Researchers at the Chen Lab, led by Prof. Shuibing Chen, cell and developmental biology, recently published a study identifying a key gene in the pathology of COVID-19. The gene, CIART, helps establish the viral infection that causes COVID-19, also known as SARS-CoV-2.
SARS-CoV-2 is a systemic respiratory virus that originates in the lungs and can spread to many other parts of the body — including the heart, liver and kidneys. These organs tend to respond differently to infection, which can have fatal consequences. The Chen research team created multiple models of small three-dimensional clusters of human tissue, called organoids, to look for common host factors that can enable infections by SARS-CoV-2 across tissue types.
Dongxiang Xue, a research associate in the Chen lab and co-first author of the study, emphasized that the multi-organoid approach was crucial in the team’s breakthrough. Over the past three years, the Chen lab had conducted single-organoid studies and found many organ-specific effects. Although results were promising, they did not offer an overall picture of the SARS-CoV-2 infection pathway.
“If we really want to block viral infection, targeting a mechanism in a single organ will not be enough,” Chen said. “We want to use this multi-organoid model to identify shared mechanisms between different organs. In future antiviral studies, we will then be able to address a target that is relevant in multiple organ systems.”
Xuming Tang, a research associate in the Chen lab and co-first author of the study, highlighted how the team used human stem cells to create models of alveolar tissue, responsible for exchanging gas in the lungs and heart muscle tissue — both of which are both known to be affected by SARS-CoV-2.
The team then infected the organoids with different concentrations of the virus. Using RNA sequencing — a technique that indicates which genes are turned “on” and “off” in a cell at different times — they were able to discover that 18 genes became consistently more active in response to viral infection across different organoids and concentrations of the virus.
Once the 18 genes were identified, the researchers used CRISPR, a genetic engineering technology, to test their specific roles in SARS-CoV-2 infection. They created “knockout cells,” where specific genes of interest were turned off.
“Using CRISPR, we knocked out genes in cardiomyocytes – heart muscle tissue – and exposed these cells to the virus to see if the absences of the genes inhibited infection,” Xue said. “Based on this, we selected the genes with the most potential.”
Thirteen genes appeared to play a role in enabling SARS-CoV-2. In knockout cells where these genes were suppressed, the virus levels were lower. The strongest enabler with the greatest effect on virus levels was CIART.
CIART is a protein that was previously known to regulate the circadian-clock feedback loop, which creates sensations of sleepiness and alertness depending on the presence of sunlight in the environment. It had never before been associated with SARS-CoV-2.
Tests demonstrated that CIART enhanced the ability of SARS-CoV-2 to reproduce and spread by enhancing the production of certain lipids via a pathway called the RXR pathway. The supply of these lipids is critical to virus replication, and the team found that by treating the organoids with an experimental RXR inhibitor before exposing them to SARS-CoV-2, they were able to successfully block the infection.
From a clinical perspective, these findings indicate that targeting CIART and the RXR pathway may be an effective treatment method for SARS-CoV-2 infection. In particular, this strategy can prove advantageous because it targets the host side of the virus-host interaction. Many current antiviral treatment pathways for SARS-CoV-2 seek to address the virus side, but the issue is that the virus can quickly adapt, with hundreds of variations already identified worldwide. It is significantly more difficult for the virus to evolve resistance on the host side, according to Robert Schwartz, co-senior author and associate professor of medicine at Weill Cornell.
Reflecting back on the study process, Chen highlighted the importance of passion and persistence as drivers of scientific discovery, especially in pioneering COVID-19 research. The team began the project in 2020, and it took around two-and-a-half years to prepare the full results for publication.
“For this project, we had a very important question to address, and it was curiosity and passion that drove us to find the answers behind SARS-CoV-2 infection,” Tang said.
Researchers in the Chen lab will continue to explore how these multi-organoid models can be used to study viral infections. Tang and Xue are pursuing two independent projects on how to model the heterogeneity of human genomes and discover more effective drug targets for SARS-CoV-2.
“The organoid model to study viral infection is a relatively new method. If you ask what researchers did five years ago before COVID-19, many used viral cell lines and animal models,” Chen said. “From COVID-19, we learned about new opportunities to study viral infection and, in a broader sense, infectious disease. We are definitely interested in building more complicated models, adding different components to make them closer to human systems.”
Kaitlin Chung is a staff writer. She can be reached at [email protected].