A new analysis of gene expression and protein content in lung and blood tissue suggests that certain variants of the ABO gene, which plays a central role in determining blood type, may also influence susceptibility to COVID-19. Researchers at the University of British Columbia, Vancouver, analyzed data from three studies to link gene and protein expression in lungs and blood with genetic regions associated with COVID-19 susceptibility.
“These genes may also prove to be good markers for disease as well as potential drug targets,” said lead author Ana Hernandez Cordero, PhD, postdoctoral fellow with the Center for Heart Lung Innovation, University of British Columbia, in a statement. Dr. Cordero presented the study at the American Thoracic Society’s virtual international conference.
Dr. Cordero noted that genomewide association studies have been used to identify genetic regions associated with COVID-19 susceptibility, but they cannot be used to identify specific genes. To pinpoint genes, the researchers employed integrated genomics, which combines Bayesian colocalization summary-based Mendelian randomization and Mendelian randomization.
Searching for candidate genes
The researchers combined genetic data and transcriptomics data, which are a measurement of the messenger RNA produced in a cell. Messenger RNA is used as a blueprint for protein production. The genetics data came from the COVID-19 Host Genetics Initiative genomewide association meta-analysis version 4 (patients with COVID-19 vs. patients without COVID-19). Blood transcriptomics data came from the INTERVAL study (n = 3301), and lung transcriptomics data came from the Lung eQTL study (n = 1038). “From the integration of these three datasets we identified the candidate genes that are most likely to influence COVID-19 through gene expression. We further investigated the most consistent candidate genes and tested the causal association between their plasma protein levels and COVID-19 susceptibility using Bayesian colocalization and Mendelian randomization,” said Dr. Cordero during her talk.
The researchers identified six genes expressed in the lung and five expressed in blood that colocalized with COVID-19 susceptibility loci. They found that an increase in plasma levels of ABO was associated with greater risk for COVID-19 (Mendelian randomization, P = .000025) and that expression of the SLC6A20 gene in the lung was also associated with higher COVID-19 risk. They also found novel associations at genes associated with respiratory diseases, such as asthma, as well as genes associated with the host immune responses, such as neutrophil and eosinophil counts.
Within the ABO gene, the research also turned up evidence that blood type O may be protective against COVID-19. “The most significant variant used for the Mendelian randomization test was in complete linkage disagreement with the variant responsible for the blood type O genotype, conferring reduced risk,” said Dr. Cordero.
The study’s method is a powerful technique, said Jeremy Alexander Hirota, PhD, who was asked to comment. “The present study uses integrative omics to determine COVID-19 susceptibility factors which would have been challenging to identify with a single technology,” said Dr. Hirota, who is an assistant professor of medicine at McMaster University, Hamilton, Ont.; an adjunct professor of biology at the University of Waterloo (Ont.); and an affiliate professor of medicine at the University of British Columbia. He trained with the senior author of the study but was not directly involved in the research.
The host response is widely believed to be most responsible for the symptoms of COVID-19, so it isn’t surprising that host genes can be identified, according to Dr. Hirota. The identification of variants in the ABO protein is interesting, though. It suggests ‘that systemic effects beyond respiratory mucosal immunity are a driver for susceptibility.’ To my understanding, ABO protein is not expressed in the respiratory mucosa, which is a common site of first contact for SARS-CoV-2. The links between blood ABO levels and initial infection of the respiratory mucosa by SARS-CoV-2 are unclear,” he said.