Abstract 660: Genome Wide DNA methylation profiling in Wilms tumor. Integration with expression and identification of molecular signatures associated with high risk blastemal type histology.
Authors: Alcaide German Marisa , Williams Richard , Charlton Jocelyn , Chagtai Tasnim , Morris Tiffany , Pearce Kerra , Pritchard-Jones Kathy 
Published: August 2014

Abstract
Introduction: Wilms tumour (WT) is the most common paediatric renal tumour, thought to arise from disruption in normal kidney development. WT typically presents triphasic histology with blastemal, stromal and epithelial components. The International Society of Paediatric Oncology (SIOP) categorises Wilms tumours based on their in vivo response to neoadjuvant chemotherapy. Tumours where a viable blastemal component predominates at nephrectomy (high risk ‘blastemal type’, BT) are associated with poorer outcome than tumours with primarily stromal, epithelial or mixed histology (intermediate risk, IR).
Although a number of WT-associated genes have been defined, most tumours do not harbour mutations in any of these genes. Global hypo-methylation as well as hyper-methylation and silencing of tumour suppressor genes have been frequently reported in cancer. In WT, several epigenetic lesions have previously been identified, particularly loss of imprinting at 11p13 and 11p15. However, to date, no genome wide comprehensive DNA methylation study in WT has been reported.
Aim: To perform genome wide DNA methylation profiling in WT and identify molecular signatures associated with BT WT.
Methods: Genomic DNA from 69 frozen clinical WT samples was extracted and bisulphite- converted with the Zymo EZ DNA Methylation Kit. The methylation levels were assessed on the Infinium HumanMethylation 450 BeadChip array, which interrogates over 480,000 CpG sites. For 56 of the samples, HumanHT-12 v3 Expression BeadChip data was available. Bioinformatic and statistical analyses were carried out using the Bioconductor minfi and limma packages. Preliminary analysis was performed integrating expression and methylation data.
Results: 930 genes showed differential methylation between BT and IR. Over 70% of the samples showed aberrant methylation at the 11p15 locus, as previously reported. 75 of these differentially methylated genes were also differentially expressed. Of interest, the well characterised WT gene, WT1, was significantly down regulated in IR, and correlated with hypermethylation in this region. Gene Ontology pathway analysis indicated that almost 50% of these 75 genes were involved in developmental processes, supporting the current model of WT.
Conclusions: This study highlighted several key genes and pathways dysregulated in BT compared to IR. Moreover, global hypomethylation was found in the BT cohort, which could be associated with genome instability or the dysregulation of DNA methyl-transferase maintenance enzymes. Further studies are required to validate these molecular routes as potential biomarkers for high risk WT.
Citation Format: Marisa Alcaide German, Richard Williams, Jocelyn Charlton, Tasnim Chagtai, Tiffany Morris, Kerra Pearce, Kathy Pritchard-Jones. Genome Wide DNA methylation profiling in Wilms tumor. Integration with expression and identification of molecular signatures associated with high risk blastemal type histology. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 660. doi:10.1158/1538-7445.AM2013-660