microRNA Expression and mRNA Transcripts in Clear Cell (Conventional) Renal Cell Carcinoma.
Amber H Hughes, Gaurav Sharma, Somak Roy, John M Krill-Burger, Christin M Sciulli, Maureen A Lyons, Lori A Kelly, Anil V Parwani, Rajiv Dhir, Teresa McHale, William A LaFramboise, Sheldon I Bastacky. UPMC, Pittsburgh, PA
Background: MicroRNAs (miRNA) are small non-protein-coding RNAs which post-transcriptionally regulate gene expression by targeting specific messenger RNAs (mRNA) for degradation. Previous studies have shown altered expression levels of miRNAs in renal cell carcinoma. The aim of this study was to simultaneously interrogate clear cell (conventional) renal cell carcinoma (ccRCC) and normal renal tissue (NRT) across the entire miRNA and mRNA transcriptomes in parallel using microarrays to identify unique miRNA and mRNA transcripts in ccRCC.
Design: We interrogated precisely annotated and classified ccRCC and NRT across the entire single nucleotide polymorphism (SNP) genome (Affymetrix 6.0 Arrays) and miRNA/mRNA transcriptomes in parallel using microarrays (Affymetrix Hu 133-2.0 plus, Exiqon MicroRNA Array), and frozen ccRCC and NRT (n=5). The data were subjected to statistical analyses and hierarchical clustering (Partek Genomics Suite) to produce discrete sets of miRNAs with increased and decreased levels in ccRCC compared to NRT. Correlational analysis of the miRNA and mRNA profiles was performed to identify reciprocal changes in miRNA linked to changes in their targets, identified using the Sanger miRBase. The mRNA targets were functionally annotated using GeneCards (Weizmann Institute of Science) and the National Institute of Health Database for Annotation, Visualization and Integrated Discovery (DAVID) program.
Results: Six miRNAs were identified with significantly altered expression levels in ccRCC compared to normal renal tissue (NRT): miR-141 (p<5.3x10-9), miR-200c (p<9.2x10-7), and miR-624 (p<2.9x10-3) were decreased, and miR-21 (p<2.1x10-7), miR-105 (p<1.8x10-6), and miR-361-3p (p<7.6x10-3) were increased. The mRNA transcripts representing targets of these miRNAs displayed significant correlated expression changes, including FAIM2, GAL3ST1, and VEGFA. Other targeted genes included transcripts encoding protein binding proteins, potassium and calcium ion channels, kinases, and transcription factors. MiRNAs encoded by chromosome 3 were found to be decreased in ccRCC, correlating with recognized chromosome 3 deletions in ccRCC, and further supported by concurrent SNP analysis.
Conclusions: In summary, this study contributes to the growing understanding of the role that miRNAs play in renal cell carcinoma, specifically ccRCC. The data identified six miRNAs with altered expression in ccRCC compared to NRT which target gene products relevant to tumorigenesis. Both the miRNAs identified and the gene products they regulate represent potentially important therapeutic and diagnostic targets in patients with ccRCC.
Category: Genitourinary (including renal tumors)
Wednesday, March 2, 2011 9:30 AM
Poster Session V # 104, Wednesday Morning