Novel epigenetic signature, molecular subtypes and insights into IGF2/H19 dysregulation in Wilms tumour revealed by methylomic and transcriptomic profiling

<title>Abstract</title> Wilms tumour (WT), the most common kidney cancer in children, results from disrupted kidney development and frequently exhibits molecular alterations at the 11p15.5 imprinted locus, affecting <italic>IGF2</italic> and <italic>H19</italic> genes. The epigenetic landscape beyond 11p15.5 suggests diagnostic and prognostic potential, but its link to transcriptomic changes is largely unexplored. To characterise this broader epigenetic and transcriptional landscape, we integrated methylomic and transcriptomic datasets of 27 primary tumours and matched normal 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 showed extensive epigenetic alterations, whereas regressive tumours were less affected. Three methylation clusters were identified, also corresponding to subtypes defined by transcriptomic profiling and characterised by distinct tumour microenvironment and chemosensitivity predictions. 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 <italic>IGF2</italic> / <italic>H19</italic> locus uncovered multiple regulatory layers of <italic>IGF2</italic> activation involving IC1 and DMR0 methylation, promoter usage, and transcriptional modulation by PLAG1 and BAHD1. These findings define the epigenetic architecture and transcriptomic heterogeneity of WT and support stratification of cases for improved prognosis and therapeutic approaches.