Protein designer awarded $2.5M to develop bioluminescent protein for deep tissue imaging

The natural glow of bioluminescence — the ability of some species to give off light — is an exciting phenomena to spot along the shores of the California coast or in the glint of a summertime firefly. Assistant Professor of Biomolecular Engineering at the UC Santa Cruz Baskin School of Engineering Andy Yeh is taking inspiration from this natural marvel to design new luminescent technology as a tool for biomedical imaging. 

With the support of a four-year, nearly $2.5 million grant from the Chan Zuckerberg Initiative, Yeh will develop completely artificial enzymes that can produce bioluminescence in the body to enable researchers to image tumors or other diseases that may be present in deep tissues at the preclinical stage. 

In addition to the artificial protein, this project will include the development of a specialized imaging system to enable high-resolution detection of the bioluminescent signal. It will explore how bioluminescence can be used in combination with CAR T-Cell Therapy techniques to better track the effectiveness of these specialized cancer treatments. Yeh will undertake this work in collaboration with UC Irvine’s Associate Professor of Biomedical Engineering Michelle Digman and Professor of Chemistry Jennifer Prescher, and Harvard Medical School’s Assistant Professor of Immunology Ming-Ru Wu. 

Exploring illumination

Since the 1960s, scientists have been investigating the biochemical mechanisms that make some living organisms glow. Scientists discovered that bioluminescence is produced via an enzyme, called luciferase, that catalyzes a chemical reaction that produces photons, or light. Despite their best efforts, researchers have not been successful in effectively transferring every bioluminescence found in nature to glow in human cells. 

Yeh specializes in de novo protein design, the process of creating new proteins completely artificially, as compared to modifying proteins found in nature. He has focused his research around developing artificial luciferases that evade the natural limitations of transferring bioluminescence to human cells and animal models. 

To do this, Yeh developed a computational method that he used to create an enzyme designed to be used to produce light in human cells. The computational method incorporates deep learning algorithms to design highly stable and efficient catalysts for high levels of light emissions. 

Last year, Yeh published evidence of his first de novo luciferase protein, which he named “LuxSit,” Latin for “let light exist,” in a paper in the journal Nature. This was an important proof of concept, showing that it is possible to create proteins that produce light at a similar activity level to what is found in nature. 

“This is the first example of us designing something that is comparable [in catalytic output] to what nature has,” Yeh said. “To design something that is as efficient as native protein, that’s a benchmark in de novo protein design.”

Designing for deep tissue 

Now, his research will focus on adapting his bioluminescent protein for deep tissue imaging, for which there is currently a lack of effective methods. 

To optimize the protein for deep tissue imaging, Yeh will engineer the protein to produce light that is shifted toward the far red or infrared end of the light spectrum. Red light is ideal for imaging in deep tissue because it allows for better penetration through the tissue — if you hold a flashlight to your hand, the light that shows through the flesh will be red, because all the other light is absorbed by the tissue. 

Red-shifting the light will create a much stronger signal that can be picked up by a detector. The researchers hope to attain deep tissue sensitivity that is significantly higher than what is currently possible in the field, which researchers could use to find and track the movement of just a small population of tumor cells that may undergo metastasis and travel through the body. 

“We believe that we are able to design a really efficient catalyst that can emit light where not only the brightness is higher, but also we can change the color of the light so it can penetrate through the tissue much more efficiently than other existing bioluminescent proteins that are produced in a lab,” Yeh said.

A team of engineers at UC Irvine including Digman and Prescher will collaborate with Yeh to develop a new method of light detection called “phasor imaging,” rather than taking the traditional approach of detecting light signals by color. The UCI researchers have proven that this technology can better differentiate light emissions and avoid severe spectral overlap, which makes it difficult to clearly separate light. 

The researchers will also collaborate with Ming-Ru Wu at Harvard University to test their probe in CAR T-Cell Therapy. This is a therapy in which synthetic biologists engineer the T-cells, an important type of white blood cells in the immune system, of a cancer patient so that they can better recognize and fight tumor cells. The lack of a sensitive method for tracking the engineered T-cell in the body is currently a hurdle for this treatment. The team hopes that Yeh’s new luminescent probes will provide an ideal method to gather information about the activity and efficacy of the treatment while it is being carried out in vivo, helping guide preclinical studies to combat cancers.