Methods for the early diagnosis of cancer are urgently needed. Liquid biopsy, the sampling of nonsolid biological tissue like blood, is gaining interest as a quick and noninvasive method for diagnosing cancers. Unlike traditional biopsies that require surgery and often general anesthesia, a liquid blood biopsy only requires blood—with minimal harm to the patient. After sampling, the blood is screened for specific markers indicating the presence of cancerous tissue.

Specific patterns of microRNA (miRNA) are associated with different types of cancer and can be used to diagnose cancers from liquid biopsies with high precision. However, the low concentration of miRNA in blood samples makes their detection challenging.

Now, researchers have developed a method for detecting miRNA expression patterns using a nanopore-based DNA computing technology.

The findings were published in the journal JACS Au in the paper, “Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations.

“DNA computing uses the biochemical reactions of the information-encoding DNA molecules to solve problems based on formal logic, in the same way that normal computers do,” said Ryuji Kawano, PhD, professor, Tokyo University of Agriculture and Technology (TUAT). “In this case, a diagnostic DNA molecule was designed to be able to bind five different kinds of miRNA associated with bile duct cancer. In the process of binding the miRNA molecules, the diagnostic DNA converts the expression pattern of the miRNAs into the information contained in the form of a nucleic acid structure.”

Specifically, the team’s system targets pattern recognition of five types of miRNAs overexpressed in bile duct cancer (BDC). The information of miRNAs from BDC is encoded in diagnostic DNAs (dgDNAs) and decoded electrically by nanopore analysis.

In this method, the DNA is passed through a nano-sized hole, or “pore.” As the molecule transits the pore, it will obstruct the flow of electrical current through the pore. These perturbations in the current through the pore can be then measured and used to deduce the properties of the passing molecule. In the case of the diagnostic DNA, the bound miRNAs will be “unzipped” from the DNA, resulting in a current inhibition of characteristic amplitude and duration.

Through statistical analysis of the unzipping data of the miRNA patterns, the scientists were able to recognize cancer-specific expression patterns even from clinical samples with extremely low concentrations of miRNA.

More specifically, they succeeded in the label-free detection of miRNA expression patterns from the plasma of BDC patients. The dgDNA–miRNA complexes could be detected at subfemtomolar concentrations, which is a significant improvement compared to previously reported limits of detection (∼10–12 M) for similar analytical platforms.

This method, nanopore decoding of dgDNA-encoded information, represents a promising tool for simple and early cancer diagnosis.