Using mathematics to provide a rare disease roadmap

Rarebase welcomed Dr. Amina Qutub to the team in January 2022 as Vice President of Computational Biology. Dr. Qutub is an accomplished neuroscientist, computational biologist, and educator, and her work has been recognized by the U.S. National Academies Keck Futures Initiative and the U.S. National Science Foundation. She is a sought-after thought leader in cellular systems biology, neuroscience, and data science and has presented more than 120 invited lectures throughout her career.

Dr. Qutub recently sat down with our team to explain her career journey and research goals at Rarebase. Read on to learn how mathematics informs our understanding of rare disease biology and how a network biology approach may help us identify unexpected therapeutic targets.

‍Computational biology, neuroscience, and rare diseases‍

When she was a child, Dr. Qutub visited her father at work at Bell Laboratories, the renowned research company credited with advancing communication and information processing technologies throughout the 20th century. “I got to see some of Bell Labs’ computing machines, and I remember one of the computers took up a whole room. As a child, I wondered, what is a machine that size doing? It spurred my imagination to think about what you can do with computing.”

Her early interests in computing later merged with a love of the natural world, and she forged a career using computers, mathematics and cell biology to deconvolute complex biological systems. “What really fascinates me – and always has – is simplifying a complex system using computing and studying human cells to conceptualize how they're responding to the environment mathematically.” Dr. Qutub joined Rarebase to focus this approach on brain cells, with the goal of advancing therapies for rare neurological disorders as quickly as possible.

The Rarebase discovery research team marries experimental and computational approaches to map the activity of thousands of genes and proteins under thousands of experimental conditions. Computation is essential to make sense of the more than 50 million data points generated by these studies and is a central component of the Rarebase Function^TM research platform. “What we're doing is looking at patterns of biology, for each individual or disease. In a sense, we’re creating a roadmap that didn’t exist before because there hasn't been a lot of rich research for many of these rare disorders.” Most rare diseases have been overlooked by the traditional pharmaceutical industry due to a lack of commercial opportunity.

Dr. Qutub has found that roadmaps are an apt analogy for the work she is leading. “You can think of molecular pathways like a collection of highways in a city. The information we get from some of these assays in the lab is like looking at all the stop lights – the red and yellow and green lights – from a satellite view. We can observe them as they change over time, and predict traffic flow.” Understanding the “stop” and “go” systems within neurons can help scientists find ways to repair damaged traffic routes or turn on alternative routes altogether when they are disrupted by gene mutations.

“You can think of molecular pathways like a collection of highways in a city. The information we get from some of these assays in the lab is like looking at all the stop lights – the red and yellow and green lights – from a satellite view. We can observe them as they change over time, and predict traffic flow.”

Dr. Qutub discovered Rarebase after searching for ways she could help a close family member affected by a neurodevelopmental disorder. After meeting the team, she recalled: “It really became clear that this is a group of like-minded people coming from all different backgrounds, with an impetus for making an impact very quickly in rare disorders.” By joining Rarebase, she saw an opportunity to contribute her unique expertise directly to this cause.

‍From roadmaps to potential therapies ‍

In less than half a year, Dr. Qutub has led major advances in the Rarebase Function^TM computational research platform. Preliminary results are now being shared with our collaborators. Over the next six months, she looks forward to “providing hope in a way that's quantitative. We have predicted compounds that have the potential to make an impact on human health in the near term. Characterizing how these compounds affect molecular and cellular pathways, in cell models tailored for each disease or individual, is the next step. Building a platform that brings the best therapies to patients and families dealing with rare disease is why I came to Rarebase, and I'm really excited to make it happen.”

‍Contact us to learn more about our Function^TM research platform for rare diseases.