Multiplexed microRNA Expression Profiling by Combined Asymmetric PCR and Label-Free Detection using Silicon Photonic Sensor Arrays

Analysis methods based upon the quantitative, real-time polymerase chain reaction are extremely powerful; however, they face intrinsic limitations in terms of target multiplexing. In contrast, silicon photonic microring resonators represent a modularly multiplexable sensor array technology that is well-suited to the analysis of targeted biomarker panels. In this manuscript we employ an asymmetric polymerase chain reaction approach to selectively amplify copies of cDNAs generated from targeted miRNAs before multiplexed, label-free quantitation through hybridization to microring resonator arrays pre-functionalized with capture sequences. This method, which shows applicability to low input amounts and a large dynamic range, was demonstrated for the simultaneous detection of eight microRNA targets from twenty primary brain tumor samples with expression profiles in good agreement with literature precedent.

Combining asymmetric PCR-based enzymatic amplification with silicon photonic microring resonators for the detection of lncRNAs from low input human RNA samples

A method for quantifying biologically relevant long-non-coding RNAs by combining nucleic acid amplification via asymmetric polymerase chain reaction (PCR) with label-free PCR product detection using silicon photonic microring resonator arrays is described. This approach eliminates the need for fluorophores, which presents a limit for spectral multiplexing in conventional qPCR methods, and rather offers potential for much higher levels of plexity by spatially arraying capture probes. Here, we demonstrate the potential of this technique to detect two differentially expressed lncRNA transcripts and an internal control mRNA transcript in different commercial human tissue specimens, as well as in a glioblastoma cell line using only nanogram input amounts of total RNA. The obtained results were validated using single-plex RT-qPCR and found to be in good agreement, demonstrating the potential of this technique for lncRNA quantification applications.

PCR-Free, Multiplexed Expression Profiling of microRNAs Using Silicon Photonic Microring Resonators

We describe an approach for multiplexed microRNA analysis using silicon photonic microring resonators to detect cDNA reverse transcription products via a subsequent enzymatic signal enhancement strategy. Key to this method is a modified stem loop primer that facilitates downstream signal amplification via enzymatic turnover and improves the sensor signal 20-fold when compared to traditional stem loop primers. This approach facilitates targeted microRNA quantification in only 2.5 h and without requiring target amplification via the polymerase chain reaction (PCR). Primers for 7 miRNA targets were orthogonally designed to avoid cross-hybridization between capture probes. This approach was applied to the detection of total RNA from human tissues and found to display differential expression profiles consistent with literature precedent. This development holds promise as an alternative to single-plex RT-qPCR methods and more expensive RNA-seq by offering a cost-effective method to analyze targeted miRNA panels in emerging diagnostic applications.