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Bacterial Biosensors Detect Cancer DNA

A recent study published in Science has unveiled the potential of engineering a well-known bacterium, Acinetobacter baylyi, to detect cancer DNA in mammals.

After four years of collaborative research between the University of California San Diego and their colleagues in Australia, a novel synthetic biology approach has emerged for the non-invasive detection, monitoring and possibly treatment of cancer in humans.

Sharing DNA is Caring

To detect or treat an illness, we often rely on traditional techniques such as pharmaceutical drugs, surgery and X-rays. However, bacterial engineering presents a way of detecting and treating illness using living cells.

Many bacteria, including A. baylyi, exhibit a trait known as natural competence. This is where an organism can take up exogenous DNA from their environment and incorporate it into their own genome. As tumours shed their DNA into the surrounding environment through routine biological processes such as apoptosis, natural competence allows bacteria to incorporate tumour DNA into their genome. This DNA is then shared among bacteria through Horizontal Gene Transfer (HGT), a mechanism where genetic material is exchanged between organisms without parent-to-offspring inheritance. HGT enables bacteria to continuously share advantageous genes, enhancing their survival – For example, propagating antibiotic resistance genes.

Cooper et al. used a CRISPR-associated transposase-enabled horizontal gene transfer (CATCH) system to instruct the biosensor bacteria to identify and assimilate specific DNA from their environment. The strategy combines the power of CRISPR-Cas technology, which can target and modify DNA, with HGT. The focus was on DNA within the KRAS gene, a known oncogene associated with human cancers. By designing genetic circuits containing CRISPR spacers, the team selectively targeted and degraded specific DNA sequences, including oncogenic mutations in KRAS.

Tumour DNA was engineered with a kanR cassette between KRAS homology arms. The sensor bacteria were also designed with matching KRAS homology arms that help them fit together with the tumour DNA. When the sensor bacteria assimilate the tumour DNA, they gain the ability to resist kanamycin. The researchers can count these bacteria in the gut’s contents by culturing them on plates with antibiotics.

Promising Results

The engineered bacteria were tested both in vitro and in vivo.

In vitro tests using simplified tumour models (cancer organoids) successfully identified mutant KRAS DNA. In vivo tests using a live mouse model of colorectal cancer, where the bacteria were introduced into the colon, also demonstrated the successful transfer of genetic material from tumour cells to bacteria through HGT.

The biosensors were able to detect very small amounts of target DNA in both instances, demonstrating their sensitivity.

“It was incredible when I saw the bacteria that had taken up the tumor DNA under the microscope. The mice with tumors grew green bacterial colonies that had acquired the ability to grow on antibiotic plates,” stated Josephine Wright, co-author of the paper.

From Detection to Treatment

The CATCH strategy successfully engineered bacterial biosensors to detect specific cancer-related DNA mutations both in vitro and in vivo, showing promise for cancer detection and monitoring. This method eliminates the need for invasive sampling and delivers more precise sequence resolution than current in vitro DNA analysis methods. Furthermore, CATCH could even be used to treat cancer through the delivery of nanobodies, peptides or other small molecules to tumour sites.

CATCH is still in its early stages and is not yet ready for use in a clinical setting. Further research is needed before the technology can be delivered orally whilst still achieving a sufficient sequence resolution in non-invasive samples such as stool or blood. There are also several safety concerns that need to be addressed, such as minimising the spread of antibiotic resistance and preventing biocontamination.

Read about other uses of CRISPR-Cas systems.