Robust MircroRNA detection by Capillary Electrophoresis

MicroRNA (miRNA) are short single-stranded RNA molecules that function as post-transcriptional regulators in gene expression, The abnormal expression of small subsets of miRNAs, termed “miRNA fingerprints”, have been found as potential biomarkers in diagnosis of various diseases including cancers. However, none of miRNA-based biomarkers has been approved yet for clinical use due to the lack of a robust quantitative method for miRNA analysis. To address this issue, there have been significant efforts towards developing robust quantitative miRNA detection methods. Among a variety of initiatives, DQAMmiR is a promising approach developed by our lab which is capable of direct, quantitative analysis of multiple miRNAs in capillary electrophoresis (CE). In my PhD project, I have been focusing on investigating and improving the robustness of DQAMmiR to increase its applicability for practical use.

Firstly, I demonstrated that DQAMmiR is capable of directly quantitating miRNA in crude cell lysates, indicating its robustness to the change of sample matrices, revealing its great potential to be used to analyzing miRNAs in biological samples directly without the need for complex sample processing. Secondly, I developed a second-generation DQAMmiR by replacing the ssDNA probes with the electrically neutral peptide nucleic acid (PNA) probes, which further improves the robustness of the assay by removing the need for single-stranded DNA binding protein (SSB) in the assay. Thirdly, to increase the applicability of the assay, I introduced a new sample preconcentration technique based on the integration of field-amplified sample stacking (FASS) and isotachophoresis (ITP) prior to CE separation in DQAMmiR, which successfully decreases its limit of quantification (LOQ) by 140 times. Lastly, I investigated the applicability of DQAMmiR for analyzing urinary miRNAs. I demonstrated that the concentration ratio of two miRNAs, miR-16 and miR-21, could be relative stable from different urine samples collected from the same person, although the individual concentrations of these miRNAs varied significantly in these samples. These findings suggests that the ratiometric measurements between multiple miRNAs in urine would serve as better biomarkers than individual miRNA concentrations for clinical diagnostic tests. And DQAMmiR would be an ideal analytical methodology for the development and use of such tests.