Cancer Identification of a MicroRNA Panel for Clear-cell Kidney Cancer David Juan, Gabriela Alexe, Travis Antes, Huiqing Liu, Anant Madabhushi, Charles Delisi, Shridhar Ganesan, Gyan Bhanot, and Louis S. Liou OBJECTIVES To identify a robust panel of microRNA signatures that can classify tumor from normal kidney using microRNA expression levels. Mounting evidence suggests that microRNAs are key players in essential cellular processes and that their expression pattern can serve as diagnostic biomarkers for cancerous tissues. METHODS We selected 28 clear-cell type human renal cell carcinoma (ccRCC), samples from patient- matched specimens to perform high-throughput, quantitative real-time polymerase chain reac- tion analysis of microRNA expression levels. The data were subjected to rigorous statistical analyses and hierarchical clustering to produce a discrete set of microRNAs that can robustly distinguish ccRCC from their patient-matched normal kidney tissue samples with high confidence. RESULTS Thirty-five microRNAs were found that can robustly distinguish ccRCC from their patient- matched normal kidney tissue samples with high confidence. Among this set of 35 signature microRNAs, 26 were found to be consistently downregulated and 9 consistently upregulated in ccRCC relative to normal kidney samples. Two microRNAs, namely, MiR-155 and miR-21, commonly found to be upregulated in other cancers, and miR-210, induced by hypoxia, were also identified as overexpressed in ccRCC in our study. MicroRNAs identified as downregulated in our study can be correlated to common chromosome deletions in ccRCC. CONCLUSIONS Our analysis is a comprehensive, statistically relevant study that identifies the microRNAs dysregu- lated in ccRCC, which can serve as the basis of molecular markers for diagnosis. UROLOGY 75: 835– 841, 2010. © 2010 Elsevier Inc. R enal cell carcinoma (RCC) is the most common neoplasm in the adult kidney, accounting for 3% of all malignancies in the United States. This year, more than 50 000 men and women will be diag- nosed with RCC and about 12 000 people will die be- cause of this disease. 1 In recent years, studies on the biological mechanisms that contribute to clear-cell RCC (ccRCC) have focused on mutations to the genome, ex- pression of protein coding genes, and epigenetic changes. Increasing evidence indicates, however, that dysregulation of a class of noncoding RNA genes, microRNAs, is also associated with cancer and their expression profiles can be correlated with diseases pathogenesis and diagnosis. 2 Dysregulation of microRNAs has been observed in many cancers, including solid tumors and hematological malig- nancies. 3 MicroRNAs are a class of naturally occurring, noncod- ing RNAs that regulate protein expression by targeting the messenger RNA of protein coding genes for either translation repression or transcriptional modulation. 3 They are a class of gene regulators that are endogenously produced to play important roles in a wide range of biological functions, including cellular differentiation, development, and apoptosis. 4 Connections between microRNA expression and can- cer have been made on several levels. Altered patterns of microRNA expression have been shown to be associated with a variety of tumors. 2 Also, microRNAs have been implicated to function as either putative tumor suppres- sors or oncogenes, and multiple microRNAs are located within cancer-associated chromosomal fragile sites, which are susceptible to point mutation, amplification, deletion, or translocation. 5 Indeed, with microRNAs estimated to regulate 30% of all gene transcripts, it is quite possible that their aberrant expression might contribute to David Juan and Gabriela Alexe are joint first authors. Gyan Bhanot and Louis S. Liou are joint corresponding authors. From the Department of Pathology, Boston University, Boston, Massachusetts; The Broad Institute of MIT and Harvard, Cambridge, Massachusetts; System Biosciences, Mountain View, California; BioMaPS Institute, Rutgers University, Piscataway, New Jersey; Departments of Molecular Biology and Biochemistry, and Physics, Rutgers University, Piscataway, New Jersey; Department of Biomedical Engineering, Boston University, Boston, Massachusetts; the Cancer Institute of New Jersey, New Bruns- wick, New Jersey; The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey; and Cambridge Health Alliance, Harvard Medical School, Cambridge, Massachusetts Reprint requests: Louis S. Liou, M.D., Ph.D., Department of Pathology, Boston University, 670 Albany Street Room 441, Boston, MA 02118. E-mail: Louis. liou@bmc.org Submitted: September 30, 2008, accepted (with revisions): October 19, 2009 © 2010 Elsevier Inc. 0090-4295/10/$34.00 835 All Rights Reserved doi:10.1016/j.urology.2009.10.033