Escherichia coli bacteria
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Using CRISPR gene editing, researchers at the University of California, San Diego (UCSD), and colleagues from Australia, have engineered bacteria that can detect the presence of tumor DNA in the colons of mice models, potentially paving the way for biosensors able to identify various diseases.

Tumor cells have been observed releasing their DNA into surrounding environments. Although laboratory technologies can already analyze purified DNA effectively, detecting nucleic acids at their release site remains a challenge.

Reporting in Science, researchers have now developed a technique called Cellular Assay for Targeted CRISPR-discriminated Horizontal gene transfer (CATCH), designed to identify specific DNA sequences outside of cells. Using an inherent bacterial skill known as natural competence, in which bacteria take up surrounding DNA using horizontal gene transfer, the researchers were able to detect cancerous sequences in the bacterial DNA.

“As we started on this project four years ago, we weren’t even sure if using bacteria as a sensor for mammalian DNA was even possible,” said Jeff Hasty, professor at UCSD School of Biological Sciences and scientific team leader. “The detection of gastrointestinal cancers and precancerous lesions is an attractive clinical opportunity to apply this invention.”

In order to establish CATCH, the researchers engineered bacteria using CRISPR to test free-floating DNA sequences on a genomic level and compare those samples with known cancer DNA sequences. After achieving positive results, the scientists genetically modified a bacterium already present in the colon to be used as a sensor for identifying DNA from KRAS—a gene mutated in many cancers.

The bacterium used—known as Acinetobacter baylyi—was programmed to distinguish between mutated and “healthy” KRAS DNA. Only bacteria that had taken up mutated copies of KRAS, as found in precancerous polyps and cancers, would survive treatment with a specific drug. This allowed the scientists to identify the location of the mutated gene by sequencing bacterial DNA present at the same site.

“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,” said Josephine Wright, senior research fellow at the South Australian Health & Medical Research Institute and co-author of the study.

The researchers believe that in the future diseases will be treated by cells rather than medicines. As a next step, the bacteria biosensor strategy will be adapted with new circuits and different types of bacteria for detecting and treating human cancers and infections.

“There’s a future where nobody need die of colorectal cancer. We hope that this work will be useful to bioengineers, scientists, and, in the future, clinicians, in pursuit of this goal,” concluded Dan Worthley, researcher at the South Australian Health & Medical Research Institute and co-author of the study.

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