Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.
Existing microarray-based approaches for screening of DNA methylation are hampered by a number of shortcomings, such as the introduction of bias by DNA copy-number imbalances in the test genome and negligence of tissue-specific methylation patterns. We developed a method designated array-based profiling of reference-independent methylation status (aPRIMES) that allows the detection of direct methylation status rather than relative methylation. Array-PRIMES is based on the differential restriction and competitive hybridization of methylated and unmethylated DNA by methylation-specific and methylation-sensitive restriction enzymes, respectively. We demonstrate the accuracy of aPRIMES in detecting the methylation status of CpG islands for different states of methylation. Application of aPRIMES to the DNA from desmoplastic medulloblastomas of monozygotic twins showed strikingly similar methylation profiles. Additional analysis of 18 sporadic medulloblastomas revealed an overall correlation between highly methylated tumors and poor clinical outcome and identified ZIC2 as a frequently methylated gene in pediatric medulloblastoma.
Pfister
Stefan
S
Department of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany.
Schlaeger
Christof
C
Mendrzyk
Frank
F
Wittmann
Andrea
A
Benner
Axel
A
Kulozik
Andreas
A
Scheurlen
Wolfram
W
Radlwimmer
Bernhard
B
Lichter
Peter
P
D002528:Cerebellar Neoplasms / Q000235:genetics* / Q000378:metabolism; D002675:Child, Preschool; D019175:DNA Methylation; D015536:Down-Regulation; D044127:Epigenesis, Genetic; D020868:Gene Silencing; D023281:Genomics / Q000379:methods; D006801:Humans; D008527:Medulloblastoma / Q000235:genetics* / Q000378:metabolism; D009687:Nuclear Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics*; D014430:Twins, Monozygotic
D009687:Nuclear Proteins; D012333:RNA, Messenger; D014157:Transcription Factors; C491812:ZIC2 protein, human