An electrochemical genosensing platform for the relative quantification of the circulating long noncoding RNA CCAT1 to aid in the diagnosis of colorectal cancer

Abstract

Long noncoding RNAs (lncRNAs) are promising biomarkers for the noninvasive diagnosis of colorectal cancer, but detection of cancer-associated changes in their expression levels is now restricted to the use of RT-qPCR. To extend the clinical applicability of these biomarkers, we developed an electrochemical platform, integrated by two different sandwich genosensors, for the relative quantification of a lncRNA called colon cancer associated transcript-1 (CCAT1) with respect to the mRNA GAPDH as an endogenous control. To achieve highly sensitive detection, and in contrast to previous sensors of this class, we use multiple fluorescein-tagged hybridization assistant probes allowing the incorporation of multiple redox enzymes per target molecule, in turn favoring the selective capture of these highly-structured targets onto the sensing platform. The resultant biosensors show high sensitivity (9.7 ± 0.3 µA nM−1 for CCAT1 and 7.3 ± 0.1 µA nM−1 for GAPDH) and low limits of detection (990 fM and 1830 fM for CCAT1 and GAPDH, respectively). Coupled to a PCR assay, we detect the lncRNA at clinically relevant concentrations. Preliminary results using total RNA extracted from the colorectal cancer cell line HT29 and spiked plasma samples from healthy individuals suggest that this new sensing architecture is sensitive and selective enough to obtain the expression level of CCAT1 simply from the ratio of outputs from the two platform sensors. We envision that the same design could be applied to detect other lncRNAs associated to various malignancies, facilitating early cancer diagnosis.