For the first time, genetically engineered bacteria in the intestines of animals have succeeded in detecting the presence of specific DNA sequences. This method can be used to create real-time sensors that provide early warning of cancer and dangerous pathogens.
“This is ideal for detecting cancer and precancerous lesions throughout the gastrointestinal tract,” said Jeff Hasty, team leader at the University of California, San Diego.
Although different groups are developing different types of biosensors for chemical detection, sensors that can detect specific DNA sequences are extremely versatile and have a variety of potential uses. This method can also be used to detect cholera in drinking water supplies, malaria in mosquito-infested areas, toxic bacteria in crops and stored foods, and to monitor disease through wastewater, Hasty said.
In the gut, it can even be designed to treat infections detected by bacteria, Hasty said. “The list of [intestinal] infections, as well as diabetic infections and vascular ulcers, that can be detected and prevented by an early direct reaction is vast.”
To create their DNA probe, Hasty worked with Daniel Worsley and others at the Colon Endoscopy Clinic in Brisbane, Australia.
First, many bacterial species actively receive DNA fragments from the environment. They usually do this to use DNA as a food source, but if the imported DNA matches part of the bacterial genome, the imported sequence can integrate into it.
Second, most bacteria also have a CRISPR immune system that can target and destroy specific DNA sequences. CRISPR gene editing uses components of these bacterial systems.
Researchers have designed a bacterium called Acinetobacter baylyi to detect single DNA letter mutations in the human gene KRAS, which is present in many cancers. First, they programmed the CRISPR mechanism of the bacterium to chew a normal copy of KRAS ingested by the bacterium. Therefore, only the mutated sequence was integrated into the bacterial genome.
Next, they confirmed that if a mutated KRAS sequence was incorporated, this would make the bacterium resistant to antibiotics. Later, researchers added bacteria to the intestines of mice. Some of them were colonic rectal tumors containing a mutated KRAS gene.
When mouse fecal samples were placed in a medium containing antibiotics, only A. baylyi from rodent tumors grew and became visible on the medium.
“As far as I know, this is the first bacterium designed to detect a specific DNA sequence in the gut,” said David Riggle of Imperial College London, who was not involved in the study. “It’s always exciting to see such progress.”
Simply sequencing DNA in stool samples is not a reliable method for early detection of intestinal cancer and pathogens, Hasty says. Because our intestines are full of enzymes that can digest anything quickly. What is Cell-Free DNA? However, if the DNA test is done locally in the intestine, it can be done before the DNA is damaged.
He said that detection systems based on antibiotic resistance are used only as proof of principle. The team is working on an easier way to determine when a bacterium encounters a target molecule. One way is to generate a visible visual signal in the stool. Another way is to make the bacteria produce harmless substances that can be detected by blood tests.
The team is also developing a genetic circuit that allows bacteria to detect one of many different mutations. This is necessary to detect most cancers. For example, KRAS mutations are found in only 13% of cases of colorectal cancer.
“It’s a really cool approach,” said Wrigley. However, he said, there are still many challenges that need to be addressed before the microbiome can become an effective diagnostic tool.