An Australian-led study has engineered bacteria capable of detecting mutated DNA released from colorectal cancer cells.
Dr Dan Worthley, Associate Professor Susan Woods and Dr Josephine Wright from SAHMRI and the University of Adelaide, worked in partnership with Professor Jeff Hasty at the University of California San Diego (UCSD), to investigate the potential of synthetic bacteria to act as an in vivo diagnostic device.
In preclinical testing, the team found that the engineered sensor bacteria, Acinetobacter baylyi (A. baylyi), was 100% accurate in differentiating between models with and without colorectal cancer, and have dubbed this technology ‘CATCH’, which stands for, Cellular Assay of Targeted CRISPR-discriminated Horizontal gene transfer.
Dr Worthley explained that some bacteria were “naturally competent” and could sample extracellular DNA directly from their environment.
“Natural competence promotes horizontal gene transfer (HGT), the exchange of genetic material between organisms outside vertical, parent-to-offspring transmission,” he said.
“Additionally, bacteria can easily access the entire gastrointestinal tract via oral administration, and they can produce outputs, which can be noninvasively measured in stool or urine, and use cellular memory such as bistable switches or genomic rearrangements that allow bacteria to store information over time.
“Acinetobacter baylyi is a highly competent and well-studied bacterium that is largely non-pathogenic in healthy humans and can colonise the murine gastrointestinal tract. It was this combination of traits that made A. baylyi a suitable candidate to test whether engineered bacteria could detect CRC-promoting DNA mutations in vivo.”
The DNA biosensor concept was developed in vitro and then validated in vivo with the sensor bacteria delivered orally or rectally to mice that had been injected with orthotopic donor CRC organoids.
HGT transfer occurred from the donor tumour to the sensor bacteria in vivo, conferring antibiotic resistance to the sensor bacteria, allowing their detection in stool, and enabling the sensor bacteria to effectively differentiate between mice with and without CRC.
“CATCH has the potential to detect bowel cancer early with the aim of preventing more people from dying of this and other cancers,” Associate Professor Woods said.
“We were thrilled to see transfer of DNA from the tumour to the sensor bacteria, as this shows that our biosensing system can be used to catch colorectal cancer DNA within a complex ecosystem, with no sample preparation or processing.”
The team noted that sampling in vivo offered important detection advantages for the gut in particular.
“The gastrointestinal tract contains significant DNase activity, which limits the lifetime of free DNA in both rodents and humans,” they said.
“However, living biosensors located in situ could capture and preserve DNA shortly after its release and before it was degraded by local DNase. In addition, biosensors could amplify target DNA in vivo through HGT-induced fitness, intercellular quorum sensing or intracellular genetic memory switches.”
While further studies are needed before progressing to clinical trials, the researchers were confident this discovery represented a significant advance in the field of living diagnostics while setting the stage for the timely and accurate delivery of targeted treatments.
“Perhaps most exciting, however, is that unlike in vitro diagnostics, detection of target DNA by a living biosensor could potentially be coupled to direct and genotype-complementary nanobodies, peptides, or other small molecules for the treatment of cancer or infection,” Dr Worthley said.
“In the future we will detect and prevent many diseases, including bowel cancer, with cells, not drugs, and we hope that this invention, of life detecting life, will be useful for clinicians, scientists and engineers to help the community wherever and whenever DNA detection is important.”