Hertz Fellow Embarking on Fantastic Voyage, Engineering Cells to be Detected with Sound Waves

January 31, 2018

by Jeremy Thomas

Remember Fantastic Voyage? The then-pioneering 1960s sci-fi flick (and its novelization by Isaac Asimov) in which a submarine crew shrinks down to microscopic size and takes a groovy trip through a scientist’s body, fixing maladies along the way?

Hertz Fellow and California Institute of Technology chemical engineering assistant professor Mikhail Shapiro certainly remembers. It happens to be the perfect analogy to the research he and his collaborators at Caltech’s Shapiro Lab published in the January issue of Nature. In the paper, Shapiro and his colleagues report successfully genetically engineering common gut bacteria with acoustic “reporter genes” allowing them to be imaged and monitored with ultrasound by reflecting sound waves, similar to sonar technology.

“Cells already do what we want the submarines to do,” Shapiro said. “We want them to be really small, we want them to go through bloodstreams, go into tissues and see signals. In the movie [Fantastic Voyage], it was really important for the submarines to be able to communicate with the doctors and scientists outside the body so they would strategize and know what to do. My vision is we will have cells acting as these submarines inside the body and what I hope we will contribute at my lab is the communications equipment that allows us to stay in touch with these submarines once they’re inside.”
The key to Shapiro’s team’s approach was genetically programming the bacteria to produce gas vesicles -- protein nanostructures commonly found in buoyant plankton and other water-dwelling microbes. Shapiro and his group discovered that by copying and pasting the genes behind the gas vesicles into bacterial cells – namely E. coli and Salmonella – these gas-filled bubbles could scatter soundwaves passing through the bacteria, and therefore could be detected and imaged using common ultrasound techniques.

Caltech electron microscopy

An illustration (left) and electron microscopy image (right) show the gas vesicles within genetically engineered
bacteria that scatter ultrasound waves, rendering the cells visible within crowded environments like the human body.
Credit: Barth van Rossum (left) and Anupama Lakshmanan (right) for Caltech.

The advantage over current technologies such as optical microscopy, Shapiro said, is that ultrasound waves can penetrate deep into the body, enabling the noninvasive study of microorganisms and cells in mammals and potentially impacting future medicine by helping to develop new ways to visualize and combat disease.

“If we really want to understand how these cells work, ideally we want to study them within a living, breathing animal rather than having these cells growing in a dish,” Shapiro said. “There’s also a big interest these days in using cells as diagnostic and therapeutic agents. A lot of medicine is based on drugs that are pretty uni-dimensional. Cells have much more diverse abilities. If you have a cell acting as a therapeutic agent then you can inject it and the cell can hone to a region of disease, it can recognize molecular signals in its environment and can make decisions based on those signals.”

Shapiro said the technology could also be useful for immunotherapy, enabling scientists to see if engineered cells reached their destination, if are they multiplying, and if they’re remaining functional. As a diagnostic tool, gene expression could be turned on and off to detect presence of, for instance, inflammation in the colon, without the patient needing a colonoscopy.

Alternative, non-invasive approaches to visualizing and manipulating biological functions occurring deep inside the tissue, like the brain or the gut, is nothing new for Shapiro, who was dissatisfied with the available tools for studying the nervous system as a neuroscience major at Brown University. Motivated to become an engineer, he earned his PhD in biological engineering at the Massachusetts Institute of Technology (MIT), where he developed the first genetically engineered molecular sensors for magnetic resonance imaging (MRI) to image neural activity. As a postdoctoral researcher at the University of Chicago and a Miller Fellow at the University of California Berkeley, Shapiro continued his work on reporters for MRI, as well as infrared stimulation of neural activity and first explored ultrasound as a tool.

“Initially, I wanted technologies that would allow me to study what’s happening in the brain noninvasively,” Shapiro said. “I’ve always been on the lookout for unusual proteins or other things that can be encoded in genes that have weird physical properties… The work on engineering these proteins and seeing how they interact with sound waves and putting them into all different kinds of cell types, I find intrinsically fascinating.”

Shapiro said his Hertz Fellowship (2004-2008) had a major impact on providing him with the ability to work on high-risk, high reward projects at MIT, where he worked on projects nobody had tried before.

“Being a Hertz Fellow made me feel free to choose whatever I wanted to do for my research, which no one was doing at the time,” Shapiro said. “Having the Fellowship allowed me to do that work and to find advisors who would let me go at it. I wouldn’t be doing anything I’m doing now if it weren’t for that.”

In addition to his scientific achievements, Shapiro embodies the Foundation’s entrepreneurial spirit. He’s founded several biotech companies, and was most recently a venture capitalist at Third Rock Ventures, a biotech venture capital firm based in Boston and San Francisco. While his involvement with those companies has ended, the experiences he’s had in the private sector have taught him.

“It was great while it lasted,” Shapiro said. “But what I’ve discovered is that I would still go to bed at night thinking about weird proteins I wanted to engineer. Having the freedom to work on these really far out ideas is something you can only really find in academia.”

Currently, about half of Shapiro’s Caltech lab is dedicated to work on MRI, a powerful technology, Shapiro said, but one that requires expensive equipment. Out of all the approaches he’s tried, Shapiro believes ultrasound may have the most promise.

“It’s kind of like picking between your children,” Shapiro said. “But I’m really excited about ultrasound because it’s a very widespread technology, it’s relatively inexpensive, you can find it in the best hospitals in Los Angeles or San Francisco, as well as the developing world. If you can give ultrasound the ability to obtain more information about what’s going on, not just anatomical but some kind of cellular or molecular information, I think that would have a lot of impact.”

Shapiro said while he and his group have only just begun demonstrating the capability of cellular ultrasound, he’s hopeful that scientists and clinicians will increasingly use genetically engineered bacteria and human cells as diagnostic and therapeutic agents. Before that happens, Shapiro said scientists will need to address a few hurdles. Besides overcoming the reservations held by some in the general public over introducing genetically engineered cells into the body, they’ll need to demonstrate that reporter genes can be added without negatively affecting the therapeutic value of the bacteria. The technology also hasn’t yet been tried in humans, and Shapiro said it may be years before it sees the light of day in a clinical setting.

“We don’t yet know whether the technology as it stands today is sensitive enough to be used clinically,” Shapiro said. “The number of cells that can be detected using this method is sufficient for some scenarios, but to make it widely usable, we’d like to further optimize these genes and the proteins that they encode to make them brighter under ultrasound so we can make this technology as sensitive as possible.”

At Caltech, Shapiro said he will continue his research into ultrasound, exploring the engineering of different types of cells to make the technology more versatile, and coupling it with other methods for cell therapies.

“We’re hopeful that our discovery of acoustic reporter genes is really just the starting point for the development of a versatile repertoire of technologies that will allow ultrasound to image things more sensitively and do more multiplexed imaging, functional sensing in the body,” Shapiro said. “If we can develop the types of tools for ultrasound or magnetic resonance that people have developed for optics at the molecular level, then we will have created categorically new capabilities for biology and potentially for medicine.”