CRISPR-Cas14a-integrated strand displacement amplification for rapid and isothermal detection of cholangiocarcinoma associated circulating microRNAs

Circulating microRNAs (miRNA) can serve as key biomarkers for early diagnose of cholangiocarcinoma. Herein, an assay that uses circulating miRNA to trigger strand displacement amplification (SDA) and a CRISPR-Cas14a system to report the SDA process has been developed. In the proposed method, SDA directly amplifies miRNAs without reverse transcription. The reporter, CRISPR-Cas14a, can reduce the risks of non-specific amplification and offers a sequential amplification that improves the sensitivity for miRNA detection. The assay, termed Cas14SDA, can discriminate miRNAs with similar sequences and can detect as low as 680 fM miR-21 (miRNAs overexpressed in cholangiocarcinoma) within 1 h. In particular, Cas14a was efficiently activated by a single-stranded SDA amplicon which improved the sensitivity by 2.86 times compared to that using Cas12a. This research has demonstrated that the Cas14SDA assay can discriminate cholangiocarcinoma patients from healthy donors by testing miR-21 in their blood samples. The Cas14SDA assay developed broadens the toolbox for miRNA biomarker analysis.