A Genomic Medicine Story (with only a little CRISPR)

Genomic technologies are transforming our understanding of biology and medicine, enabling the precise manipulation and comprehensive analysis of genetic material. Duke University is investing in the development and use of genomic technologies through the Center for Advanced Genomic Technologies (CAGT), supported by the Pratt School of Engineering, the Trinity School of Arts & Sciences, and the Duke University School of Medicine.

CAGT launched in the fall of 2019. Under the direction of Charles Gersbach, the John W. Strohbehn Distinguished Professor of Biomedical Engineering, it is focused on developing and applying cutting-edge genomic technologies to address critical biomedical questions and advance human health. 

Perhaps the best known of these genomic technologies is CRISPR, which, in the last 12 years, has been revolutionary for both biomedical research and medicine and has shown promise in helping to treat and potentially even cure a wide range of genetic disorders, such as cystic fibrosis, sickle cell anemia, muscular dystrophy and more.

CRISPR’s discovery, though, is just the beginning of a field that continues to expand. “There is a misconception that CRISPR is transformative because of gene editing. While that is true, it’s potential is much wider,” Gersbach said. “CRISPR is transformative because of the ability to precisely target these molecular machines to specific regions of the genome. Gene editing is one basic operation these machines can perform on our genome, but there are many other ways to control genome structure and function that CRISPR technology enables.”

CAGT focuses its efforts on epigenomics of disease, gene regulation, drug responses to gene regulation, genome engineering technologies, and genome structure and function. While CRISPR gets a lot of attention, it is only one of many genomic technologies the center is pursuing in the hopes of speeding up science innovation and pushing the boundaries of what is possible to revolutionize the way we treat multiple conditions, including cancer.

Although their approaches are different, John Hickey and Emma Chory, both assistant professors of biomedical engineering at Duke, have a common goal: develop better, more effective ways to deliver chimeric antigen receptor (CAR) T-cell therapy using genomic technologies. 

CAR T-cell therapy isn’t a new idea. It’s a way to use a person’s own T cells—a type of white blood cell—to fight cancer by changing them in the lab so they can find and destroy cancer cells. However, it doesn’t work for all people or all types of tumors. For example, CAR T-cell therapy works best in liquid tumors, like leukemias, while solid tumors like sarcomas, carcinomas and lymphomas are harder to penetrate, making CAR T therapy less responsive. 

A Picture is Worth a Thousand Data Points

Hickey is using spatial relationships and computational strategies to better understand how solid tumors are organized so he can figure out better ways to attack them. 

Using an imaging technique called multiplex imaging, Hickey can add DNA barcodes to antibodies that recognize specific molecules. This allows him to make as many unique combinations of DNA barcodes as needed, and the antibodies act as a paint to differentiate as many proteins and molecules each cell is expressing as needed, which can provide information about its function and identity as well as where it is spatially.

Previously, researchers could only take cells, mash them up, harvest the RNA or DNA, and sequence it. “But essentially, what that’s doing,” Hickey said, “is taking a beautiful fruit platter, throwing it all together and getting a fruit smoothie.” When single cell technology came along, they were able to isolate each cell and characterize it, like isolating a piece of fruit on that fruit platter. What Hickey can do, though, is look at the fruit platter, see what fruit is next to what, and gain a better understanding of the relationships between the fruit. 

Then, using computational methods, Hickey can figure out the relationships between cells at different scales, like protein-protein or cell-cell interactions.

Recently, the Hickey lab used two different cell therapies in a mouse model with solid tumors. When they took the tumors out, they wanted to see why one cell therapy worked better than another. “What we found was that both cell therapies created similar cell proportions,” Hickey said. “The number of cells was relatively similar, but the organization of the tumors was different.”

In the cell therapy that worked well, the T-cells were able to get into the tumor and cause tumor inflammation, which stopped the tumor from growing. It also secreted inflammatory cytokines that recruited other immune cells close to them to create a boundary around the tumor. And while there are still some questions to be answered, Hickey said that it appeared that the T-cells were fighting for a while, then leaving to rest before returning. “It provides a large environment to improve tumor killing,” he said.

The other tumor, with the less effective therapy, didn’t have large areas of immune cells next to them and were more broken up. T-cells also created both anti-inflammatory and inflammatory molecules, which was less effective. Without Hickey’s technology, he would not have been able to see the spatial relationships nor determine why one treatment worked better than the other.

Speeding Up Evolution

Emma Chory’s research takes a slightly different approach: integrating robotics with evolutionary biology.     

Chory uses protein engineering to develop drugs, understand how genetic elements work, and answer basic questions about evolution and the genetic underpinnings of cancer. 

“Cancer is the biggest gene regulatory question that encompasses the three main focuses of our lab: therapeutics, genetic elements and understanding evolution,” Chory said. “Fundamentally, cancer consists of cells that are genetically diverse and misregulated, competing within a mixed population—this is a fundamental aspect of evolution.”

Using robots typically found only in pharmaceutical companies, Chory and her lab conduct experiments that would normally require large bioreactors to study how populations change over time. “With our custom robotics, we can test a thousand different experimental conditions with the same group of cells and see if some grow faster or if some might even die,” Chory said. “We can hopefully use robotics to grow cell lines continuously with much more precision and gain deeper insights into their biological responses.”

Currently, with CAR T-cell therapy, only one methodology is applied to growing the cells, but, as Chory notes, “sometimes those methodologies can make the cells stop growing such that they almost don’t even work by the time you transplant them back into the patient.” 

Chory’s robots can screen a lot of different drugs and can also screen the conditions to make the cell-based therapies. “So, if you think of the drug as being the patient’s own cells,” Chory said, “we could not just personalize the cell itself, but also the conditions under which we cultivate the cells to ensure the best outcomes when reintroduced into the patient.” Her tools give her the ability to not only screen the types of cells but also the environments in which they grow.