Researchers at Massachusetts General Hospital (MGH) and the Broad Institute of MIT and Harvard have identified the protein “signature” of severe COVID-19, which they describe in a new study published in Cell Reports Medicine. “We were interested in asking whether we could identify mechanisms that might be contributing to death in COVID-19,” said MGH infectious disease expert and Broad associate member Marcia Goldberg, who studies interactions between microbial pathogens and their hosts. “In other words, why do some patients die from this disease, while others — who appear to be just as ill — survive?” Goldberg is co-senior author of the study together with MGH Center for Cancer Immunotherapy director and Broad institute member Nir Hacohen.
In March 2020, when the first patients with symptoms of COVID-19 began arriving at MGH’s emergency department (ED), Goldberg was contacted by her colleague, Michael Filbin, an attending physician and director of clinical research at MGH’s ED, an associate member at the Broad, and co-first author of the study with Arnav Mehta, a postdoctoral fellow at the Broad and Dana-Farber Cancer Institute. Filbin and Goldberg had earlier begun collaborating with Hacohen to develop methods for studying human immune responses to infections, which they had applied to the condition known as bacterial sepsis. The three agreed to tackle this new problem with the goal of understanding how the human immune system responds to SARS-CoV-2, the novel pathogen that causes COVID-19.
A massive collection effort
To undertake this study, the MGH team used proteomics, which is the analysis of the entire protein composition (or proteome) of a cell, tissue or organism. In this case, proteomic analysis was used to study blood specimens taken from patients arriving at the hospital’s ED with respiratory symptoms consistent with COVID-19. Collecting these specimens required a large team of collaborators from many departments, which worked overtime for five weeks to amass blood samples from 306 patients who tested positive for COVID-19, as well as from 78 patients with similar symptoms who tested negative for the coronavirus. (Read more about this extraordinary effort.)
Next, Mehta was brought on board to oversee interpretation of the complex data produced by the proteomic analysis. Mehta also works in Hacohen’s lab, and the two had long been interested in using proteomic analysis of blood as an alternative to biopsies (which are invasive and painful). “We have been asking, What can we learn about what’s happening in the body just by looking at protein signatures in the blood?” Mehta said.
The study found that most patients with COVID-19 have a consistent protein signature, regardless of disease severity; as would be expected, their bodies mount an immune response by producing proteins that attack the virus. “But we also found a small subset of patients with the disease who did not demonstrate the pro-inflammatory response that is typical of other COVID-19 patients,” Filbin said, yet these patients were just as likely as others to have severe disease. Filbin, who is also an assistant professor of emergency medicine at Harvard Medical School (HMS), noted that patients in this subset tended to be older people with chronic diseases, who likely had weakened immune systems.
Signatures of severity
The next step was to compare the protein signatures of patients with severe disease (defined as those who required intubation or who died within 28 days of hospital admission) with patients with less-severe cases of COVID-19. The comparison allowed the researchers to identify more than 250 “severity associated” proteins. Importantly, Mehta noted, blood was drawn from patients three times (on enrollment, then three and seven days later). “That allowed us to look at the trajectory of the disease,” he said. Among other revelations, this showed that the most prevalent severity-associated protein, a pro-inflammatory protein called interleukin-6 (IL-6) rose steadily in patients who died, while it rose and then dropped in those with severe disease who survived. Early attempts by other groups to treat COVID-19 patients experiencing acute respiratory distress with drugs that block IL-6 were disappointing, though more recent studies show promise in combining these medications with the steroid dexamethasone.
However, Hacohen, who is a professor of medicine at HMS and director of the Broad's Cell Circuits Program, noted that many of the other severity-associated proteins the analysis identified are likely important for understanding why only a portion of COVID-19 develop severe cases. Learning how the disease affects the lungs, heart, and other organs is essential, he said, and proteomic analysis of the blood is a relatively easy method for getting that information. “You can ask which of the many thousands of proteins that are circulating in your blood are associated with the actual outcome,” he said, “and whether there is a set of proteins that tell us something.”
Goldberg, who is a professor of emergency medicine at HMS, believes that the proteomic signatures identified in this study will do just that. “They are highly likely to be useful in figuring out some of the underlying mechanisms that lead to severe disease and death in COVID-19,” she said, noting her gratitude to the patients involved in the study. Their samples are already being used to study other aspects of COVID-19, such as identifying the qualities of antibodies that patients form against the virus.
The study was supported by the Cystic Fibrosis Foundation Postdoctoral Fellowship; a gift from Sandra, Sarah and Arthur Irving; the American Lung Association (COVID-19 Action Initiative); the Executive Committee on Research at MGH; the Chan-Zuckerberg Initiative; and the Harvard Catalyst/Harvard Clinical and Translational Science Center (National Center for Advancing Translational Sciences, National Institutes of Health).