UCSF Labs Are Hard At Work

Monday, May 25, 2020

From tracing viral spread to fast tracking drugs to studying infected cells, labs on UCSF’s Mission Bay campus have been working tirelessly through the shutdown to tame the effects of COVID-19. On May 18, the Bakar Computational Health Sciences Institute hosted an online meeting to present ongoing work around the COVID-19 crisis.

Fast tracking drugs for COVID-19

Brian Le, PhD, of Marina Sirota’s lab at UCSF spoke about using computational inference to identify drugs more quickly as potential treatment for COVID-19. By taking FDA-approved drugs that have already been tested in humans for safety and side effects, researchers can identify promising candidates and repurpose them for clinical trials to treat COVID-19.

Previously, this genetic approach has been helpful in identifying new drugs for diseases like inflammatory bowel disease and liver cancer.

The idea is to take the “fingerprint” of genes that are changed during COVID-19 infection and find drugs that help create opposing effects.

While this is still a bet, as we do not know which gene changes are the most important for COVID-19 in infecting and damaging the body, the drugs in the database are already approved by the FDA and could quickly move to clinical trials for COVID-19, saving months in testing.

Le said the aim is to identify drugs which reverse gene dysregulation and help treat COVID-19.


Douglas Arneson, PhD, of Atul Butte’s lab demonstrated the use of their new publicly available tracker of COVID-19’s spread.

The site offers a more granular focus by tracking individual counties rather than just states or countries, and allows users to interact with the data to highlight specific counties of interest or to zoom back and see the bigger picture.

Data is taken in on an ongoing basis from the New York Times COVID-19 database and Kaiser Health News to display metrics like doubling time and estimated intensive care beds needed.

As shelter in place is lifted, the website could be used to government officials to better estimate trends in infection and future healthcare needs. More information is at https://covidcounties.org/.

COVID-19 Tissue Atlas project

Reports have suggested that COVID-19 has direct or indirect effects across the whole body, not just the lungs.

Dr. Franklin Huang talked about how his lab is creating an atlas which identifies the specific cell types in each organ that are infected by SARS-CoV-2, the virus that causes COVID-19, and how infected cells change their gene expression.

His lab is first looking for where SARS-CoV-2 shows up in tissues from patients with COVID-19 using labels for the viral protein and RNA.

Next, they will see how the patient’s body reacts to SARS-CoV-2 by sequencing RNA from patient tissue samples and seeing how the body changes with infection.

This could lead to a better understanding of how SARS-CoV-2 is affecting the entire body and where doctors should focus to prevent damage.