Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma

Abstract

BackgroundEpigenetic mechanisms such as DNA methylation and histone modifications are important regulators of gene expression and are frequently involved in silencing tumor suppressor genes.MethodsIn order to identify genes that are epigenetically regulated in neuroblastoma tumors, we treated four neuroblastoma cell lines with the demethylating agent 5-Aza-2'-deoxycytidine (5-Aza-dC) either separately or in conjunction with the histone deacetylase inhibitor trichostatin A (TSA). Expression was analyzed using whole-genome expression arrays to identify genes activated by the treatment. These data were then combined with data from genome-wide DNA methylation arrays to identify candidate genes silenced in neuroblastoma due to DNA methylation.ResultsWe present eight genes (KRT19, PRKCDBP, SCNN1A, POU2F2, TGFBI, COL1A2, DHRS3 and DUSP23) that are methylated in neuroblastoma, most of them not previously reported as such, some of which also distinguish between biological subsets of neuroblastoma tumors. Differential methylation was observed for the genes SCNN1A (p < 0.001), PRKCDBP (p < 0.001) and KRT19 (p < 0.01). Among these, the mRNA expression of KRT19 and PRKCDBP was significantly lower in patients that have died from the disease compared with patients with no evidence of disease (fold change -8.3, p = 0.01 for KRT19 and fold change -2.4, p = 0.04 for PRKCDBP).ConclusionsIn our study, a low methylation frequency of SCNN1A, PRKCDBP and KRT19 is significantly associated with favorable outcome in neuroblastoma. It is likely that analysis of specific DNA methylation will be one of several methods in future patient therapy stratification protocols for treatment of childhood neuroblastomas.

Neuroblastoma epigenetics: From candidate gene approaches to genome-wide screenings

“…However, only four publications perform a genome-wide expression study after a pharmacologic unmasking screening strategy. 28,31,32,34 In all four publications, this led to the discovery of previously undescribed DNA-methylation biomarkers in NB. In all other research papers, re-activation is shown by (quantitative) PCR for a limited set of genes of interest, in order to demonstrate the link between DNA-methylation and transcriptional silencing in NB cell lines.…”

“…A frequently used high-throughput platform, making use of different probe types for methylated vs. unmethylated bisulfite treated DNA is the Illumina Infinium HumanMethylation27 BeadChip. This technique with over 27,000 methylation-specific probes has recently been applied on NB primary samples 34 and has led to the identification of several novel methylation biomarkers that show potential for prognostic use.…”

Hypermethylation of collagen α2 (I) gene (COL1A2) is an independent predictor of survival in head and neck cancer

“…Structural integrity and coordinated biosynthesis of the two chains are critically important for tissue morphogenesis, growth, homeostasis, and repair [11]. Hypermethylation of COL1A2 has been described in many cancers, mainly adenocarcinomas, including colorectal cancer [12], melanoma [13], bladder cancer [14], neuroblastoma [15], medulloblastoma [16,17], breast cancer [18], and hepatoma [19]. The investigation for oncogenic mechanism by COL1A2 gene inactivation was also recently progressing.…”

Emerging Roles of Atypical Dual Specificity Phosphatases in Cancer

“…The dusp23 gene is highly methylated and decreased dusp23 mRNA expression is observed in neuroblastoma [107]. Interestingly, dusp23 mRNA levels were lower in tumors from deceased patients than patients exhibiting no clinical symptoms, suggesting that DUSP23 levels could be a prognostic marker for neuroblastomas [107].…”

“…Interestingly, dusp23 mRNA levels were lower in tumors from deceased patients than patients exhibiting no clinical symptoms, suggesting that DUSP23 levels could be a prognostic marker for neuroblastomas [107]. The generality of dusp23 functioning as a tumor suppressor is called into question by observations that it is amplified in many other cancers, including breast, colon, lung, squamous carcinoma, pancreatic, brain, esophageal, stomach, bladder, kidney, skin, ovary, prostate, and testicular cancers [108], and selective over-expression of dusp23 in MCF7 cells increased proliferation while knock-down of dusp23 decreased proliferation [108].…”