ISCRM Research Sheds New Light on COVID-19 and Kidney Health

Kidney Organoid
Kidney organoid infected with SARS-CoV-2 (green). Arrowheads indicate specific infection in proximal tubule cells (purple) but not podocytes (red). (c) American Society for Clinical Investigation

It has been nearly two years since the World Health Organization declared the accelerating spread of COVID-19 a global pandemic. At the time, much of the concern focused on the respiratory system. While it is true that many patients arriving at hospitals and health clinics had life-threatening breathing difficulties, we now know that the virus can inflict serious damage to other organs as well, including the heart, brain, and the kidneys.

Last year, for example, UW Medicine investigators from the Institute for Stem Cell and Regenerative Medicine (ISCRM) and the Department of Immunology used stem cell technology to demonstrate that the virus is capable of infecting heart cells directly, helping to explain why so many COVID-19 patients experience short and long term cardiovascular complications. Attention has also turned to the kidney, another organ vulnerable to the effects of COVID-19.

In fact, COVID-19, which is particularly dangerous for people with underlying health problems,  severely exacerbates a health crisis that was already worsening – kidney disease. According to the CDC, chronic kidney disease, a condition that commonly leads to kidney failure, impacts nearly one in every 15 adults in the United States. Sadly, as incidence rises in an aging, ailing population, treatment options remain limited to dialysis and transplantation, both of which are expensive, temporary, and physically hard on patients.

Does COVID-19 Affect Kidneys Directly?

Two scientists
ISCRM faculty member Beno Freedman, PhD and graduate student Louisa Helms

While it is well known that COVID-19 can affect kidney health, how exactly the virus targets the kidneys has remained a question. Now, a new study led by ISCRM faculty member Beno Freedman, PhD, Associate Professor of Medicine/Nephrology, reveals more about the threat COVID-19 poses to kidneys. Louisa Helms, a PhD student in the Freedman Lab, is the lead author of the paper, which was published in the journal JCI Insight.

“COVID-19 continues to cause patient suffering around the world,” says Freedman. “Our hope was to produce insights on the kidney’s vulnerabilities to the virus as a step toward protecting future patients from this disease. We’re grateful to our ISCRM colleagues and our collaborators across the university for their partnership in this effort.”

In the investigation, the researchers used kidney organoids to demonstrate that the SARS-CoV-2 virus is capable of infecting kidney cells directly, a conclusion that was supported by a cross-validation experiment involving clinical data collected from COVID patients.

To establish whether the virus that causes COVID-19 can affect kidneys directly, Freedman and his research team added green fluorescent SARS-CoV-2 to kidney organoids in a petri dish. One cell population, proximal tubules, turned green, indicating an infection.  Not surprisingly, the cells that make up these structures express ACE2, a receptor that the virus uses as a gateway to infect cells in other organs, including the heart and lungs.

PKD Organoid
SARS-CoV-2 infection (green) in a cystic kidney organoid (0.5 mm diameter) with polycystic kidney disease mutations. (c) American Society for Clinical Investigation

Digging further, Freedman partnered with colleagues in the Murry Lab to demonstrate that ACE2 was the point of attack for the virus. When the researchers applied  SARS-CoV-2 to kidney organoids that were edited to disrupt ACE2, they saw no signs of infection. Freedman believes his team is among the first to show that SARS-CoV-2 binds to ACE2 receptors in the kidney, just as it does in the heart and lungs.

The researchers also wondered how COVID-19 might impact patients with polycystic kidney disease (PKD), a disorder in which fluid-filled cysts impair kidney functioning. When they exposed PKD organoids to the virus, they observed clear evidence of infection – specifically replicating virus, cell death, and abnormal cell morphology. The finding that cysts can be infected may help explain why patients with kidney disease can be particularly vulnerable to COVID-19.

Clinical Data Supports Observations in Organoids

Kidney organoids are useful models for learning how a virus affects living cells and systems. However, organoids still lack the full complexity of cells taken from actual patients. To confirm what they had seen in organoids, the researchers collaborated with Pavan Bhatraju, MD, an Assistant Professor of Medicine/ Pulmonary, Critical Care and Sleep Medicine. Together, they analyzed data extracted from more than 100 ICU patients, 61 of whom had COVID-19.

Looking at urine samples, Bhatraju analyzed 5,000 proteins in each individual patient. He found that certain proteins were more prominent in patients with COVID-19. This result suggested an inflammatory signature associated with the body’s immune response to the virus.  It also matched a pattern of upregulated genes the team observed in kidney organoids, validating that SARS-CoV-2 can infect the kidney directly. “The clinical patient results highlight the importance of interferon signaling pathways in leading to kidney injury in COVID-19 and potentially demonstrate therapeutic targets for future study,” says Dr. Bhatraju.

Blocking Infection with Designed Proteins

Having shed light on how SARS-CoV-2 attacks the kidneys, the researchers set out to test whether a synthetic protein designed by the Institute for Protein Design (IPD) might be capable of preventing infection. In this experiment Freedman enlisted the help of Hannele Ruohola-Baker, PhD, Professor of Biochemistry and Associate Director of ISCRM. Once again, kidney organoids were exposed to the virus. This time, the researchers added a computer-designed peptide built specifically to interact with parts of the spike protein that the virus uses to attach itself to healthy cells. After three days, the results were visible in the lab. The peptide had essentially blocked the virus from docking by disrupting the receptor binding domain.

The collaboration between Freedman and Ruohola-Baker is supported in part by a $3.4 million Department of Defense grant that is allowing the ISCRM researchers to explore multiple designed regeneration approaches to preventing and treating COVID-19

“In the organoids treated with the peptide, we saw a dose dependent decline in the infectivity of the virus,” says Freedman.  “At least in organoids, the peptide appears to be very promising. We also believe the platform can be used to test other new drugs in organs besides kidneys.”


This work was supported by NIH awards R01DK117914 (BSF), R01DK130386 (BSF), U01DK127553  (BSF),  UH3TR002158  (JH),  UG3TR003288  (JH  and  MK),  Department  of Defense award W81XWH2110007 (BSF and HRB), a gift from the Northwest Kidney Centers to the Kidney Research Institute (BSF), the Lara Nowak Macklin Research Fund (BSF), the Robert B. McMillen Foundation (CEM, SM), start-up funds from the University of Washington (BSF),  K23DK116967  (PKB),  R01DK124063  (PKB),  the  CDC  Foundation  (PKB),  Roche Diagnostics (PKB), and the Bill and Melinda Gates Foundation (PKB). Yan Ting Zhao was supported by NIH T90DE021984. Louisa Helms was supported by NIH 5TL1TR002318-04 (Whitney) and NIH F31DK130550.