Methods for the early diagnosis of cancer are urgently needed. Liquid biopsy, the sampling of non-solid biological tissue such as blood, is gaining interest as a rapid and non-invasive method of diagnosing cancers. Unlike traditional biopsies that require surgery and often general anesthesia, a liquid blood biopsy requires only blood — with minimal harm to the patient. After sampling, the blood is screened for specific markers that indicate the presence of cancerous tissue.
Specific patterns of microRNA (miRNA) are associated with different cancers 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 nanopore-based DNA computing technology.
The findings were published in the journal JACS Au in the newspaper, “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 at Tokyo University of Agriculture and Technology (TUAT). “In this case, a diagnostic DNA molecule was designed to be able to bind five different types of miRNA associated with bile duct cancer. While binding the miRNA molecules, the diagnostic DNA converts the expression pattern of the miRNAs into the information in the form of a nucleic acid structure.”
The team’s system specifically targets pattern recognition of five types of miRNAs that are overexpressed in bile duct cancer (BDC). The information from miRNAs of BDC is encoded into diagnostic DNAs (dgDNAs) and electrically decoded by nanopore analysis.
In this method, the DNA is passed through a nano-sized hole or “pore”. If the molecule passes through the pore, it will impede the flow of electrical current through the pore. These perturbations in the flow through the pore can then be measured and used to infer the properties of the passing molecule. In the case of the diagnostic DNA, the bound miRNAs will be “unpacked” from the DNA, resulting in a current inhibition of characteristic amplitude and duration.
By statistically analyzing the extract data from 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 managed to detect unlabeled 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 detection limits (∼10-12 M) for comparable analytical platforms.
This method, nanopore decoding of dgDNA-encoded information, represents a promising tool for simple and early diagnosis of cancer.