Researchers from across campus join in creation of online portal to serve as an open science ‘path to discovery’
Last spring, as healthcare providers and scientists around the world scrambled to treat a surge of patients infected with a virus that experts knew little about, one thing quickly became clear: SARS-CoV-2 strikes people differently.
Faced with solving a mega-puzzle on a timer when minutes cost lives, clinical practice early in the pandemic became a fervent game of trial and error.
Now, on the University of Colorado Anschutz Medical Campus, where the then-new Vice Chancellor for Research Thomas Flaig, MD, had the fortitude and resources to create a biobank of samples from some of the state’s first COVID-19 patients, a promising venture has sprung.
Named the COVIDome Project, creators call it a groundbreaking research approach capable of accelerating life-saving COVID-19 discoveries around the world. The venture is a partnership between the Office of the Vice Chancellor for Research and the CU School of Medicine (SOM).
“This is an effort to fast-track and accelerate a precision-medicine approach to COVID-19,” said Joaquin Espinosa, PhD, who co-led the project with Flaig. “Nothing in the study of COVID-19 makes sense except under the light of personalized medicine.”
‘No two persons are the same’
Precision medicine uses information on an individual’s genes, molecules, metabolism, lifestyle and environment to create personalized treatments and preventive measures against disease. It’s frequently used in cancer care to analyze a person’s tumor at the molecular level before making a treatment plan.
“The public needs to understand that COVID-19 is not one entity,” Espinosa said. “COVID-19 manifests very differently across individuals. And in order for us to make a difference in the clinic, we need to understand the mechanisms driving this heterogeneity.”
“Nothing in the study of COVID-19 makes sense except under the light of personalized medicine.” – Joaquin Espinosa, PhD
To do that, scientists must dig deep. Why did a grandmother rely for months on a respirator to survive when her husband rode out the virus at home? What differences lie in the biological samples of a Black patient who died compared with a white person who had cold-like symptoms for a week?
“No two persons are the same,” Espinosa said. “We all harbor important differences in our genes, metabolism and immune systems. Why did this person respond to this drug, and this one didn’t?”
Project amasses datasets and experts
The hugely collaborative effort, which began with the help of two of the campus’ major hospitals – UCHealth University of Colorado Hospital and Children’s Hospital Colorado – involved collecting biological samples from COVID-19 patients at the two hospitals, from serum and nasal swabs to urine and DNA isolates, and creating a series of sophisticated datasets using these samples.
Experts in different areas of biomedical research across campus created these multidimensional datasets in their labs, which were then collected and combined to be shared through a public online portal called the COVIDome Explorer.
From a Transcriptome (RNA datasets) to a Proteome (protein datasets) and from Cytokines (markers of immune function) to Metabolomics (informing about metabolism), researchers can quickly access this work to further their own hypotheses more efficiently.
“They helped us a lot,” said Federica Piani, MD, a postdoc fellow from Italy who used the COVIDome Explorer for research she and CU SOM Professor Richard Johnson, MD, are conducting. “They performed the analysis that we requested, and it was really fast. In one week, we already had the results we were asking for,” she said, referring to the large research team behind the project.
Piani and Johnson of the Division of Renal Diseases and Hypertension are studying how and why uric acid is higher in COVID-19 patients with poorer outcomes. “We have found some interesting pathways,” Piani said.
COVID spurs rapid response
Launched in November, the COVIDome Project went live in five months, thanks to the outpouring of research volunteers and the foundation that was already laid by Espinosa and his team at the Linda Crnic Institute for Down Syndrome.
“Everybody said yes,” Espinosa said of his fellow researchers from disciplines across campus, who enthusiastically contributed to the effort. After leading the five-year construction of the similar Human Trisome Project for Down syndrome research at the Crnic Institute, Espinosa brought the COVIDome Project together quickly.
Offering one of the deepest datasets in COVID-19 research to date, the concept opens scientists’ work up to the public before it’s published. “Nobody has a portal where they have given access to this amount and type of data ahead of publication,” Espinosa said. “It’s counterculture.”
But, particularly important now, with an urgent need for discovery during a pandemic immobilizing the world, Espinosa predicts the open science concept’s time has come.
“I think it’s the future,” Piani said. “You have a lot of data, and you share ideas,” she said, adding that having the multidisciplinary expertise of the COVIDome team reduces her background work, such as searching for past articles. “You can ask them, and they know. They can tell you if someone else is working on the same topic.”
‘This is the fastest path to discovery’
Because the online portal is public, meaning users are not required to sign in, 100% reliable numbers on distinct users is not possible, said Kyle Bartsch, an Information Services IT principal professional, who helped compile the portal data.
“At the end of the day, if you are mission-aligned, this
is the fastest path to discovery.” – Joaquin Espinosa, PhD
However, analytics show there have been at least 350 users and 590 unique sessions since the COVIDome Explorer launched. Users have come from 10 countries and across the United States.
Given the enthusiasm he has seen, Espinosa said he hopes to see the concept expand to fields of study across the campus, from cancer to cardiology.
“It makes you wonder, after COVID-19, what else can we do in this highly collaborative fashion? What else can we tackle through open science principles without the pressure of a pandemic? At the end of the day, if you are mission-aligned, this is the fastest path to discovery.”