Global and targeted microRNA expression profiling in clear cell renal cell carcinoma tissues potentially links miR-155-5p and miR-210-3p to both tumorigenesis and recurrence [discovery phase]

About 30% of renal cell carcinoma (RCC) patients undergoing nephrectomy experience disease recurrence. This study aimed to profile microRNAs (miRNAs) that are dysregulated in clear cell RCC (ccRCC) tumor tissues and predictive of recurrence. The expression levels of 800 miRNAs were assessed in paired tumor and normal tissues from a discovery cohort of 18 ccRCC patients via the NanoString assay platform. MiRNAs found to be differentially expressed were further examined in a validation set of 205 patients using quantitative real-time PCR. Tumor-normal data from 64 patients in The Cancer Genome Atlas were used for external validation. Results showed 28 miRNAs were consistently dysregulated in tumor tissues. Dichotomized analyses indicated patients with high levels of miR-155-5p and miR-210-3p displayed increased risk of ccRCC recurrence (HR, 2.64; 95% CI, 1.49-4.70; P=0.0009 and HR, 1.8; 95% CI, 1.04-3.12; P=0.036, respectively) and shorter median recurrence-free survival times than patients with low levels (log rank test P<0.01). A risk score was generated based on expression levels of miR-155-5p and miR-210-3p, and the trend test was significant (P for trend=0.005). Pathway analysis revealed target genes regulated by miR-155-5p and miR-210-3p were mainly enriched in inflammation-related pathways. In summary, we identified and validated multiple miRNAs dysregulated in ccRCC tissues. MiR-155-5p and miR-210-3p were predictive of ccRCC recurrence pointing to potential utility as biomarkers and underlying biological mechanisms. Study consists of a dual-phase design for discovery and validation. In the discovery phase, total RNA was isolated from paired tumor and adjacent normal tissues from 18 ccRCC patients (9 with disease recurrence and 9 without recurrence) and then subjected to NanoString miRNA profiling. MiRNAs dysregulated in tumors were selected for further validation using the quantitative real-time PCR approach. During the validation phase, total RNA isolated from paired tumor/normal tissues from additional 205 ccRCC patients (63 with disease recurrence and 142 without recurrence) was subjected to Fluidigm real-time PCR quantification. MiRNAs dysregulated in tumors in both discovery and validation phases were identified and analyzed for their association with risk of ccRCC recurrence. The results of altered miRNAs in tumor tissues were further validated using the ccRCC miRNA dataset in The Cancer Genome Atlas. Cumulative effect of altered miRNAs was assessed by developing a risk score, and pathway analysis was conducted to identify potential target genes and enriched pathways.