16 Aug Engineered Bacteria Can Act as Biosensors to Detect Cancer DNA
MedicalResearch.com Interview with:
Dr. Worthley
Daniel L. Worthley
MBBS (Hons), PhD, MPH, FRACP, AGAF
Gastroenterologist
Associate Professor
University of Adelaide
MedicalResearch.com: What is the background for this study?
Response: Cells are revolutionising healthcare, from modern faecal microbial transplantation in the gut to CAR-T cells fighting cancers, life healing life. Some aspects of cellular care are so entrenched in medicine that they are almost overlooked for the miraculous cellular therapies that they are, such as stem cell transplantation to treat haematological malignancies and, of course, in vitro fertilization, life creating life. Modern medicine is slowly, but surely, pivoting from pills to cells. Professor Siddhartha Mukherjeee, oncologist, scientist, and author, provides a beautiful thesis of this in his book Song of the Cell and in his TED talk on the cellular revolution in medicine (https://youtu.be/qG_YmIPFO68?feature=shared). I was lucky enough to have trained with Sid as a post-doc at Columbia and this concept was really drummed into me. But, as a gastroenterologist, perhaps it was the bacterial cells, rather than the blood cells, that had most to offer in the management of bowel disorders? Around the same time, Professors Jeff Hasty, Tal Danino and Omar Din from UC San Diego had been inventing and publishing, in my opinion, the best bacterial engineering work that has ever been produced to specifically target cancer. I remember when we first reviewed their 2016 Nature paper in our lab meeting (https://www.nature.com/articles/nature18930#citeas), it was like – “We gotta meet these guys!”. Through Tal, who was by then, working at Columbia, I was introduced to Jeff and I attended his lab meeting back in 2019. That was where our project began after a lab meeting in La Jolla. Rob Cooper had presented his work on horizontal gene transfer. Everything that comes out of Jeff’s lab is both practical and reproducible but also beautiful. Beautiful in a scientific self-evident way that instantly communicates the purpose, approach and outcomes of an experiment.
Rob’s presentation that day was a case-in-point. Rob was studying genes and gene transfer in bacteria (see part of Rob’s fascinating presentation here, https://youtu.be/5nBsRF-BsA8?feature=shared). Genes are the fundamental unit of heredity and gene transfer (or inheritance) the process by which genes are passed from one cell to another. Genes may be inherited vertically when one cell replicates its DNA and divides into two, now separate, cells (reproduction). Genes are the stuff, and vertical gene transfer is the process, by which you receive your mother’s laugh and your father’s eyebrows. Genes may also, however, be inherited horizontally when DNA is passed between unrelated cells, outside of parent to offspring inheritance. Horizontal gene transfer is quite common in the microbial world. Certain bacteria can salvage genes from cell-free DNA found within its environment. This sweeping up of cell-free DNA, into a cell, is called natural competence. So, competent bacteria can sample their nearby environment and, in doing so, acquire genes that may provide a selective advantage to that cell. Like cellular panning for flecks of gold in a stream. After Rob’s presentation, Jeff, Rob and I started to discuss the possibilities. If bacteria can take up DNA, and cancer is defined genetically by a change in its DNA then, theoretically, bacteria could be engineered to detect cancer. Colorectal cancer seemed a logical proof of concept as the colorectal lumen is full of microbes and, in the setting of cancer, full of tumour DNA. When a biophysicist, a scientist and a gastroenterologist walk into a bar, after a lab meeting, this is what can happen! Professor Susi Woods and Dr Josephine Wright, superb cancer scientists from Adelaide, Australia, were quickly recruited in as essential founding members of the group. We all got to work. Australian and US grants, lots of experiments, early morning Zoom calls across the Pacific, inventing new animal models and approaches, i.e. a many year, iterative process of design-build-test-learn, that got us all to where we are now.
MedicalResearch.com: What are the main findings?
