gms | German Medical Science

Question: Small non-coding RNAs (sncRNA; < 200nt) modify gene expression and thereby regulate various cellular processes. sncRNA expression profiles are changing during carcinogenesis. We therefore performed Next Generation Sequencing to identify clear cell renal cell carcinoma (ccRCC) specific sncRNA profiles.

Method: Small RNA Sequencing was utilized to determine the expression pattern of miRNA, piRNA, tRNA and snRNAs in 18 corresponding normal and ccRCC tissue samples. Subsequently, validation was performed in an independent cohort of 118 ccRCC and 74 normal renal tissues with quantitative real-time PCR.

Result: Differential expression (fold change >2, false discovery rate < 0.05) was observed for 151 miRNA (upregulation: 75, downregulation: 76) and 98 tRNAs (upregulation: 44, downregulation: 54); in contrast, piRNA and snRNA counts were overall low and quantification thus not feasible. Read length analysis indicated that tRNA reads mapped in the 30-36nt fraction, and not as expected to 73-95nt. Thus, tRNA are truncated to 5'-tRNA-halves, most probably due to enzymatic cleavage within the anticodon region. Subsequent PCR experiments confirmed overexpression of miR-122-5p and miR-142-3p as well as downregulation of 5'tRNA4-ValAAC in ccRCC. Furthermore, miR-122-5p expression levels were higher in patients with metastatic ccRCC, and 5'tRNA4-ValAAC levels were negative correlated with pathological stage and grade.

Conclusion: sncRNA expression profiles are different in ccRCC and normal renal tissue. We demonstrate for the first time that truncated tRNAs are involved in renal carcinogenesis. Although their functional role has to be elucidated, published studies indicate involvement in the regulation of angiogenesis.