In a study posted to the medRxiv* preprint server, a team of interdisciplinary research groups identified a genome-wide significant association (GWAS) for long coronavirus disease (COVID) at the FOXP4 locus, which has been previously associated with cancer, severe COVID 2019 (COVID-19), and lung function.
Study: Genome-wide Association Study of Long COVID. Image Credit: NiphonSubsri/Shutterstock.com
*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
Background
Long COVID is also called post-acute sequelae of COVID-19. It is more common in patients hospitalized or admitted to an intensive care unit due to COVID-19 infection. However, it can also occur in patients who have mild COVID-19 symptoms.
The COVID-19 Host Genetics Initiative (HGI) has identified 51 distinct genome-wide significant loci linked to COVID-19 pathophysiology ranging from infection to hospitalization.
To understand the underlying causes of long COVID, it is imperative to assess these variants to elucidate viral pathways and entry mechanisms.
About the study
In this collaborative study, researchers performed the first GWAS focussing on long COVID. They conducted 24 independent GWAS conducted in 16 countries representing populations of 6 ancestries, 6,450 people with long COVID diagnoses, and 1,093,995 controls.
They conducted four GWAS meta-analyses based on a test-verified infection, which was listed as a strict case definition (included 11 studies, N = 3,018) and a self or clinician-reported SARS-CoV-2 infection listed as the broad control definition (all contributing 994,582 studies).
Individuals who survived SARS-CoV-2 infection without long COVID were classified as tight controls, while samples that were genetically ancestry-matched and had no long COVID were classified as population controls.
Additionally, a questionnaire-based approach was followed for symptom assessment.
Results
The analysis discovered a strong genome-wide relationship at the FOXP4 gene. It was also identified that the C allele at rs9367106 was linked to a higher risk of long COVID. Concordant results (although not genome-wide) were observed in all three meta-analyses. The rs9367106-C at the FOXP4 locus also demonstrated to have high epidemiological variability.
The genomic area surrounding the primary variation linked to long COVID (+/-100 kilobases) comprises four genes (FOXP4-AS1, FOXP4, MIR4641, LINC01276).
Since all the variants in linkage disequilibrium (LD) with the lead variant were non-coding, the authors scanned the variants connected to nearby genes with differential expression spanning a 100 kb window.
They identified that rs12660421-A (a proxy allele that correlates with rs9367106-C, the long COVID risk allele) is connected to an increase in the expression of FOXP4 in the lung.
Since FOXP4 has a robust expression in nearly all tissues, including lung cells and immune cells, a colocalization analysis confirmed the same differential expression of long COVID.
Furthermore, the COVID meta-analyses and Biobank Japan labeled the variants in this region as risk factors for COVID-19-related hospitalization. Colocalization analysis conducted by the authors correlated the FOXP4 risk haplotype COVID-19 severity haplotype.
Furthermore, single-cell sequencing analysis suggested that FOXP4 is abundantly expressed in type 2 alveolar cells, which mount robust innate immune responses, secrete surfactant, maintain the alveoli dry, and act as progenitor cells in injured epithelium replenishment.
Additionally, granulocytes that regulate innate immunity also share the same level of FOXP4 expression.
The authors extracted data from the VannoPortal, Regulome, and ENCODE databases and discovered four variants of interest through Chip sequencing. POLR2A and EP300 bound rs2894439 at the start of the risk haplotypes, and EP300 and FOXA1 bound rs7741164 and rs55889968, among others.
Finally, one variant (rs9381074) was shown to be directly associated with DNA methylation signatures in immune and lung cells (H3K27me3 and H3K4me1, H3K27ac, H3K4me3, H3K4me2, H3K4me3), indicating that they are situated at the euchromatin.
A phenome-wide association study between all Biobank Japan phenotypes and rs9367106 identified that the long COVID risk allele was linked to lung cancer.
Additionally, the known risk mutations for lung cancer in non-smoking Asian women and non-small cell lung carcinoma in European and Chinese populations are in LD with the long COVID risk allele.
Colocalization analyses showed that lung cancer and long COVID shared the same genetic signal within 500 kb of rs9367106. Interestingly, the authors also found significant genetic associations between long COVID and symptoms of depression, asthma, and diabetes.
They also suggested that the FOXP4 signal demonstrated an unusually stronger association with long COVID, which cannot be caused by COVID-19 severity alone.
Conclusion
The present research offers direct genetic evidence that lung pathology could contribute substantially to the emergence of long COVID.
Like other post-viral conditions, long COVID is a heterogeneous disease entity where both genetic and epigenetic factors decide the patient's fate in terms of disease risk, severity, and hospitalization.
Since FOXP4 is expressed in various tissues, including the lungs and gut, its polymorphisms can affect lung diseases like long COVID and cancer and other diseases.
Thus, this study paves the way for future research and gives more insight into the biological processes that underlie long COVID.
*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
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