A surgical biopsy can be crucial to tracking the damage of disease and infection in the body, but the procedure can take its own toll on the patient.
A Cornell-led collaboration has developed a non-invasive blood test that uses cell-free DNA to gauge the damage that COVID-19 inflicts on cells, tissues, and organs, and could help aid in the development of new therapies.
The team’s paper, “Cell-Free DNA Tissues-of-Origin by Methylation Profiling Reveals Significant Cell, Tissue and Organ-Specific Injury Related to COVID-19 Severity,” published Jan. 16 in Cell Med. The co-lead authors are doctoral student Alex Cheng; Dr. Matthew Pellan Cheng, assistant professor of medicine at McGill University Health Center; and Wei Gu, assistant professor of pathology at Stanford University.
“A lot of what we’ve learned about the involvement of the virus with different organs is from invasive biopsies, postmortem biopsies,” said corresponding author Iwijn De Vlaminck, an assistant professor in the Meinig School of Biomedical Engineering. “But a liquid biopsy is potentially very useful as a biological measurement, a way to study what is going on in patients who have different types of symptoms, for example.
“It could be used to assess disease severity and help stratify patients in the care system,” De Vlaminck said. “It could also potentially be a surrogate biomarker that you could include in randomized controlled trials of various anti-COVID therapies and anti-virals.”
For several years, De Vlaminck and Cheng have been exploring the biomedical applications of cell-free DNA – dead fragments of DNA that drift around the bloodstream and urine. The fragments are relatively easy to collect via the body’s plasma. By profiling the DNA molecules and logging the occurrence of methylation marks – a chemical modification that results from the expression of different genes – the researchers can follow the fragments, much like a trail of breadcrumbs, back to the source of injury or infection.
In 2019, they developed a test that used the technique to identify the presence of urinary tract infections in kidney transplant patients while also quantifying the degree of damage to the kidney and bladder.
As the COVID-19 pandemic emerged, the researchers realized their test could help search out and quantify the impact of COVID-19 on patients’ lungs and other organs and tissues.
Working with partners at McGill University and the Dana-Farber Cancer Institute, the researchers profiled 104 plasma samples from 33 COVID-19 patients, then compared the results with patients who had other viral infections, as well as healthy controls.
As expected, they found evidence of injury to the lungs, as well as the liver. More surprisingly, they noted an increase in DNA from red blood cell progenitors and found that a high concentration of cell-free DNA in the blood was itself a strong prognostic marker for severe COVID-19 cases.
“The total concentration of the free DNA in the blood is something that can be measured pretty quickly,” De Vlaminck said. “If you’re not interested in figuring out where it’s coming from, or using complex genomic assays, it’s potentially useful for preclinical diagnostic workflows and workups because it can be integrated fairly easily.”
While liquid biopsies are often utilized in connection with cancer, they remain understudied in other diseases, Cheng said.
“When there’s a new virus that emerges, it’s not always clear what to look for,” Cheng said. “Clinicians are looking for specific injury to the kidney or the liver or the lungs. I think that an unsupervised assay like ours during a pandemic setting, when we don’t really know much about what’s going on, is important because it’ll tell us where we can start to look for more information.”