Rice University: Feds back probe of understudied gut nervous system

Rice University neurobiologist Rosa Uribe will be hitting the books for her latest study of the digestive system, but some of the pages in her books are a billion years old.

Uribe, an assistant professor of biosciences, has won a five-year, $2 million R01 grant from the National Institutes of Health to study how the enteric nervous system forms.

If you didn’t realize you had an enteric nervous system, you’re not alone.

“Most people don’t realize they have it until there’s something wrong with it, and they have to go to the gastroenterologist,” Uribe said. “It is basically the nervous system that resides within your entire gut. It is separate from your spinal cord, and it is separate from your brain. Meaning, it can function on its own to help move the food that you digest from one end of the gut the other in a healthy way.”

Uribe, who was recruited to Rice in 2017 with a CPRIT Scholar grant from the Cancer Prevention and Research Institute of Texas, specializes in studying the development of the enteric nervous system. When that development goes awry, it can lead to chronic and sometimes life-threatening illnesses, including neuroblastoma, a common pediatric cancer, and Hirschsprung disease, a congenital condition that frequently causes chronic intestinal obstructions and severe constipation.

Rice Neurodevelopmental biologist Rosa Uribe
Neurodevelopmental biologist Rosa Uribe is a CPRIT Scholar and assistant professor of biosciences at Rice University. (Photo by Jeff Fitlow/Rice University)

“We know an embarrassingly small amount of information about how the enteric nervous system forms,” Uribe said. “We have a long way to go to understand the fundamental mechanisms of how it forms, and that’s the major goal of this R01.”

It is impossible to directly study the development of the enteric nervous system in humans. For ethical reasons, human embryos cannot be studied beyond the 14th day after fertilization, which is well before most of the development of the enteric nervous system takes place. Instead, Uribe and her students use zebrafish, small egg-laying fish whose translucent embryos develop outside the female’s body. Using a variety of microscopes and genetic tools, Uribe and her students can peer directly inside the embryos and make detailed observations of the neural crest cells, the embryonic stem cells that give rise to the enteric nervous system.

During enteric nervous system development, neural crest cells migrate down the gut. At each step in their journey, they’re prompted with biochemical cues that tell them whether to keep moving or stop, and what cells to become when they stop. The transformation from a malleable neural crest stem cell into a working neuron or one of the many other cell types in the enteric nervous system is a multistep process, and deciphering the mechanisms of this process is the main aim of the project.

microscope image of embryonic zebrafish gut
A microscope image of the entire embryonic zebrafish gut with enteric nervous system cells highlighted in blue and green. (Photo by Akshaya Venkatesh/Rice University)

The five-year study builds upon a major breakthrough Uribe’s lab achieved in February with a new tool called single-cell transcriptomics, which allowed them to build the first open catalog of activated genes in neural crest cells at many stages on the enteric development path.

“It really is like a library, where you have both books and a catalog of what’s in those books,” Uribe said. “And when you open a book, you see the content and information within that book. But here in our situation, a book is a cell.”

Joshua Moore and Rosa Uribe
Rice University graduate student Joshua Moore examines zebrafish embryos with a microscope in the lab of Rice neurodevelopmental biologist Rosa Uribe (right). Uribe’s lab recently won an R01 grant from the National Institutes of Health to study enteric nervous system development in zebrafish. (Photo by Brandon Martin/Rice University)

Single-cell transcriptomics creates the books in Uribe’s library by measuring messenger RNA in a way that allows biologists to see which genes are activated in individual cells in a sample. In Uribe’s case, the samples are surgically removed portions of zebrafish embryos in which neural crest cells are developing. Thanks to a proprietary process that dissociates, isolates and individually bar-codes each cell, Uribe’s team was able to catch neural crest cells in the act becoming neurons or glial cells.

“We did this for about 100 embryos,” Uribe said. “All of the cells were grouped in one single-cell suspension, and all of the data was mapped back to the zebrafish genome. We ended up with massive lists of genes that were either expressed or not expressed in those cells, and that has helped us start to see the bigger picture, because we’re not looking at just one or two cells, we’re looking at thousands of cells. And with the power of thousands of cells, you can pull out potentially interesting patterns about gene expression and how, in our case, a developing embryo forms itself.”

The results were published in the journal eLife, and Uribe said the work will continue during the R01.

“We will continue to leverage this for various questions for subpopulations of cells at different stages of development,” she said. “For example, you can take an embryo and expose it to some type of experiment, like a pharmacological reagent or a genetic alteration, and then you can see what those changes do. Using the single-cell transcriptomic method, you can compare it to the books in your library and see how you’re editing the story with those changes. What pages are different and how? And does it change the number and type of books in the library?”