Researchers Find that Unique Nano-Scale DNA Signature Could be Common to All Cancers

Researchers from the University of Queensland’s Australian Institute for Bioengineering and Nanotechnology (AIBN) have found a distinctive nano-scale DNA signature that seems to be common to all cancers.

On the basis of this finding, the researchers have developed an innovative technology that allows fast and easy detection of cancer from any tissue type, such as blood or biopsy.

The study—supported by a grant from the National Breast Cancer Foundation and reported in the journal Nature Communications—offers fresh insights about how epigenetic reprogramming in cancer controls the chemical and physical properties of DNA and could result in a completely new approach to point-of-care diagnostics.

Because cancer is an extremely complicated and variable disease, it has been difficult to find a simple signature common to all cancers, yet distinct from healthy cells.

Dr Abu Sina, Researcher, AIBN.

In order to overcome this challenge, Dr Sina and Dr Laura Carrascosa, who are working with Professor Matt Trau at AIBN, concentrated on something known as circulating free DNA.

Akin to healthy cells, cancer cells are always in the process of dying and renewing. When they die, they essentially burst and liberate their cargo, including DNA, which then circulates.

There’s been a big hunt to find whether there is some distinct DNA signature that is just in the cancer and not in the rest of the body,” says Dr Carrascosa.

Therefore, the team investigated epigenetic patterns on the genomes of healthy cells and cancer cells. Simply put, they looked for patterns of molecules, known as methyl groups, which decorate the DNA. These methyl groups are vital to cell function since they serve as signals that control the selection of specific genes to be switched on and off at any specified interval.

These methyl groups are widely spread across the genome in healthy cells. However, the AIBN researchers discovered that a cancer cell genome is fundamentally sterile except for intense clusters of methyl groups at very precise locations.

This unique signature—which they termed the cancer “methylscape”, for methylation landscape—was present in all types of breast cancer they investigated and was also present in other forms of cancer, such as lymphoma, colorectal cancer, and prostate cancer.

Virtually every piece of cancerous DNA we examined had this highly predictable pattern.

Matt Trau, Professor, AIBN.

According to him, if a cell is considered as a hard-drive, then the new discoveries suggest that cancer requires specific genetic programmes or apps in order to function.

It seems to be a general feature for all cancer,” he says. “It’s a startling discovery.”

Furthermore, the team discovered that when the intense clusters of methyl groups were placed in solution, they make cancer DNA fragments to fold up into three-dimensional nanostructures that essentially like to stick to gold.

The researchers exploited this to design an assay, which uses gold nanoparticles that immediately change color depending on whether or not these 3D nanostructures of cancer DNA are present.

This happens in one drop of fluid,” says Trau. “You can detect it by eye, it’s as simple as that.”

Moreover, the technology has been adapted for electrochemical systems, which enables inexpensive and portable detection that could ultimately be carried out using a mobile phone.

To date, they have tested the new technology on 200 samples across various types of human cancers, and healthy cells. In certain cases, the accuracy of cancer detection reaches as high as 90%.

It works for tissue derived genomic DNA and blood derived circulating free DNA. This new discovery could be a game-changer in the field of point of care cancer diagnostics.

Dr Abu Sina, Researcher, AIBN.

The team says that it is not perfect yet, but it can be a promising start and will only get better with time.

We certainly don’t know yet whether it’s the Holy Grail or not for all cancer diagnostics, but it looks really interesting as an incredibly simple universal marker of cancer, and as a very accessible and inexpensive technology that does not require complicated lab based equipment like DNA sequencing.

Matt Trau, Professor, AIBN.

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