A computational approach to cancer

A computational approach to cancer

Toni-Ann Nelson transformed remote summer research into an opportunity to learn a new set of tools for analyzing tumors.

Raleigh McElvery
August 20, 2020

Toni-Ann Nelson has wanted to find a cure for cancer ever since she was nine years old and lost her grandfather to the disease. “I remember thinking there must be something that the doctors and scientists were missing,” she recalls. “It just couldn’t be that complicated.” Now one semester away from earning her degree in molecular biology, Nelson is realizing cancer is just that — complicated. After conducting cancer research during MIT’s Summer Research Program in Biology (MSRP-Bio), she understands much more about the intricacies of tumors and metastasis. But she’s also glimpsed just how many cellular puzzles remain to be solved.

Growing up in Jamaica, Nelson enjoyed all her science classes, but preferred biology because she knew it would provide the foundation to probe cancer. She graduated as the valedictorian of her high school class, and earned a scholarship to Alcorn State University in Mississippi, where she began in the spring of 2017.

Alcorn doesn’t have any cancer research facilities, so Nelson secured a position as an undergraduate researcher in Yan Meng’s plant tissue culture lab. For three years, Nelson aimed to improve viral disease resistance in sweet potatoes. Even though she wasn’t conducting clinical research, she mastered key molecular biology techniques like PCR, gel electrophoresis, and tissue culture.

“Fundamental research is important because many times finding a cure requires starting with the basics, and understanding what’s going on inside the cell,” she says.

When Nelson was accepted into MSRP-Bio as a Gould Fellow and assigned to work in Tyler Jacks’ lab, she was elated to get her first hands-on cancer research experience. But in April 2020 — two months before the program was slated to begin — MIT’s campus temporarily shut down due to the COVID-19 pandemic, and MSRP-Bio 2020 became a remote learning experience.

As a result, Nelson and her MSRP-Bio cohort conducted their research from home. She took on a computationally-intensive project that was conducive to remote work and required taking an online quantitative methods class. In a manner of weeks, she learned an entirely new set of skills, including programming languages like Python.

“I always thought that I wouldn’t need those types of computational tools as part of my cancer research,” she explains. “But working at MIT was enlightening, because it showed me that they are key to understanding disease. I can definitely see myself using them on my own projects in the future.”

Pink and purple histology image
Light micrograph of a lung adenocarcinoma. Credit: Vasilena Gocheva/Jacks Lab, Koch Institute

The Jacks lab studies the genetic events that contribute to cancer, and Nelson’s project centered on lung adenocarcinoma. The predominant form of non-small cell lung cancer, it begins in alveolar type II (AT2) cells. Past studies showed that, as the tumor progresses, AT2 cells change state and lose their original identity. Nelson wanted to determine which genes and proteins underlie this evolution. Her analyses showed that genetic markers characteristic of AT2 cells tend to decrease over time, while markers denoting faster-growing “high grade” tumors become more prevalent.

“The kinetics of these gene expression changes that are happening early on are still poorly understood,” she explains. “It just goes to show how complicated this pathology is, which I find even more fascinating.”

Once researchers can pinpoint the genes and proteins that drive changes in cancer cell state, they’ll be better equipped to design drugs that target and prevent metastatic processes.

Although Nelson couldn’t visit the lab in person, as on-campus research slowly began ramping up again, her graduate student mentor Amanda Cruz would show her around during their video conference calls. Cruz also helped Nelson explore the scientific literature, choose studies for the lab’s journal club, and perform computational analyses.

Given the unprecedented circumstances, Nelson says having a solid support system was key to her success. Nelson and her MSRP cohort also relied on one another for encouragement, and were each assigned a graduate student “pal” for guidance outside of lab.

“The program catered to our every need, and it’s structured to ensure that someone will always check up on you if you’re feeling alone,” Nelson says. “I never expected to get so much from this experience, especially because I’m not physically on campus. But what I learned this summer was so much more than I could ever have anticipated.”

Her time in the Jacks lab has solidified her fervor for cancer research, and she intends to apply to cancer biology PhD programs in order to continue this line of inquiry. “I’ve realized there’s still so much more to learn,” she says, “but we’re getting there.”

Top image courtesy of Toni-Ann Nelson
Posted: 8.19.20