Finding the Genes that Enable Worm Cell Migration
Vida Praitis, professor of biology, Sam Naik ’21, Sarina Kopf ’22, Stephany Dos Santos ’21, and Sarah Weltz ’21 planned to research in the lab together during the summer of 2021. Then the pandemic began and access to the Noyce Science Center and the labs within was restricted.
So, Praitis, Naik, Kopf, Dos Santos, and Weltz did a “dynamic pivot.” Joined by Jasper Yang ’21, whose internship plans were canceled because of the pandemic, they turned to their laptops. Through those laptops, they carried out bioinformatics research to find genes that likely play a role in cell migration during worm development.
From Worm Cell Migration to Human Cancer and More
“A huge part of how we become a complex organism … has to do with the fact that cells come together in particular ways,” says Praitis. She studies how cells come together, how cells “migrate.”
Cell migration plays an important role in development and the immune system. Additionally, parts of the cancer process seem to be the reverse of parts of the cell migration process. As a result, “understanding the pathway in one direction, we hope will actually give us information about how that pathway works in the opposite direction during cancer,” says Praitis.
Praitis researches cell migration in Caenorhabditis elegans, a worm often used as a model organism in biological research. “We can do research in a really simple system to ask questions about cell behavior that occurs in more complicated systems where it’s more difficult to really understand what’s going on,” she explains. So, by advancing our understanding of worm cell migration, her research also advances our understanding of human cell migration.
Asking Difficult Questions
Praitis is not alone in studying C. elegans development. In 2019, Packer et al. published an article in Science that included a database of which genes are expressed, or “turned up or down,” in which cells at different developmental stages. That database was the starting point for Praitis’ teams’ research.
Praitis’ team wanted to use the database to find which genes are expressed during cell migration but not expressed during other stages, i.e., which genes specifically enable cell migration. Praitis thought, “I know that I can ask some really interesting questions using this dataset. Can we actually answer them?”
Lighting Their Own Path
In the end, they did answer some of those questions, but the path to the answers was not an easy one. “The students came in with really good skill sets,” says Praitis. Despite that, they had much to learn before they could answer their questions.
The sheer amount of data they had to sort through made their work even more difficult. “The database has tens of thousands of data points in it, so even downloading it so we could work with it was non-trivial,” says Praitis.
After downloading the data, they created a list of migrating cells to focus on, which Praitis says “took a lot of patience and perseverance to build.” For each migrating cell, they also chose a nonmigrating cell to use as a control.
Then Praitis’ team “magically” turned the database into a list of genes that likely enable cell migration — magically meaning they spent hours, days, and weeks reading relevant literature, programming, troubleshooting, and doing statistics. Kopf describes this experience: “I felt like I was wandering around in the dark for all 10 weeks of the summer, but I feel like that was a good thing to realize about research itself.”
While wandering around in the dark, they were lighting the path for themselves and for those who will come after them. The methods they used were new and, as a result, their work helped develop and improve those methods, which may even be used in research beyond cell migration.
This work would not have been possible in the lab alone. They were able to study many more genes in much less time than they would have otherwise been able to. Kopf explains this powerful approach: “You can cut [the scientific] process short by doing a bunch of computational work and then hybridizing that with lab work. I think that’s really a cool concept and also where the future is going.”
To Be Continued
“Science takes time, and it takes effort. Just seeing a story come together is pretty cool,” says Praitis. Finding genes that likely enable cell migration was the first part of the research story. Many of those genes are known to be involved in cell migration, which is a promising sign that their methods were accurate. However, they are interested in the genes that are not known to be involved in cell migration. For those genes, they need to do further research.
That research will be the second part of the story and will take place in the lab. There, Kopf will validate that the genes they found are involved in cell migration by observing how mutating those genes affects cell migration.
This pivot was a pandemic silver lining; not having access to the lab made Praitis’ team get creative. In doing so, her team advanced our understanding of cell migration and, therefore, our understanding of development, the immune system, and cancer. As Praitis says, “sometimes it takes difficult circumstances to encourage you to take a leap.”
Vishva Nalamalapu ’20 is the content specialist fellow in the Office of Communications and Marketing at Grinnell College. She loves writing about scientific research in a way that is accessible and interesting to readers with or without science backgrounds. Her series on scientific research projects focuses on doing just that. If you are a Grinnell College professor or student interested in having your scientific research project featured or think someone else’s project would be a good fit, please contact her.