Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma

Abstract

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.

An Epigenetic Genome-Wide Screen Identifies SPINT2 as a Novel Tumor Suppressor Gene in Pediatric Medulloblastoma

“…The first genome-wide approach to the MB (32) identified aberrant methylation affecting f6% and 1% of genes in MB cell lines and primary tumors respectively. Three additional genomewide studies have been published (29,30,33). Waha and colleagues (30) performed a differential methylation hybridization technique, from which they identified secretory granule neuroendocrine protein 1 (SGNE1/7B2) as a putative TSG that is methylated in MB.…”

Epigenetic mechanisms regulating neural development and pediatric brain tumor formation

“…86 Epigenome-wide studies have identified different genes suppressed by DNA hypermethylation, such as ZIC2, COL1A2, and KLF4. 3,107,117 The work by Northcott et al 110 suggested that chromatin modifications contribute to medulloblastoma development. The authors described new amplifications and homozygous deletions targeting genes involved in histone lysine methylation, particularly H3K9: for example, amplifications of histone lysine demethylases (JMJD2C and JMJD2B), deletions of histone lysine methylatransferases (EHMT1 and SMYD4), and deletions in genes of the Polycomb group (L3MBTL2 and L3MBTL3).…”

Expression status of Zic family member 2 as a prognostic marker for oral squamous cell carcinoma

“…Dopamine receptor D1 stimulates adenylyl cyclase and cyclic AMP-dependent protein kinases and regulates neuronal growth, development, and dopamine receptor D2-mediated events (Missale et al 1998). Up-regulated ZIC2 has been reported in invasive human tumors, such as lung cancers, endometrial cancers, pediatric medulloblastoma and synovial sarcoma (Gure et al 2000;Bidus et al 2006;PWster et al 2007;Fernebro et al 2006). In addition, ZIC2 antibody was isolated in sera obtained from patients with small cell lung cancer (Gure et al 2000;Sabater et al 2008;Vural et al 2005).…”