Knight Campus alum adapting cancer research to COVID-19

adrian bubie in the lab

 

 

Knight Campus alum adapting cancer research to COVID-19

Adrian Bubie’s career is marked by nimble professional growth, with each experience building toward the next.  

Most recently, that means the 2018 graduate of the Knight Campus Graduate Internship Program is playing a key role on a team converting a newly developed tool for tracking the progression of cancer viruses so that it can also be used to identify different strains of the novel coronavirus.

“Linking this approach with COVID-19 is important to us,” Bubie said. “The disease is a big deal in New York City now, and our lab is trying to jump in and help in the ways that we can.”

Bubie, who completed his master’s degree in the Bioinformatics and Genomics track of the Knight Campus program, serves as a bioinformatician in the lab of institute geneticist Bojan Losic in the Department of Genetics and Genomic Sciences at the Mount Sinai Icahn School of Medicine in New York City. It’s a position that grew out of Bubie’s internship at Mount Sinai, a nine-month, required component of the Knight Campus program, where 90 percent of graduates are employed in their fields within three months of graduating.

adrian bubie
Adrian Bubie, ’18 M.S.

Track: Bioinformatics and Genomics

What drew you to the program? “I was looking for a master’s program that would allow me to jump into high-density coursework quickly, but also had an applied or experiential piece. The Knight Campus's Graduate Internship Program program really stood out with both.”

On continued support: Program director “Stacey Wagner is integral to linking up students with opportunities and offering advice. Even now, she continues to help maximize opportunities for us.”

 

Initially, Losic’s team focused on creating a tool to explore at a fundamental level the evolution of liver cancers in patients also infected with hepatis B. They’ve since applied it to cervical cancer progression in patients with the human papilloma virus.

Bubie has been studying shifts in tumor expression profiles, such as what genes are stimulated or turned off as these cancers and co-infections grow and recruit immune responses.

The tool, he said, gathers nuggets of information from tumor RNA-sequencing, drawn from biopsies, that previously were unreadable. That information, it turns out, opens a window on specific genes and phenotypes – the observable characteristics – of viruses involved in a disease’s path. It also uncovers mutations that drive the evolution of new strains of a virus.

“This tool allows us to correlate viral phenotypes of tumors and model patient survival using a combined set of clinical and viral variables,” Bubie said. “Our research is focused on understanding how different strains of a virus influence how patients will react when they are infected and how they may fare during the progression of the disease process.”

The work draws heavily on Bubie’s experiences in the Knight Campus program, which solidified his knowledge in genomics and programming with a grounding of statistics and linear modeling.

After graduating from Case Western Reserve University with a degree in biomedical engineering, Bubie went to work at a startup, where he began teaching himself how to code in python, while also starting to comprehend the intricacies of genomics. But he knew he needed a graduate program to take his career to the next level.


 

“I couldn’t do what I’m doing now without the UO and the program. I had to prepare myself for the research I’m doing now.”

— Adrian Bubie


In a preprint of a paper the lab will publish soon, Bubie, Losic and five colleagues describe the tool and how the text-based information it returns provides clues about disease trajectory that, in turn, link to potential health outcomes of patients with liver, cervical and head and neck cancers in combination with other viral infections.

How the refocused research translates into clinical importance, including therapeutic treatments, is not yet determined, Bubie said, but he and colleagues have begun discussions.

“We’d like to know what the viral expression profiles look like in vivo – in the tissues of COVID-19 patients, and whether it differs based on the viral strain and/or differing mixtures of viral strains,” Bubie said. “Our thought is that the outcome of this test done with our new tool would have diagnostic importance. It could help clinicians, for example, understand how at-risk a particular patient may be for a strong immune response that could potentially exacerbate the patient’s symptoms and suggest how bad the disease is going to be for the patient.”

A big challenge, Bubie added, is that the COVID-19 virus is evolving differing strains as it emerges in new populations in different geographic locations.

“The virus has a closed-off trajectory within each individual population,” he said. “Strains in Nebraska and Oklahoma will look different than those in France and Italy. This is also true for the human papilloma virus. The goal is to try and identify which strains of this coronavirus are likely to be more problematic in the future.”

lab work
Knight Campus Graduate Internship Program

Touting an impressive 98 percent graduation rate and average internship salary of $57,000, this program merges two longstanding and successful UO programs, the Master’s Industrial Internship Program and the Bioinformatics and Genomics Master’s Program. Students receive rigorous and experiential coursework and internship-based training in one of five technical areas: optical materials and devices; molecular sensors and probes; polymer science; semiconductor and photovoltaic device processing; or bioinformatics and genomics. Additionally, students engage in comprehensive professional development trainings, which include resume writing, active listening, and inclusion and diversity. Upon opening of the first Knight Campus building this fall, students and staff in the program will have access to cutting-edge facilities. The program is the driving force behind the UO’s top national ranking for the number of master’s degrees in physics awarded.

knight campus facade
Knight Campus

The Phil and Penny Knight Campus for Accelerating Scientific Impact defines the University Oregon as a hub for translational and applied research, a place where cross-disciplinary, scientific entrepreneurship pushes the frontiers of science. Seeded with a $500 million gift from Penny and Phil Knight and augmented with $70 million in state funds, the campus operates at the intersection of science and society, with a first building set to open in the fall of 2020.