Response: A tiny bit more background, Acinetobacter baylyi, a naturally competent bacteria, was chosen to be the experimental biosensor, the bug to detect cancer in this project. The A. baylyi genome was modified to contain long sequences of DNA complementary to a human cancer gene that we were interested in capturing from the tumour. These complementary DNA sequences functioned as sticky landing pads so that when any specific tumour DNA was taken up by the bacteria it was more likely to integrate into the bacterial genome. We conducted a series of experiments in which bacterial biosensor and tumour cells were brought together, in increasingly complex systems. Initially, the biosensor was simply incubated with purified tumour DNA. It detected the cancer DNA. Next, the biosensor was co-cultured with living tumour cells. It detected the cancer DNA. Ultimately the biosensor was delivered into the colorectum of mice. The engineered biosensor perfectly discriminated between mice with and without colorectal tumours, through sampling, integrating and reporting through the synthetic biology genetic circuit that we engineered. Further engineering allowed discrimination of single base pair changes within the tumour DNA. We called this technology CATCH, a Cellular Assay for Targeted, CRISPR-discriminated Horizontal gene transfer.
MedicalResearch.com: What else can engineered bacteria detect?
Response: Diseases/incidents defined by a specific genetic sequence, present in the disease/incident situation, but absent in health/normality. That is why cancer and infection are the lowest hanging fruit to apply this system to healthcare, because cancer and infections, fundamentally develop from a unified common ancestor cell that genetically defines the condition. We engineered a competent bacterium to detect and respond to mutant cell-free tumour DNA: other medical applications are detecting and responding to other cancer mutations in bacterial accessible sites such as the nasopharynx, the genitourinary tract, other parts of the digestive tract (stomach, oesophageal and pancreatic cancer), infections defined by bacterial DNA perhaps C. difficile, DNA viruses. This is, however, fundamentally a synthetic biology paper, as the applications are not limited to healthcare. 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. Wherever genetic detection is important, continuous surveillance is desirable, or an immediate and biologically-generated response at the time and place of detection would be beneficial.
MedicalResearch.com: What should readers take away from your report?
Response: For cells to replace tablets, the right cells (chassis) need to process (circuits) a disease signal (input) and deliver an appropriate therapy (output). Cell-free DNA is an excellent disease signal, particularly for cancer & infection. In our paper we developed and describe a new synthetic biological technique to allow cell-free DNA to be used as a signal, an input, for a range of future applications. Although there is more work to do, engineered-bacterial healthcare will revolutionise digestive healthcare in the coming decades.
MedicalResearch.com: What recommendations do you have for future research as a results of this study?
Response: We have designed and are testing better circuits to create more sensitive biosensors, we are integrating the detection of cancer-DNA with other biological signals to improve the sensitivity and specificity of our biosensors, and, perhaps most importantly, we are coupling disease detection to treatment. Any diagnostic lab can detect DNA. But, what a diagnostic lab can’t do, and can never do, is to directly treat a disease at the time and at the place of detection. That is the extraordinary potential of cellular therapy.
MedicalResearch.com: Is there anything else you would like to add? Any disclosures?
Response: There is more work to do, but we have an extraordinary team that is committed to developing, testing and applying this work to realise a future where nobody dies of colorectal cancer. Jeff Hasty is a cofounder and board member of, and Jeff Hasty, Dan Worthley, and Susis Woods have equity in, GenCirq Inc., which focuses on cancer therapeutics. Dan Worthley, Jeff Hasty, Rob Cooper, Susi Woods, and Josephine Wright are inventors on a provisional patent application, “Detecting disease-associated target nucleic acids in a mammal and treatment thereof,” filed by the University of California San Diego with the US Patent and Trademark Office (application no. 63/528,234). Also, if you could please link to our website www.catch.contact and to our video https://youtu.be/yS7sqiXegL4?feature=shared
Citation:
Robert M. Cooper et al.,
Engineered bacteria detect tumor DNA.Science
381,682-686(2023).DOI:10.1126/science.adf3974
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