Wilms' tumour (WT) is a pediatric tumor of the kidney that arises via failure of 
the fetal developmental program. The absence of identifiable mutations in the 
majority of WTs suggests the frequent involvement of epigenetic aberrations in 
WT. We therefore conducted a genome-wide analysis of promoter hypermethylation 
in WTs and identified hypermethylation at chromosome 5q31 spanning 800 kilobases 
(kb) and more than 50 genes. The methylated genes all belong to alpha-, beta-, 
and gamma-protocadherin (PCDH) gene clusters (Human Genome Organization 
nomenclature PCDHA@, PCDHB@, and PCDHG@, respectively). This demonstrates that 
long-range epigenetic silencing (LRES) occurs in developmental tumors as well as 
in adult tumors. Bisulfite polymerase chain reaction analysis showed that PCDH 
hypermethylation is a frequent event found in all Wilms' tumor subtypes. 
Hypermethylation is concordant with reduced PCDH expression in tumors. WT 
precursor lesions showed no PCDH hypermethylation, suggesting that de novo PCDH 
hypermethylation occurs during malignant progression. Discrete boundaries of the 
PCDH domain are delimited by abrupt changes in histone modifications; 
unmethylated genes flanking the LRES are associated with permissive marks which 
are absent from methylated genes within the domain. Silenced genes are marked 
with non-permissive histone 3 lysine 9 dimethylation. Expression analysis of 
embryonic murine kidney and differentiating rat metanephric mesenchymal cells 
demonstrates that Pcdh expression is developmentally regulated and that Pcdhg@ 
genes are expressed in blastemal cells. Importantly, we show that PCDHs 
negatively regulate canonical Wnt signalling, as short-interfering RNA-induced 
reduction of PCDHG@ encoded proteins leads to elevated beta-catenin protein, 
increased beta-catenin/T-cell factor (TCF) reporter activity, and induction of 
Wnt target genes. Conversely, over-expression of PCDHs suppresses 
beta-catenin/TCF-reporter activity and also inhibits colony formation and growth 
of cancer cells in soft agar. Thus PCDHs are candidate tumor suppressors that 
modulate regulatory pathways critical in development and disease, such as 
canonical Wnt signaling.