AbstractBackgroundWilms tumor is the most common pediatric renal malignancy, but the parameters that are important to its invasion capacity are poorly understood. The aim of this study was to identify new proteins associated with the invasion capacity of Wilms tumor.ProcedureGene expression profiles for 15 primary Wilms tumor samples were determined by Affymetrix Genechip® Human Genome Ul33A microarray analysis. The gene expression profiles for selected genes was further confirmed by quantitative RT‐PCR analysis. Immunohistochemical analysis was performed on 25 Wilms tumor cases to confirm expression for Bcl2A1, EphB2, MSX1, and RIN1.ResultsUsing microarray analysis 14 genes showed differential expression (P < 0.05) comparing stage 1 non‐invasive Wilms tumor to stages 2–4 invasive Wilms tumor. The differential expression for Bcl2A1, EphB2, MSX1, and RIN1 was confirmed by quantitative RT‐PCR. MSX1 protein was statistically significantly lower in stages 2–4 invasive Wilms tumor cases compared to stage 1 non‐invasive cases (P = 0.013). EphB2 protein was higher in stages 2–4 Wilms tumor cases compared to stage 1 cases (P = 0.006). There was no statistically significant difference between stages 1 and 2–4 Wilms tumor for Bcl2A1 (P = 0.230) or RIN1 (P = 0.969) at the protein level.ConclusionOur results indicate that MSX1 may be associated with the invasion capacity of Wilms tumors. RIN1 is a downstream effector of RAS and Bcl2A1 functions as an anti‐apoptotic protein. EphB2 is an ephrin receptor and is up‐regulated in invasive tumors but its role needs to be confirmed in further cases of Wilms tumors. Pediatr Blood Cancer 2011; 57: 950–957. © 2011 Wiley‐Liss, Inc.