What genes can tell us about COVID-19 mortality rates
By Tracy Gale
Why are more men than women around the world dying from COVID-19? This is the question Dr. Ana Conesa Cegarra and a team of researchers and clinicians from the U.S. and Europe are trying to understand.
“The mortality rate is higher for men worldwide, even though infection rates are very similar,” says Conesa. We are looking to explain these differences so we can identify new ways to combat the virus and help determine treatment.”
Conesa joined the University of Florida in 2014 as a professor of bioinformatics. Her research focus is on gene expression and understanding the progression of complex diseases. She and her lab have current funded projects from the National Institutes of Health, the Juveniles Diabetes Research Fund, NASA, and the Florida Space Grant Consortium. While this research continues, the urgency of COVID-19–understanding, containment of and hopefully eradication–is also at the forefront of her research efforts.
Conesa and her collaborators are now analyzing the clinical data of around 1,000 COVID-19 patients. The data is from Italian patients treated at hospitals in Verona and Milan, and includes information on existing conditions, blood testing, and treatment plans while they were in hospital.
Two lines of research
What clinical parameters behave differently in man and women as disease progresses?
Working with the medical staff of IRCCS Ospedale Sacro Cuore Don Calabria (Verona) and Istituto Clinico Humanitas (Milan) and a team of statisticians to find clinical biomarkers of gender differences
What underlying physiology may play a role in gender differences to the disease?
If being a woman or a man can be considered as a pre-existing condition, can we identify differences for COVID-19 relevant genes in the healthy population and if so, who these genes behave in COVID-19 patients?
With the help of a grant investment from the University of Florida’s Covid-19 emergency research funding program of 15 compute cores and 15 terabytes of storage on HiPerGator, the University of Florida’s supercomputer, Conesa and her collaborators are now analyzing the gene expressions as well as all of the factors collected about the patients to find answers to their lines of inquiry. With the analysis strategy in place, Conesa says she expects to share some initial research findings in September.
“Through UF and IFAS’s One Health Center of Excellence, we have the necessary resources to work with clinicians in Italy and the U.S.” Conesa says. “We have the facilities at UF to store and analyze great amounts of data. And the more patient data we can include, the better our research findings will be.”
UF’s research ecosystem has many resources to help faculty advance their science. Conesa has formed a strong partnership with UF Information Technology’s team of supercomputing consultants. Many of the research and clinical investigations underway pertaining to COVID-19 are supported by UFIT Research Computing, the department that manages HiPerGator and provides consulting, application, and training support.
“My research is computational biology, so I rely heavily on UFIT’s Research Computing staff,” notes Conesa. “We engage in very heavy computation tasks and work with terabytes of data. Through the help of Facilitator and Biocomputing Specialist Alex Moskalenko, we’ve been able to work with extremely large data sets. Alex has solved technological problems for me and my lab staff, figuring out ways to install many applications, like the PacBio data sequencing software, and getting them to work with our data. Without his involvement we would have lost a lot of valuable time.”
Research Computing Director Erik Deumens is enthusiastic about how UF can enable COVID-19 research.
“We have the technical resources to make our researchers’ lines of inquiry a reality. Recent storage upgrades and the addition of NVIDIA’s DGX™ A100 system gives UF research the world’s most advanced artificial intelligence (AI) capabilities.”
“This is truly a place that fosters international collaboration. One Health puts these activities together and makes research activities like this happen without the volume of administrative overhead that exists at other universities. While I’m coordinating the Center’s gender research lines of inquiry on COVID-19, there are seven other researchers investigating COVID-19 as part of the E-ellow Submarine initiative that One Health sponsors. UF can quickly provide the resources to get a research project like this up and running.”
The One Health Center of Excellence at UF is an integrative effort between UF Institute of Food and Agricultural Sciences (IFAS) and UF Health, with the mission of co-advancing the health of humans, animals, plants and the environment using innovative approaches. This circular health approach exploits the big data environment and critical thinking to accelerate interdisciplinary research and drive data-driven decision-making in health policy. Dr. Ilaria Capua, professor and director of the One Health Center of Excellence, is impressed with Conesa’s research and collaborative efforts.
“Ana Conesa is working with a group of medical doctors, data scientists, and economists to unveil aspects of COVID-19 as it relates to sex and gender. Her leadership in advancing and coordinating highly interdisciplinary teams will enhance scholarship on COVID-19 and have global impact. This is what UF and the One Health Center of Excellence are all about.”
At their best, research activities are designed with regional, national or global impact. 2020 has shown that the scientific community can quickly coalesce, and UF research faculty are at the forefront of contributing to the knowledge base the world needs to solve the challenges brought by COVID-19.