An engineered bacterium in the gut of an animal has successfully detected the presence of a specific DNA sequence for the first time. The approach could be used to create living sensors that provide early warnings of cancers or dangerous pathogens.
鈥淚t is perfect for the detection of cancer and precancer throughout the entire gastrointestinal tract,鈥� says team leader at the University of California, San Diego.
Many groups are developing various kinds of biosensors for detecting chemicals, but ones that could spot specific DNA sequences would be extremely versatile and could have all kinds of potential uses. Hasty says this approach could also be used to detect cholera in drinking water sources, malaria in waters where mosquitoes breed and toxic fungi on crops or stored food, as well as for monitoring diseases via sewage.
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In the gut, the bacteria could even be designed to treat infections that they detect, says Hasty. 鈥淭he list of [intestinal] infections, or even diabetic or vascular ulcer infections, that could be detected and thwarted by an early and direct response are vast.鈥�
To create their DNA detector, Hasty worked with at the Colonoscopy Clinic in Brisbane, Australia, and others to exploit two things.
Firstly, many bacterial species actively take up DNA fragments from the environment. They usually do this to , but when the imported DNA matches part of the bacterial genome, the imported sequence can get integrated into it.
Secondly, most bacteria also have CRISPR immune systems that can target and destroy specific DNA sequences 鈥� CRISPR gene editing uses components from these bacterial systems.
The researchers engineered a bacterium called Acinetobacter baylyi to detect a single-DNA-letter mutation in a human gene called KRAS,聽found in many cancers. They first programmed the bacterium鈥檚 CRISPR machinery to chew up any normal copies of KRAS the bacterium took in, so only mutant sequences could be integrated into the bacterial genome.
Next, they ensured that if any mutant KRAS sequences were integrated, this would make the bacteria antibiotic resistant. The researchers then added the bacteria to the guts of mice, some of which had colorectal tumours containing the mutant KRAS听驳别苍别.
When faecal samples from mice were put on a medium containing an antibiotic, only聽A. baylyi聽from the rodents with tumours grew on the medium and became visible.
鈥淭o my knowledge, this is the first example of bacteria being engineered to detect specific DNA sequences while living in the gut,鈥� says at Imperial College London, who wasn鈥檛 involved in the research. 鈥淚t鈥檚 always exciting to see advances such as this one.鈥�
Simply sequencing the DNA present in faecal samples isn鈥檛 a reliable way to detect gut cancers or pathogens early on, says Hasty, because our guts are full of enzymes that rapidly chew up any free DNA. But if the DNA detection happens in situ in the gut, it can be done before the DNA is destroyed.
The antibiotic-resistance-based detection system was used just for proof of principle, he says. The team is working on ways to make it simpler to tell when the bacteria have encountered a target molecule. One approach would be to make them generate visual signals that could be seen in faeces; another would be to get the bacteria to produce harmless substances that could be detected by blood tests.
The team is also developing genetic circuitry that would allow the bacteria to detect any one of many different mutations. This will be necessary to detect most cancers: the mutant KRAS is found in only 13 per cent of colorectal cancers, for instance.
鈥淭his is a really nice approach,鈥� says Riglar. But there are still a number of challenges to solve before the bacterial system could become an effective diagnostic tool, he says.
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