Sep 10, 2019, 5:21 pm SGT

SINGAPORE – A team of researchers from the National University of Singapore (NUS) has developed a technology that promises to make biopsies more informative and less invasive for cancer patients.

Called Sequence-Topology Assembly for Multiplexed Profiling (Stamp), it works by generating 3D DNA “barcodes”. Just as a barcode, when scanned, contains information about a product and its price, a chain of DNA can tell scientists about the nature of cells.

The DNA used in Stamp is specially engineered such that it can be folded and unfolded. Assistant Professor Shao Huilin from the NUS Institute for Health Innovation & Technology (iHealthtech), who led the project on developing the technology, likens it to origami where a flexible piece of paper can be folded into a rigid 3D shape.

Here is how Stamp works. A long chain of DNA is first folded into a pyramid-like structure to give it stability. This is then exposed to a small sample of cells extracted from a patient. The DNA attaches to the proteins in the cells and, when it does this, the DNA barcode changes.

When the DNA is later unfolded to be read and analysed, the barcode changes can tell scientists what proteins were present and where they were located within the cell. This information determines if cancer is present, its subtype and its aggressiveness.

As Stamp only requires a small sample and can measure billions of proteins in a single test, both the patients and their doctors will be able to receive comprehensive reports about the condition earlier to facilitate timely treatment.

Conventionally, early diagnostic biopsies require a fine needle to be inserted into a suspicious growth to extract samples. These are then sent for tests, to determine if the growth is cancerous.

This means that patients may not know the subtype of their cancer nor its aggressiveness until large portions or the entire growth are surgically removed for further analysis. This process may take weeks for conclusive results.

Prof Shao explains that this uncertainty can often lead to great patient anxiety and lesser informed health decisions. Some female patients, for example, may choose to remove their entire breast only because of the possibility that their cancer may be at an advanced stage.

The NUS iHealthtech team hopes that their technology will allow for tailored therapies to begin earlier. Mr Noah Sundah, a doctoral student at NUS iHealthtech and a member of the research team, cited drug therapies that target particular proteins, or the use of chemotherapy to shrink specific tumours.

The 10-member research team’s paper was published as the cover story of this month’s issue of Nature Biomedical Engineering. The scientists conducted clinical trials using samples from 69 breast cancer patients and found that Stamp had a diagnostic accuracy of above 94 per cent, comparable to gold-standard tissue pathology which only reveals clinical information post-surgery.

Prof Shao’s team are currently discussing with industry partners to further develop and commercialise their technology. They expect to bring Stamp to the market within the next five years. Further research is also being done by the team to validate its applications in other types of cancer including lung and colorectal cancer.