A research team led by Gage Crump, PhD , at the Keck School of Medicine of USC has received a $3.3 million grant from the National Institutes of Health (NIH) to study congenital anomalies affecting head development. The R01 grant will fund research into the role that short stretches of DNA known as enhancers play in the development of these anomalies.
Genes in coding regions of DNA provide the blueprints for proteins, which the body uses both as signals and as the building blocks for its structures and organs. In noncoding regions of DNA, regulatory elements such as enhancers turn the genes that code for proteins on and off. While the logic of how mutations in coding regions affect development is well understood (for example, by changing the make-up of proteins), researchers understand much less about the effects of mutations in the noncoding regulatory regions.
“For me, it’s one of the big unsolved mysteries of biology,” said Crump , professor and vice-chair of the Department of Stem Cell Biology and Regenerative Medicine. “What is the logic of how these regulatory elements work?”
The team will use zebrafish to methodically explore craniofacial enhancers to understand which are critical to the development of anomalies.
Previously, much work has relied on cultures of individual cells to probe the logic of how enhancers function. This new grant project will study how enhancers operate in a developing zebrafish embryo. Zebrafish develop and reproduce quickly, making it affordable for researchers to test thousands of enhancers. “We can start to scale up work in animals to really understand the logic that controls not only cell type but also regional specificity in the head,” Crump said.
In zebrafish, noncoding genes outnumber coding genes nearly one hundred to one.
“Now the time is right to start looking at these noncoding regulatory elements and developing zebrafish as a more high-throughput vertebrate model to understand these regulatory regions,” Crump said.
The team will determine the genetic codes of many individual cells, as well as use machine learning to capture patterns and make predictions from the massive amounts of data. Coinvestigator Emma Farley, a molecular biologist at UC San Diego, will help Crump’s team interpret the gene regulatory program for the head.
The researchers will also look at evolutionary variation across other organisms, such as mice, lizards, amphibians and other species of fish, to identify the core similarities underlying enhancer activity. “The genes that control head development are fairly similar across all vertebrates, so we think the enhancers that control how these genes are expressed are also going to function similarly in each vertebrate, including humans,” Crump explained. “Evolution keeps shuffling the DNA sequence while keeping the logic the same, so we can get at what’s important versus what’s random background noise.”
The group will collect enhancers from across the various vertebrate groups and insert them into the zebrafish genome to assess what types of cells they are active in. The team has chosen to test the enhancers in zebrafish because of the powerful genetic techniques available and because the fish share many cell types and genes for head development with humans.
If the enhancers have the same activity in zebrafish, “then we can understand what’s common between them and get to the core of the logic,” he said.
By understanding these enhancers, the team hopes to inform new ways to predict various conditions, advise families who have children with a condition on which mutation may have caused it, or determine which family members may harbor relevant mutations.
They are also interested in understanding how various developmental genes and regulatory elements, particularly the enhancers, have changed over the course of evolution.
“What’s common, and what are some unique specializations of the human head that make it different than other animals?” Crump said.
Ultimately, they would like to know enough to be able to assemble an enhancer in the lab from the components of DNA. “That would show we know enough of the rules to use them to build new enhancers,” Crump said. These new enhancers could control in what tissue a gene produces a protein and for how long, which could be useful for developing gene therapy treatments for congenital anomalies.
Crump describes this work as basic research that could lead to new translational breakthroughs over the next decade.
“We’re understanding fundamental mechanisms that I think will be very important,” he said. “I’m thankful that NIH continues to fund discovery research projects such as ours that will inform the therapies of the future.”