Both Epimutations and Chromosome Aberrations Affect Multiple Imprinted Loci in Aggressive Wilms Tumors.

Laura Pignata,Orazio Palumbo,Enrique De Álava,Gaetano Verde,Josep Roma,Andrea Riccio,Soledad Gallego,Flavia Cerrato,Jaume Mora,Basilia Acurzio,Massimo Carella

doi:10.3390/cancers12113411

Abstract

Simple SummaryAbout 7% of all children’s malignancies are represented by the embryonal renal cancer Wilms tumor (WT). Since methylation imprinting alterations at multiple loci dictated by chromosome copy-number variations have been recently demonstrated in adult cancers, we investigated the presence of similar alterations in pediatric malignancies. Our results demonstrated that 35% of WT cases were affected by methylation abnormalities of multiple imprinted loci. However, differently from adult cancers, they were associated with either chromosome aberrations or normal chromosome profiles. Epigenotype–phenotype correlations indicated that these epimutations were more frequent in highly aggressive tumors, suggesting the use of multiple methylation imprinting defects as a new informative marker for WT.The embryonal renal cancer Wilms tumor (WT) accounts for 7% of all children’s malignancies. Its most frequent molecular defect is represented by DNA methylation abnormalities at the imprinted 11p15.5 region. Multiple imprinted methylation alterations dictated by chromosome copy-number variations have been recently demonstrated in adult cancers, raising the question of whether multiple imprinted loci were also affected in WT. To address this issue, we analyzed DNA methylation and chromosome profiles of 7 imprinted loci in 48 WT samples. The results demonstrated that methylation abnormalities of multiple imprinted loci occurred in 35% of the cases, but that they were associated with either chromosome aberrations or normal chromosome profiles. Multiple imprinted methylation changes were correlated with tumor stage and presence of metastasis, indicating that these epimutations were more frequent in highly aggressive tumors. When chromosome profiles were affected, these alterations were extended to flanking cancer driver genes. Overall, this study demonstrates the presence of multiple imprinted methylation defects in aggressive WTs and suggests that the mechanism by which they arise in embryonal and adult cancers is different.

Highlights

Wilms tumor (WT) is a pediatric renal cancer, which typically affects 1 child per 10,000 worldwide before the age of 15 years
In order to investigate whether imprinted methylation outside of the 11p15.5 locus (H19/IGF2:IG-differentially methylated region (DMR) and KCNQ10T1:TSS-DMR) is affected in WT, we analyzed the DNA methylation profile of five further imprinted DMRs (PLAGL1, GNAS, MEST, GRB10 and MEG3) in 48 WTs and 23 normal kidney tissues, by bisulfite conversion and pyrosequencing
The results demonstrated that methylation imprinting defects were present at more than one imprinted region in 35% of tumors(Wilms tumor with multi-locus imprinted methylation aberration, WT-MLIMA), while 38% of the cases showed gain and/or loss of methylation only at a single locus (Wilms tumor with single-locus imprinted methylation aberration, WT-SLIMA,), and only 27% showed a methylation profile similar to normal kidneys at all tested imprinted regions (Wilms tumor with normal imprinted methylation, WT-NIM,) (Figure 1A)

Summary

Introduction

Wilms tumor (WT) is a pediatric renal cancer, which typically affects 1 child per 10,000 worldwide before the age of 15 years. This malignancy is generally sporadic, with only 1–2% of familial cases [1]. DNA methylation abnormalities of chromosome 11p15.5 are very common in WTs [4,5,6,7]. This region contains a cluster of genes controlled by genomic imprinting, a mechanism causing a gene to be expressed only from its maternal or its paternal allele. The imprinted gene cluster located at 11p15.5 is functionally divided into two domains containing an ICR each, namely the

Methods

Results

Conclusion