Programmable Cells Poised to Benefit Biology, Disease Detection
In the brave new world plausibly envisioned by MIT’s Dr. James Collins in a recent Covid-19 scientific interest group lecture, wearable sensors may one day detect the arrival of whatever pandemic will almost certainly succeed Covid-19 as a global threat, and even the mask one dons on such an occasion might be capable of diagnosing what that bug tangled in the fibers happens to be.
That’s thanks to the maturing field of synthetic biology, in which investigators are adapting the logic of the electronic circuit board to make gene circuits capable of rewiring living cells and endowing them with novel functions. So-called “wet circuits” are now being designed and built by scientists such as Collins, who is the Termeer professor of medical engineering & science at the Massachusetts Institute of Technology.
Starting with relatively simple genetic toggle switches, Collins and colleagues have created a range of chemical switches that “open up tremendous possibilities for biosensors…Synthetic gene circuits have opened up a whole range of logical functions to use in cells.”
The technology enables programmable cells, or living technology, that can sense their environment, make a decision and act on it. Standing to benefit are not only medicine, but also energy, the environment, first responders, the military and agriculture, to name a few fields.
Yet multiple times throughout the hour of his lecture, Collins paused to remind listeners, “No matter how clever we think we are, biology still gets in the way of our best intentions and aspirations in synthetic biology.”
Nonetheless, we are poised on the doorstep of an era of living diagnostics and living therapeutics, he said.
Proof of concept for the MIT team was their response years ago to a challenge from the Gates Foundation to create an inexpensive way to diagnose and treat cholera. Engineering, in mice, the bacteria Lactococcus lactis, the researchers invented a “theranostic,” that responds only to the presence of cholera. By modifying the pH in cells, the therapy thwarts the dumping of cell fluids into the intracellular space, which is the hallmark of that nasty gut pathogen.
Virtues of the therapy are that it is “eminently manufacturable, inexpensive and can be lyophilized into pills or spiked into yogurt,” Collins said. “These innovative developments in synthetic biology could make a difference for controlling pathogen outbreaks.”
Thanks to the wizardry of a number of collaborators skilled in manipulating cell-free extracts, Collins described the possibility of encoding RNA switches within freeze-dried, paper-based systems—which don’t require refrigeration—to create paper-based diagnostics that could be mailed around the globe to identify pathogens. It could tell first responders—within the “golden hour” when treatment is most effective—which antibiotic to reach for, and which to avoid.
Several years ago, Collins and collaborators pivoted from diagnostic work on bacteria and antimicrobial resistance to a focus on Ebola, to help with an outbreak in Africa. Within a day of taking on the challenge, his team had crafted a 24-sensor system at a cost of only 2 cents per sensor, capable of detecting multiple strains of Ebola.
Fifteen months later, in January 2016, they embarked on creation of a paper-based diagnostic for Zika virus. It took less than 2 months to create a freeze-dried amplification system embedded with RNA sensors that could tell Zika from dengue, chikungunya and yellow fever.
Almost inevitably, the scientists also began using CRISPR-cas9 gene editing technology to make a Zika diagnostic capable of teasing out its various strains; it debuted in 2016.
Collins described another paper-based diagnostic created to detect the gut microbiome and host response, to identify species present in stool samples.
“It was easy, inexpensive and provides a rapid readout of results,” he said.
“But what we build doesn’t always function,” Collins cautioned. He and colleagues are now exploring “deep learning” platforms that can harness neural networks to improve synthetic biology, particularly with respect to Covid-19.
Working with collaborators at Harvard and the Wyss Institute, Collins is now searching for design rules, new components and novel gene circuits that will enable the platforms to quickly diagnose diseases such as Covid. They are using a kind of regulator known as a “toehold switch,” which, according to Wyss “enables precise control over the expression of a gene of interest in response to a defined environmental stimulus in diverse synthetic biology applications.”
A refinement of CRISPR known as SHERLOCK, pioneered by scientists at MIT and the Broad Institute, uses a variety of enzymes beside cas9 to detect substances at the sensitivity of a single molecule. It forms the basis of a diagnostic system enabling not only species identification, but also discrimination between strains and mutants within a strain, said Collins. Uses are not limited to bacteria, but viruses as well.
He envisioned a 4-pot multiplex system that could evaluate serum, urine, saliva and plasma simultaneously, with results as rapid as today’s pregnancy tests.
Last May, the FDA issued the first CRISPR-dependent emergency use authorization for a Covid-19 diagnostic, reported Collins. “Ours compares well to the PCR-based test,” he said. “You get output in less than an hour, which is much faster, and at only one-quarter of the cost.”
Collins predicts a coming era of “wearable synthetic biology,” wherein gene circuits could be inserted into clothing to see if a person is exposed to a pathogen or toxin, and perhaps even measure a bug’s biological effect on the host. Already, a synthetic gene circuit has been developed that serves as a universal sensor for nerve toxins.
The “lab coat of the future” could be tailored with biosensors, and even johnnies—those embarrassing gowns worn by inpatients at hospitals everywhere—could include sensors enabling hospital epidemiologists to pinpoint sources of in-house infection.
Masks, too, could include inserts that respond to and analyze the water vapor in exhalations—such a system is now in demonstrations, said Collins.
“Any porous media, not just paper” can host biosensors, he continued. Freeze-dried pellets could be encapsulated into portable field systems that can make vaccine antigens on the spot, Collins noted. A model has already been created, using diphtheria as an example. “We could have portable on-demand biomolecular factories.”
Observing that the Moderna vaccine against Covid-19 has its origins in synthetic biology, Collins said work has started on a BCG-based Covid vaccine. (BCG, or bacillus Calmette-Guérin, has long been used as a tuberculosis vaccine.)
“This is not Operation Warp Speed, but Operation Slow Speed,” he quipped. Tweaked using synthetic biology, the BCG-based vaccine would be “inexpensive, safe, easy to make, requires no refrigeration and involves only one shot,” said Collins. “We don’t know if it will be ready in time, but it could address the next pandemic, which is coming, but we don’t know when or where.”
Collins and colleagues are also taking a deep-learning approach to the discovery of novel antibiotics.
“Our antibiotic arsenal is declining while antibiotic resistance is increasing,” he said. “What features, if we look bond by chemical bond, contribute to bactericidal behavior?” Applying their technology to larger and larger libraries of compounds, they are identifying hundreds of new candidates.
“We would like to extend our work to the design of novel antibiotics,” Collins concluded, “and to antivirals, and to new treatments for cancer and other complex diseases.”
During a brief Q&A moderated by Collins’s first postdoc, Dr. Carson Chow, now at NIDDK, who described the talk as “Marvel-level science,” Collins was asked if biofabrics will be affordable for everyone.
“Our hope is that this new technology will be as cost-effective as possible,” he said. “Face masks can be made for small numbers of dollars. The more complicated clothing could be quite expensive. But wristbands are very low-cost. Athletes at the high school level could use them for monitoring their workouts.”
The complete talk—a great way to get excited about science all over again—is available at https://videocast.nih.gov/watch=38876.