Supplementary Material for: Identification of Genes Targeted by CpG Island Methylator Phenotype in Neuroblastomas, and Their Possible Integrative Involvement in Poor Prognosis

<i>Background/Aims:</i> CpG island (CGI) methylator phenotype (CIMP) is strongly associated with poor prognosis in neuroblastomas (NBLs; hazard ratios 7–22). Methylation of nonpromoter CGIs is useful to detect the presence of the CIMP, while the poor prognosis is considered to be caused by gene silencing due to promoter methylation. Here, promoter CGIs targeted by the CIMP were searched for. <i>Methods:</i> A genome-wide screening was performed by methylation-sensitive representational difference analysis of CIMP(+) and CIMP(–) NBLs. <i>Results:</i> Promoter CGIs of 9 genes were methylated in CIMP(+) NBL cell lines and caused silencing of their downstream genes. On analysis of 90 clinical specimens, <i>CYP26C1,</i><i>FERD3L </i>(<i>N-TWIST</i>), <i>CRYBA2</i> and <i>PCDHGC4 </i>were methylated at significantly higher incidences in CIMP(+) NBLs than CIMP(–) NBLs, while the difference was unclear for <i>NPY</i>, <i>SPAG6</i>, <i>DDIT4L</i>, <i>CHR3SYT</i> and <i>C6Orf141</i>. Methylation of <i>CYP26C1 </i>and <i>FERD3L</i> was significantly associated with poor prognosis, but weaker than the presence of the CIMP. Treatment of an NBL cell line with a demethylating agent caused demethylation of multiple promoter CGIs, and enhanced 13-<i>cis</i>-retinoic acid-induced neuronal differentiation. <i>Conclusion:</i> Our results indicate that the CIMP causes poor prognosis of NBLs by inducing methylation of multiple promoter CGIs with various incidences.