Mohd Karim, a computational biologist from the Wellcome Sanger Institute, and his team combined proteome and genome-wide association approaches to analyze datasets from COVID-19 patients and identify proteins that associate with severe COVID-19. They recently detailed their findings in medRxiv, supporting proteins identified in previous studies such as the red blood cell surface markers ABO and introducing novel proteins such as the cell death protein FAS (1). Their study provides potential severe COVID-19 biomarkers for researchers to investigate.
“They’re not just generating this genomic data, they’re actually trying to combine it with another type of information, this proteomic information,” said Nevan Krogan, a systems biologist from the University of California, San Francisco, who was not involved in this study. “Putting orthogonal data types together is really powerful, so they’re pushing in this direction in this paper.”
For genome-wide association studies (GWAS), researchers scan the genomes of individuals with a particular disease to identify genetic variants overrepresented in the diseased population. Theoretically, these gene variants can serve as biomarkers to predict the likelihood that a particular patient will develop the disease. For example, patients carrying a specific mutation in the Huntingtin protein will develop Huntington’s disease, a severe neurological disorder that causes the nerves to break down over time.
However, how a particular variant causes a disease is often unclear. Associating variants identified using GWAS with a patient’s protein levels or phenotype helps pinpoint what pathway the variants may be involved in and how they may contribute to disease pathology.
“It’s a relatively new method for understanding associations. Previously, we were just looking at, okay, we found this genetic variant, let’s look at whether it’s associated with these diseases or these proteins,” said Karim.
Karim is a strong proponent of connecting genetic and protein information. He began using these analyses last year to understand the underlying mechanisms of severe COVID-19 and to explore why blood type affects COVID-19 severity.
Karim noted a GWAS study that identified a variant of the ABO gene, which determines a person’s blood type (2). He expanded upon this study by examining the phenotypes and circulating protein levels in patient samples amassed from several studies of non-COVID patients with cardiovascular problems (3). The ABO variant associated with strokes and pulmonary embolisms, which were both observed in cases of severe COVID-19. Individuals with this ABO variant also had higher protein levels of a dendritic cell receptor known as CD209.
In his team’s medRxiv study, Karim reported on the relevance of the association between the ABO variant and CD209 protein for patients with severe COVID-19.
He found that ABO genetic variants predicted to cause changes in ABO protein levels significantly associated with increased susceptibility to COVID-19 and a likelihood for developing a severe case. In a follow-up proteome-wide association analysis, one specific ABO variant highly correlated with high plasma concentrations of CD209 in COVID-19 patients.
“That’s cool because there are some other reports suggesting that it’s not just ACE2, but also CD209 that could be an entry receptor for COVID-19 by binding to the spike protein,” said Kliment Verba, a biochemist from the University of California, San Francisco who was not involved in this study. “It gives interesting directions for more mechanistic studies.”
Karim collaborated with Jarrod Shilts, a biochemist at Wellcome Sanger Institute, to determine if CD209 interacted with the COVID-19 spike protein, the main protein required for COVID-19 entry into the cell. Shilts showed that the COVID-19 spike protein could bind to both CD209 in a test tube and in cells at a similar level to that of ACE2.
“Using some of the assays we’ve developed for looking at particular pathogen-host interactions, we could find a direct binding between this protein that was identified just by genetic evidence,” said Shilts. “That can really help emphasize potential targets that can be expanded off of this. Now we have not just a protein, but a potential pathway, and some guesses or hypotheses about why it might be leading to more severe disease as well.”
Karim identified other proteins to study as well. FAS, a protein involved in regulating cell death, associated with a higher risk for developing severe COVID-19. Karim and Shilts are interested in exploring the role of apoptosis in the COVID-19 immune response and hope that other researchers will follow suit.
Some, however, thought that Karim’s analyses could have gone a step further.
“There’s a lot of other data types that can compare to this to as well,” said Krogan. “They could have done a more sophisticated, more comprehensive, comparative analysis across more data sets because there's so much out there.”
Krogan expects that Karim’s paper will need more comprehensive analyses and mechanistic studies of the identified proteins before it will be published in a peer-reviewed journal.
Karim is up for the challenge. “This is not something that's set in stone. It's very preliminary research, but it sort of bolsters the need to study these particular proteins in more depth,” he said.
- Karim, M.A. et al. A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance. medRxiv (2021).
- The Severe COVID-19 GWAS Group. Genomewide Association Study of Severe Covid-19 with Respiratory Failure. NEJM. 383, 1522-1534 (2020).
- Karim, M.A. et al. Correspondence: Mining a GWAS of severe COVID-19. NEJM. 383, 2599-2589 (2020).