Zhou
Jun 30, 2019·Molecular Cytogenetics·Christoph StandfußAndreas Klein
Apr 30, 2017·Journal of Pediatric Hematology/oncology·Xiao-Feng Duan, Qiang Zhao
Jul 14, 2018·Scientific Reports·Yoon ChoJae-Chun Ryu
Mar 3, 2020·Frontiers in Physiology·Shubha Gururaja RaoHarpreet Singh
Jul 31, 2020·International Journal of Molecular Sciences·Cara-Lynne Schengrund
Sep 12, 2018·Children·Erin K Barr, Mark A Applebaum
Dec 11, 2019·Bioscience Reports·Yonghu XuGuofeng Xu
Sep 10, 2020·Cancer Management and Research·Yanping HuXiaomin Zhang
Dec 15, 2019·Cancer Metastasis Reviews·Daniel A WeiserMark A Applebaum
Jun 9, 2020·PLoS Genetics·Tajana Tešan TomićFrida Abel
Jan 30, 2018·Japanese Journal of Clinical Oncology·Akira NakagawaraMasanori Nishi
Feb 28, 2019·BMC Medical Genetics·Flora CimminoMario Capasso
Apr 12, 2019·Interdisciplinary Sciences, Computational Life Sciences·Anil Kumar TomarBishwajit Kundu
May 11, 2021·Frontiers in Pharmacology·Zhichao LiuWeida Tong
Nov 10, 2021·Future Oncology·Abdulazeez GiwaHocine Bendou

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Datasets Mentioned

BETA
GSE54719
GSE45547
GSE62564
GSE54720

Methods Mentioned

BETA
PCR

Software Mentioned

R
Phenogram
R NMF package
package ChAMP
GenomeStudio
ChAMP
BeadStudio
DAVID
INRG
Gene Probe

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