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A Gene Expression Signature for Relapse of Primary Wilms Tumors

¹ Department of Genetics, Case Western Reserve University; ² Department of Cancer Biology, Cleveland Clinic Foundation, Cleveland, Ohio; ³ Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada; ⁴ Department of Biochemistry, University of Otago, Dunedin, New Zealand; and ⁵ Pediatric Haematology/Oncology, Starship Children's Hospital, Auckland, New Zealand

Requests for reprints: Bryan R.G. Williams, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195. Phone: 216-445-9652; Fax: 216-444-3164; E-mail: williab{at}ccf.org.

Anaplastic histology and metastasis are each associated with higher relapse and mortality rates in Wilms tumor patients. However, not all anaplastic tumors relapse and some nonanaplastic tumors relapse unexpectedly. To identify more accurate early prognostic indicators, we analyzed expression of 4,900 cancer-related genes in 26 primary Wilms tumors. This analysis revealed that expression of a set of four genes predicts future relapse of primary Wilms tumors with high accuracy, independent of anaplasia. Random permutation testing of this prognostic gene expression signature yielded P = 0.003. Real-time reverse transcription-PCR analysis of the four genes in an independent primary tumor set resulted in correct prediction of future relapse with an accuracy of 92%. One of the four genes in the prognostic signature, CCAAT/enhancer binding protein ß (C/EBPB), is expressed at higher levels in both primary relapsing tumors and metastatic tumors than in primary nonrelapsing tumors. Short interfering RNA–mediated down-regulation of C/EBPB expression in WiT49, a cell line derived from a metastatic Wilms tumor, resulted in spontaneous apoptosis. These findings suggest that C/EBPB is a critical survival factor for Wilms tumor cells and that its expression contributes to the prognosis of Wilms tumor patients.

Key Words: Wilms tumor • profiling • molecular signature • relapse • C/EBP ß

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