Cancer DNA detected at low levels with CRISPR-based liquid biopsy

A new method for identifying small amounts of DNA from cancer cells in the blood may offer further opportunities for early cancer detection.

Researchers from the Korea University College of Medicine in Seoul showed that a sensitive CRISPR-based method called MUTE-Seq, which removes DNA without mutations at specific regions, can be used to amplify DNA from cancer cells. The researchers highlight the potential of these techniques for early detection and disease monitoring.

'Our findings suggest that the MUTE-Seq method has considerable potential for developing diagnosis panels aimed at detecting multiple low-frequency ctDNA [circulating tumour DNA] for MCED [multi-cancer early detection], CDx [companion diagnostics], and MRD [minimal residual disease]' said clinical assistant professor, Dr Junseok Hur, who led the study published in Advanced Materials.

Techniques for finding cancer using DNA taken from liquid biopsies, such as blood, may be useful as non-invasive tools for detecting and monitoring cancer. However, as little as 0.01 percent of this DNA is expected to come from tumour cells, especially in the early stages of cancer. Most techniques are unable to identify DNA at this frequency, limiting their clinical potential.

To increase the amount of tumour DNA for analysis, the researchers developed MUTE-Seq, a method involving a precise CRISPR enzyme which depletes any DNA that perfectly matches a given region, meaning that mutated tumour DNA is not affected. This allowed for the detection of mutations present in as few as one in every 20,000 cells, which would not be captured using standard sequencing methods.

To demonstrate the clinical relevance of MUTE-Seq, the researchers showed that residual disease of acute myeloid leukaemia could be found by identifying rare mutations in NRAS, a frequently mutated gene in leukaemia.

This was followed by a 'multiplex mode', which searched for mutations in other cancer-related genes such as EGFR and KRAS. Using these markers, MUTE-Seq was able to identify rare mutations in patients with lung cancer and pancreatic cancer.

'Results suggested that even minute mutations can be detected using MUTE-Seq if they are present in blood samples,' said Dr Hur.

Within the paper, the researchers stated that MUTE-Seq: 'demonstrated a significant improvement in the sensitivity of simultaneous mutation detection and highlighted its clinical utility for early-stage cancer patients with extremely low levels of circulating tumour DNA'.

The researchers acknowledged that one current limitation of MUTE-Seq is that the current method checks for mutations in specific pre-defined cancer 'hotspots', which may not be applicable for many patients. Looking forward, the researchers are hoping to expand the scope of MUTE-Seq to improve early multi-cancer detection and patient-specific disease monitoring.