A recent computational study from India implied a deregulated vitamin D pathway in the pathobiology of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – and opened the door for experimental validation of these observations. The article is currently available on bioRxiv* prepress server.
A major public health calamity due to coronavirus disease (COVID-19), which is a fatal disease caused by SARS-CoV-2, mobilized the global research community to decipher fundamental mechanisms and cellular pathways responsible for the variety of symptoms, severity and progression of the disease, as well as recovery or death.
Vitamin D is a steroid hormone with multiple cellular functions; although a defective vitamin D pathway has been linked to the pathobiology of SARS-CoV-2, the status of the genes modulated by vitamin D in the lung cells of infected patients remains undetermined.
In short, the cellular effects of vitamin D derive from its non-genomic / cytoplasmic effects, but also from its genomic / nuclear effects. Consequently, a myriad of receptors, enzymes and factors are involved in how it modulates inflammation and feedback cycles.
That is why the researchers, led by Dr. Bijesh George of the Rajiv Gandhi Biotechnology Center (Trivandrum) and the Manipal Academy of Higher Education in India, conducted a study to assess the exact status of the vitamin D pathway in SARS-CoV- 2 -infected patients using public transcriptomic data sets and rigorous computational approaches.
Cell lines, transcriptomic approaches and network analysis
The researchers initially evaluated the levels of expression of the major components of the vitamin D pathway in different models of viral infection, using the data sets of the Signaling Pathways (SPPD) project – a set of biocured transcriptomic data sets by the Signaling Atlas Organization Nuclear Receiver (NURSA).
Subsequently, the lung cells of patients with COVID-19 were analyzed to evaluate the central molecules of the vitamin D pathway in three transcriptomic data sets based on RNA sequencing of bronchoalveolar lavage fluid (BALF) cells, but also in A549 cells. , Calu3 and NHBE of human lung lines that express SARS-CoV-2.
Finally, the network analysis of several sets of genes was performed using the Network Analyst 3.0 tool. In addition, the functional enrichment analysis was performed using Reactome, a free online path database with intuitive bioinformatics tools.
Reduced expression of components of the vitamin D pathway
In summary, the results of this study support the notion of a supposed association between SARS-CoV-2 infection and reduced expression of different components of the vitamin D pathway. More specifically, there was a reduction in vitamin D and retinoid X receptors, as well as CYP27A1 (belonging to the cytochrome P450 gene family) in BALF cells of patients infected with the virus.
Expression of genes regulated by vitamin D in COVID19 patients. a) Number of genes found overlapping genes regulated by vitamin D and three SARS-COV-2 data sets are indicated. b) 43 genes have been identified that are common to 3 SARS-COV-2 data sets and also regulated by Vitamin D, c) The bar diagram shows the summary of Metascape’s SARS-COV-2 enrichment analysis. d) The bar diagram shows the summary of Metascape’s functional enrichment analysis. e) The expression status of these 43 genes in the SARS-COV-2 patient data is plotted as a thermal map. f) Analysis of the network of 12 genes found to be positively regulated in all three patient data sets and also regulated by vitamin D is provided. The analysis of functional enrichment of 12 genes using Reactome identified “Activation of the pre-replicative complex” as primary enrichment (classification 1, hits 9/32 pavlue 3.5e-11), network analysis of 12 negatively regulated genes in all three SARS -COV- 2 patient transcriptome data sets. The genes are found functionally related to the immune system (classification 57, 131/1140 pvalue 1.31e-21) are observed.
In addition, by identifying 107 differentially expressed and mainly negatively regulated genes, modulated by vitamin D in transcriptomic data sets of patient cells, the role of direct and indirect mechanisms of gene expression by unregulated vitamin D was established.
A detailed analysis of the network of such differentially expressed genes revealed the pathways of the immune system, the NF-kB / cytokine signaling and the regulation of the cell cycle as primary predictive events that can be affected in the cells of such patients.
Another notable new observation is the positive regulation of PAK1 expression (but not from another AKT family of survival kinases) in the same sets of SARS-CoV-2 samples with reduced expression of components of the vitamin D pathway, suggesting a potential relationship correlative between these two phenomena “, say the study authors.
A step towards experimental validation
That said, it is clear how this study provides important information about a potentially causal association between a compromised multi-layered vitamin D pathway with SARS-CoV-2 infections in patients, resulting in deregulation of the pathways downstream of vitamin D.
This deregulation is characterized by both negative and positive regulation of vitamin D cellular genes, which involves molecules that are involved in the pro-inflammatory Th1 response and immune regulation.
These preliminary results now set the stage for experimental validation of observations and postulations made using computational approaches, “conclude the study authors based on the results of their study.
In any case, the scenario is set by this research effort for larger studies that will confirm whether a compromised vitamin D pathway can in fact influence the susceptibility of lung cells to SARS-CoV-2 and elucidate its exact role in the multiform manifestations of COVID-19.
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