And hence downregulation of PDE4B, may contribute to the sensitivity
And hence downregulation of PDE4B, may contribute to the sensitivity to apoptosis observed in WT1 mutant cells. Although the true expression relationships between WT1 and these genes awaits experimental validation, the SVM predictions provide insight into the possible targets of WT1 and can help in guiding further experimentation. For the results of additional analysis using the DAVID annotation system see Additional File 5 (genes related to cellular adhesion, cytoskeleton, or motility) and Additional File 6 (genes related to the nervous system).Disease associated chromosomal loci are significantly enriched in predicted WT1 targets In recent years it has become clear that there are distinct pathways of tumor formation in syndromatic versus sporadic tumors. As mentioned earlier, syndromatic tumors often contain a mutation in WT1 (Denys Drash and WAGR syndromes) or loss of the nearby region 11p15.5 (Beckwith-Wiedemann syndrome) [127,127]. The WT1 gene is located in 11p13, and naturally explains why disruption of this region contributes to tumor formation [139-142]. The syndromes resulting from these abnormalities and their associated chromosomal changes are listed in Table 1.Only 10?5 of sporadic tumors have a WT1 mutation [112,113,115,121,122]; however, sporadic cases tend to have a variety of other genomic changes including loss of heterozygosity (LOH) and loss of imprinting (LOI). In sporadic tumors LOH occurs in 11p15 where the maternal copy PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27484364 of 11p15 is lost, often in conjunction with duplication of the paternal copy [128,143]. This causes the overexpression of some genes and the silencing of others, notably IGF2 [144-147] which is often upregulated, H19 [148-150] which is often silenced, and p57 [151-153]. Besides 11p15 [128], LOH in sporadic cases occurs in 1p, 4q, 7p, 11q, 14q,16q, and 17p [123]. LOI is an early stage event in sporadic tumors, and occurs in several regions including 11q, 16q, 4p, and 7p [123]. Figure 5 depicts some of the genetic changes which may lead to tumor formation by the syndromatic or sporadic pathways. These data suggest that regions shown to undergo LOH harbor genes buy SC144 regulated by WT1 or downstream effectors, yet these observations currently have no cohesive framework relating them. We show that by combining published data and the newly identified WT1 targets reported here, past observations on sporadic and syndromatic tumors can be tied together, relating them in molecular detail to misregulation or a loss of WT1 and/or modification of its targets. Strikingly, examining the predicted targets of WT1 shows that these genes occur more frequently than expected by chance in several genomic regions including cytobands 11p15.5 (p = 6.3e-5, 8 new predictions), 1p36.3 (p = 6.3e4, 3 new predictions), and 4p16.3 (p = 4.3e-3, 5 new predictions) (analysis in DAVID [33], see Methods). Three of the new targets for WT1 in 11p15.5 are possible tumor suppressors: RNH1 [154], IGF2AS [155], and CD151 [156,157]. If in fact WT1 normally activates these genes it could explain why inactivation of WT1 or loss of genes in 11p15.5 contributes to cancer formation, since in both cases expression of these tumor suppressors would be abolished. Also in these regions are 2 possible oncogenes (1 previously known GF2, 1 ew HRAS), one gene expressed in the fetal kidney which may be involved in adhesion (MUCDHL [158]), and one known to contribute to cancer progression (FGFR3 [159-161]). Of particular interest in 11p15.5 is MUCDHL, the cadher.
