“Specially trained” microbes could enable earlier cancer diagnoses in the future: Researchers have modified bacteria in such a way that they can detect cancerous areas in the body that are difficult to detect based on released tumor DNA. They have already successfully used the concept to detect colon cancer in a mouse model. Their system could be adapted to diagnose various diseases and even open up locally targeted treatment options, the scientists say.
Detected early – danger averted: early diagnosis is the key to successful treatment for many types of cancer. Malignant tissue can also be recognized by certain genetic mutations that are often associated with the proliferating potential of these cells. It is known that tumor tissue also releases its special genetic material into the environment. This detached cancer DNA can already be detected by genetic engineering. But this method is problematic for the diagnoses. Because in the body – for example in the intestinal tract – the free DNA is broken down relatively quickly by enzymes. Therefore, a method would be desirable that records the genetic cancer traces directly at the release site and then shows them.
This is exactly what the method that a team of US and Australian researchers is now presenting can apparently achieve. For their biosensor system, they have cleverly exploited the potential of a type of bacteria that naturally belongs to the harmless inhabitants of the human intestinal system. What is special about Acinetobacter baylyi is a feature that is referred to as natural competence: These bacteria like to snap up free DNA from the environment and incorporate it at a specific point in their genome. This can be useful for the microbes, because it can sometimes result in beneficial traits. In technical terms, this form of transmission of hereditary factors is called horizontal gene transfer.
Microbial tumor DNA collectors
“Knowing that cell-free DNA can act as an input, we set out to engineer bacteria that respond locally to tumor DNA,” says co-author Dan Worthley of the South Australia Health and Medical Research Institute in Adelaide. Using genetic engineering methods, the researchers have specifically adapted the integration region in the genome of Acinetobacter baylyi: Using certain modules, a special genetic sequence is now integrated there when the bacterium has picked it up in its environment. It is a section of a gene called KRAS, which is typically mutated in colorectal cancer.
The fact that the spy microbes actually picked up a piece of the cancer-mutated version of KRAS is made clear by a reporter function, the scientists explain: through sophisticated genetic constructions at the installation site, they have built in a switch function. A genetic program is only activated when the mutated form is integrated: the tumor DNA switches on an antibiotic resistance gene that makes the microbes insensitive to treatment with the active ingredient kanamycin. In the case of sensor bacteria, which have only incorporated the “healthy” version, the resistance is not activated and they die on culture medium with the antibiotic. In other words: This effect makes the “cancer finding” detectable.
Proof of function in the mouse model
To what extent this concept works in practice, the researchers first tested on organoids from cancer cell tissue and then finally in a mouse model. These were animals in which the formation of intestinal tumors that have a KRAS mutation was induced. The researchers injected the sensor bacteria into the intestines of these animals and healthy controls. Later, the intestinal contents were then removed and analyzed: solutions were applied to culture media containing kanamycin.
It turned out that no sensor bacteria grew in the samples from healthy mice, which only have the normal KRAS gene, due to the lack of activation of the reporter resistance. However, many of the microbes from the Krebs mice were able to grow because they had successfully integrated the mutated sequence. “It was incredible when I saw under the microscope the bacteria that had taken up the tumor DNA,” says co-first author Josephine Wright of the South Australia Health and Medical Research Institute in Adelaide.
However, as the researchers emphasize, their concept is only in an early phase of development: Before it can be used clinically, questions about the safety and practical use of the method still have to be clarified. But they see considerable potential for medicine. The team emphasizes that the system can also be quickly adapted to detect other types of cancer or infectious diseases. It also seems possible that the sensor bacteria can even be designed in the future so that they can also carry out treatments on site. “An exciting aspect is that once the target DNA is captured, it could be coupled with the direct delivery of nanobodies, peptides or other molecules to treat cancer or infection,” the scientists write.
Source: University of California – San Diego, professional article: Science, doi: 10.1126/science.adf3974