DNA methylation and transcriptomic profiles of Wilms tumour reveal new deregulated genes and epigenetic processes relevant for tumour stratification and management

Wilms tumour (WT), the most common kidney cancer in children, presents features of altered kidney development and frequently exhibits molecular alterations at the 11p15.5 imprinted locus, affecting the IGF2 and H19 genes, which contribute to tumour growth and may also act as predisposing events that require additional hits for tumour initiation. The epigenetic landscape beyond 11p15.5 suggests diagnostic and prognostic potential, but its link to transcriptomic changes is largely unexplored. We integrated methylomic and transcriptomic datasets of 27 primary tumours and matched non-neoplastic kidneys. DNA methylation profiling identified around 9,000 differentially methylated CpG sites distinguishing neoplastic from non-neoplastic tissue and other pediatric cancers, thus representing a novel WT-specific epigenetic signature. We found that cases with Imprinting Centre 1 (IC1) gain of methylation exhibited the most extensive epigenetic alterations, LOH tumours showed intermediate changes, whereas regressive tumours with largely normal 11p15.5 status displayed limited methylation abnormalities. Three methylation clusters corresponding to transcriptomic subtypes were identified, characterised by distinct tumour microenvironment and chemosensitivity predictions: a regressive-enriched group with high immune infiltration and predicted susceptibility to paclitaxel, a proliferative group with high tumour purity and predicted sensitivity to doxorubicin, and a stromal-like group with intermediate predicted sensitivity to both drugs. Combined analysis of methylation and expression data revealed more than 900 genes under epigenetic control, which contributed to defining the WT subtypes. Analysis of the IGF2/H19 locus uncovered multiple regulatory mechanisms underlying IGF2 activation, including imprinting defects at IC1, methylation changes at DMR0, differential promoter usage, and transcriptional modulation by PLAG1 and BAHD1. These findings define the epigenetic architecture of WT, encompassing genome-wide methylation changes, subtype-specific patterns, and their integration with gene expression, supporting stratification of cases for improved prognosis and therapeutic approaches.