title: Genome-wide methylation analyses in glioblastoma multiforme.
abstract: Few studies had investigated genome-wide methylation in glioblastoma multiforme (GBM). Our goals were to study differential methylation across the genome in gene promoters using an array-based method, as well as repetitive elements using surrogate global methylation markers. The discovery sample set for this study consisted of 54 GBM from Columbia University and Case Western Reserve University, and 24 brain controls from the New York Brain Bank. We assembled a validation dataset using methylation data of 162 TCGA GBM and 140 brain controls from dbGAP. HumanMethylation27 Analysis Bead-Chips (Illumina) were used to interrogate 26,486 informative CpG sites in both the discovery and validation datasets. Global methylation levels were assessed by analysis of L1 retrotransposon (LINE1), 5 methyl-deoxycytidine (5m-dC) and 5 hydroxylmethyl-deoxycytidine (5hm-dC) in the discovery dataset. We validated a total of 1548 CpG sites (1307 genes) that were differentially methylated in GBM compared to controls. There were more than twice as many hypomethylated genes as hypermethylated ones. Both the discovery and validation datasets found 5 tumor methylation classes. Pathway analyses showed that the top ten pathways in hypomethylated genes were all related to functions of innate and acquired immunities. Among hypermethylated pathways, transcriptional regulatory network in embryonic stem cells was the most significant. In the study of global methylation markers, 5m-dC level was the best discriminant among methylation classes, whereas in survival analyses, high level of LINE1 methylation was an independent, favorable prognostic factor in the discovery dataset. Based on a pathway approach, hypermethylation in genes that control stem cell differentiation were significant, poor prognostic factors of overall survival in both the discovery and validation datasets. Approaches that targeted these methylated genes may be a future therapeutic goal.
authors.affiliation: Departments of Neurology, Neurosurgery and Preventive Medicine, University of Southern California, Los Angeles, California, United States of America.
authors.forename: Rose K
authors.initials: RK
authors.lastname: Lai
authors.affiliation: Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America.
authors.forename: Yanwen
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Guan
authors.affiliation: Departments of Neurology, Neurosurgery and Preventive Medicine, University of Southern California, Los Angeles, California, United States of America.
authors.forename: Darryl
authors.initials: D
authors.lastname: Nousome
authors.affiliation: Department of Radiation Oncology, Columbia University, New York, New York, United States of America.
authors.forename: Charu
authors.initials: C
authors.lastname: Sharma
authors.affiliation: Departments of Pathology, Columbia University, New York, New York, United States of America.
authors.forename: Peter
authors.initials: P
authors.lastname: Canoll
authors.affiliation: Departments of Neurosurgery, Columbia University & Bartoli Brain Tumor Research Laboratory, Columbia University, New York, New York, United States of America.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Bruce
authors.affiliation: Department of Neurological Surgery, University Hospitals-Case Medical Center, Case Western Reserve University, United States of America.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Sloan
authors.affiliation: New York Brain Bank, Columbia University, New York, New York, United States of America.
authors.forename: Etty
authors.initials: E
authors.lastname: Cortes
authors.affiliation: Departments of Pathology, Columbia University, New York, New York, United States of America ; New York Brain Bank, Columbia University, New York, New York, United States of America.
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Vonsattel
authors.affiliation: Pathology Core, Herbert Irving Cancer Center, Columbia University, New York, New York, United States of America.
authors.forename: Tao
authors.initials: T
authors.lastname: Su
authors.affiliation: Department of Environmental Health Sciences, Columbia University & Biomarker Core, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, United States of America.
authors.forename: Lissette
authors.initials: L
authors.lastname: Delgado-Cruzata
authors.affiliation: Department of Environmental Health Sciences, Columbia University & Biomarker Core, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, United States of America.
authors.forename: Irina
authors.initials: I
authors.lastname: Gurvich
authors.affiliation: Department of Environmental Health Sciences, Columbia University & Biomarker Core, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, United States of America.
authors.forename: Regina M
authors.initials: RM
authors.lastname: Santella
authors.affiliation: Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America.
authors.forename: Quinn
authors.initials: Q
authors.lastname: Ostrom
authors.affiliation: Feinstein Institute of Medical Genetics, North Shore University Hospital, Manhasset, New York, United States of America.
authors.forename: Annette
authors.initials: A
authors.lastname: Lee
authors.affiliation: Feinstein Institute of Medical Genetics, North Shore University Hospital, Manhasset, New York, United States of America.
authors.forename: Peter
authors.initials: P
authors.lastname: Gregersen
authors.affiliation: Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America.
authors.forename: Jill
authors.initials: J
authors.lastname: Barnholtz-Sloan
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001921:Brain / Q000473:pathology*; D001932:Brain Neoplasms / Q000235:genetics* / Q000473:pathology; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D055106:Genome-Wide Association Study; D005909:Glioblastoma / Q000235:genetics* / Q000473:pathology; D006801:Humans; D008297:Male; D008875:Middle Aged; D011401:Promoter Regions, Genetic