Can bacteria be living biosensors? In a recent paper, Cooper et. al. describe a remarkable approach to engineer bacteria to detect cancerous DNA in models of colorectal cancer. By incorporating a clever antibiotic resistance construct specific to cancerous DNA mutations, the detection mechanism is a simple bacterial growth assay on an antibiotic-containing agar plate.
The bacteria that live on, in, and all around us have remarkably diverse interactions with our health. Some are obviously pathogenic (S. aureus, for example), while others have been shown to be beneficial (Lactobacillus in the gut). The world of bacteria becomes even more interesting when we begin to engineer bacteria to help us.
A remarkable recent example includes engineering a strain of commensal skin bacteria to produce a cancer-fighting immune response. Bacteria can also be engineered to take advantage of a unique microbial property called horizontal gene transfer (HGT). In contrast to the typical flow of genetic information from parent to offspring, HGT allows microbes to pass DNA between each other, or even to sample and integrate DNA present in their environment.
Engineering Sensor/Donor Constructs to Detect Cancer DNA
This property could be particularly useful in detecting DNA shed by cancerous cells, taking a very different approach to “liquid biopsy” or proteomics-based methods. In a recent paper published in Science, Cooper et. al. describe engineering Acinetobacter baylyi to detect colorectal cancer DNA using HGT.
A. baylyi is a “naturally competent” bacterial strain, meaning it can easily take up DNA from its environment, and also contains an endogenous CRISPR system for DNA degradation. The authors first designed cancer cell lines, organoids, and mouse models of colorectal cancer with CRISPR degradation sites around the wild-type KRAS genotype and an antibiotic-resistant construct associated with cancerous KRAS-mutated DNA.
A. baylyi bacteria were engineered with complementary KRAS homology arms that allow for genetic recombination with donor DNA taken up via HGT. The result is that wild-type KRAS DNA taken up by the bacteria is degraded, while cancer-specific mutant KRAS DNA is incorporated into the bacterial genome, along with the antibiotic resistant construct. Bacteria then isolated from the cell lines or colorectal lumen in the mice are plated on agar plates containing the antibiotic. A simple readout of bacterial growth indicates the presence of cancerous DNA, while absence of growth means absence of cancerous DNA.
Successful Detection of Non Engineered Cancer DNA
For application to real-world cancer detection, this approach must also work for non-engineered cancer DNA. To engineer living bacterial biosensors for real-world cancer detection, the authors inserted a tetR repressor construct in the bacterial KRAS homology arms and an output gene of antibiotic resistance controlled by that repressor.
Recombination of the bacterial sensor’s DNA with the DNA taken up through HGT effectively deletes the repressor. If the incorporated KRAS sequence is wild-type, the bacterial CRISPR system can recognize and degrade it. If the KRAS sequence is mutated, however, the CRISPR system can no longer recognize its motif and thus, the downstream output gene is expressed. Once again, this produces the same readout of bacterial growth on an antibiotic plate as confirmation of cancerous DNA detection.
The creativity and efficacy of this technique is remarkable, and provides a new avenue for engineering bacterial biosensors for disease. Early detection of cancer is critical, this paper adds another tool to oncology researchers’ toolbox to develop new avenues for cancer detection!
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Jane Cook, Biochemist & Content Writer, Bridge Informatics
Jane Cook, the leading Content Writer for Bridge Informatics, has written over 100 articles on the latest topics and trends for the bioinformatics community. Jane’s broad and deep interdisciplinary molecular biology experience spans developing biochemistry assays to genomics. Prior to joining Bridge, Jane held research assistant roles in biochemistry research labs across a variety of therapeutic areas. While obtaining her B.A. in Biochemistry from Trinity College in Dublin, Ireland, Jane also studied journalism at New York University’s Arthur L. Carter Journalism Institute. As a native Texan, she embraces any challenge that comes her way. Jane hails from Dallas but returns to Ireland any and every chance she gets. If you’re interested in reaching out, please email [email protected] or [email protected].