Predicting the presence of breast cancer using circulating small RNAs, including those in the extracellular vesicles

Abstract

Emerging evidence indicates that small RNAs, including microRNAs (miRNAs) and their isoforms (isomiRs), and transfer RNA fragments (tRFs), are differently expressed in breast cancer (BC) and can be detected in blood circulation. Circulating small RNAs and small RNAs in extracellular vesicles (EVs) have emerged as ideal markers in small RNA‐based applications for cancer detection. In this study, we first undertook small RNA sequencing to assess the expression of circulating small RNAs in the serum of BC patients and cancer‐free individuals (controls). Expression of 3 small RNAs, namely isomiR of miR‐21‐5p (3′ addition C), miR‐23a‐3p and tRF‐Lys (TTT), was significantly higher in BC samples and was validated by small RNA sequencing in an independent cohort. Our constructed model using 3 small RNAs showed high diagnostic accuracy with an area under the receiver operating characteristic curve of 0.92 and discriminated early‐stage BCs at stage 0 from control. To test the possibility that these small RNAs are released from cancer cells, we next examined EVs from the serum of BC patients and controls. Two of the 3 candidate small RNAs were identified, and shown to be abundant in EVs of BC patients. Interestingly, these 2 small RNAs are also more abundantly detected in culture media of breast cancer cell lines (MCF‐7 and MDA‐MB‐231). The same tendency in selective elevation seen in total serum, serum EV, and EV derived from cell culture media could indicate the efficiency of this model using total serum of patients. These findings indicate that small RNAs serve as significant biomarkers for BC detection.

isomiRs–Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them?

“…The accumulated evidence shows that the analysis of isomiRs expression pattern can differentiate tumor cells from normal, and moreover to discriminate amongst different tumor types and subtypes [118,119]. This strongly suggests isomiRs as potentially valuable diagnostic and prognostic biomarkers in cancer diagnostics [119][120][121].…”

“…The accumulated evidence shows that the analysis of isomiRs expression pattern can differentiate tumor cells from normal, and moreover to discriminate amongst different tumor types and subtypes [ 118 , 119 ]. This strongly suggests isomiRs as potentially valuable diagnostic and prognostic biomarkers in cancer diagnostics [ 119 , 120 , 121 ]. Furthermore, the combination of isomiR features with state-of-the-art algorithms effectively differentiated normal from cancer cell lines [ 118 , 122 ].…”

tRNA-derived RNA fragments in cancer: current status and future perspectives

“…Meanwhile, the detection of the functional tRF-Leu-CAG in the serum of NSCLC is related to progression stage, suggesting that it may be a new diagnostic marker and potential therapeutic target for NSCLC [72]. Circulating tRF-Lys and another two miRNAs in EVs can discriminate early-stage BCs at stage 0 from controls with an AUC (area under the curve, a criterion for judging the pros and cons of a binary classification prediction model) of 0.92 [90]. All these studies indicated that tRFs have great potential as clinical biomarkers for cancer diagnosis and prognosis.…”

tRNA-derived small RNAs: novel regulators of cancer hallmarks and targets of clinical application

“…Another study revealed that tRF-32-XSXMSL73VL4YK was significantly upregulated, and tRF-32-Q99P9P9NH57SJ and tRF-17-79MP9PP were significantly downregulated in breast cancer tissues [ 95 , 96 ]. Kio and his colleagues combined the miRNA and tsRNA pools and found that the expression of miR-21-5p, miR-23a-3p, and tRF-Lys, was significantly higher in breast cancer samples and these results could be validated in an independent cohort by small RNA sequencing [ 97 ]. Circulating tsRNAs have also received attention.…”