Signature in Renal Carcinoma Figure 4. Adipogenic differentiation signature in clear cell renal cell carcinoma. a. Heatmap showing adipogenic gene expression signature in ccRCC. Upregulation of genes is indicated in red, downregulation is indicated in green, and similar expression is indicated in black. b. IHC showing lipid-laden clear cell morphology of ccRCC, increased expression of ADFP, and decreased expression of GATA2 in ccRCC. Sum scores are shown with n, as indicated. *p,0.01 when comparing ccRCC to normal match. doi:10.1371/journal.pone.0010696.g004 list of genes known to be involved in EMT [24] and selected 40 EMT genes from our ccRCC data set that represented an EMT genotype (Fig. 7a). Well known upregulated molecular markers include N- cadherin (CDH2, M34064), fibronectin (FN1, AK026737), trans- forming growth factor b1 (TGFb1, BC000125) and vimentin (VIM, A1922599) (Fig. 7a). We validated vimentin (VIM) and N-cadherin (CDH2) at the protein level (Fig. 7b). Vimentin protein expression in ccRCC has been previously described by us and others [25,26]. Our results agree with previously reported findings that reveal upregulated expression of fibronectin in ccRCC at the gene and protein levels [11,27,28]. In summary, the pattern of directional alterations in our gene set indicates for an EMT gene expression signature and is consistent with an EMT phenotype. We further validated our findings by comparing a publicly available gene expression database (GSE#15641) of early-stage ccRCC against normal renal samples (Fig. S3). Cellular differentiation model in pathogenesis of ccRCC Based on our cumulative data, we propose a model for aberrant cellular differentiation events in renal carcinogenesis that includes PLoS ONE | www.plosone.org 7 May 2010 | Volume 5 | Issue 5 | e10696