A recent computational study in India involved an irregular pathway of vitamin D in the pathobiology of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – and opened the door to experimental validation of these observations. The paper is currently available on BioRx* prepress server.
A major public health disaster due to coronavirus disease (COVID-19), a life-threatening disease caused by SARS-CoV-2, has mobilized the global research community to decipher the fundamental mechanisms and cellular pathways that are responsible. of the variety of symptoms, the 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 modulated vitamin D genes in the lung cells of infected patients remains undetermined.
In short, the cellular effects of vitamin D come from its nongenomic / cytoplasmic effects, but also from its genomic / nuclear effects. Consequently, a multitude of receptors, enzymes and factors are involved in how it modulates inflammation and feedback loops.
That is why researchers, led by Dr. Bijesh George of the Rajiv Gandhi Center for Biotechnology (Trivandrum) and the Manipal Academy of Higher Education in India, conducted a study to assess the exact state of the vitamin D pathway in SARS-CoV- 2 -infected patients using public transcriptomic data sets and strict computational approaches.
Cell lines, transcriptomic approaches and network analysis
The researchers initially assessed the expression levels of the basic components of the vitamin D pathway in various models of viral infection using signaling pathway design data sets (SPPDs) – a set of transcriptomic data sets biocured by Atlas Signaling Organization nuclear receptors (NURSA).
Subsequently, the lung cells of patients with COVID-19 were analyzed to evaluate the basic molecules of the vitamin D pathway in three sets of transcriptomic data based on RNA sequencing of bronchoalveolar lavage fluid (BALF) cells, but also in human lung cells A549 , Calu3 and NHBE lines expressing SARS-CoV-2.
Finally, the network analysis of the different gene sets was performed using the Network Analyst 3.0 tool. Moreover, the functional analysis of enrichment was done by using Reactome, an online database accessible online, with intuitive bioinformatics tools.
Reduced expression of vitamin D pathway components.
In summary, the results of this study support the notion of an alleged association between SARS-CoV-2 infection and reduced expression of various components of the vitamin D pathway. More specifically, there was a reduction in vitamin D receptors and retinoids X, as well as CYP27A1. (belonging to the cytochrome P450 family of genes) in the BALF cells of patients infected with the virus.
Expression of vitamin D-regulated genes in patients with COVID19. a) The number of genes found overlapping with the regulated genes of vitamin D and three SARS-VOC-2 data sets are indicated. b) 43 genes were identified that are common to 3 SARS-VOC-2 data sets and also regulated by vitamin D, c) Bar chart summarizes the enrichment analysis in SARS-VOC-2 from Metascape . d) The bar chart summarizes the functional enrichment analysis in Metascape. e) The expression status of these 43 genes in the data of SARS-VOC-2 patients is represented as a heat map. f) Network analysis of 12 genes found regulated upward in all three patient data sets and also regulated by vitamin D is given. Functional analysis of 12 gene enrichment using Reactome identified “Activation of the pre-replicative complex” as primary enrichment (rank 1, hits 9/32 pavlue 3.5e-11), Network analysis of 12 genes regulated in the three SARS-VOC-2 patient transcriptome data sets. Genes are found to be functionally linked to the immune system (rank 57, 131/1140 pp. 1.31e-21).
Moreover, by identifying 107 differentially expressed and mainly down-regulated genes modulated by vitamin D in the transcriptomic data sets of patients’ 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 immune system pathways, NF-κB / cytokine signaling, and cell cycle regulation as primary predictive events that may be affected in the cells of these patients.
Another notable new observation is the upregulation of PAK1 expression (but not another AKT kinase survival family) in the same SARS-CoV-2 sample sets with reduced expression of vitamin D pathway components, suggesting a potential correlative relationship. between these two phenomena, “say the study’s authors.
A step towards experimental validation
All that being said, it is clear how this study provides important information about a potentially causal association between a compromised multilayered vitamin D pathway with SARS-CoV-2 infections in patients, resulting in a downstream pathway of vitamin D. .
This disorder is characterized by both downward regulation and upward regulation of vitamin D cell genes, which involve molecules that are involved in the proinflammatory response Th1 and immune regulation.
These preliminary results now establish the stage of experimental validation of the observations and postulates made using computational approaches “, conclude the study authors based on the results of their study.
In any case, the stage is set by this research effort for further studies to confirm whether a compromised pathway of vitamin D can indeed influence the susceptibility of lung cells to SARS-CoV-2 and elucidate its exact role in COVID protein manifestations. . -19.
*Important Note
medRxiv publishes preliminary scientific reports that are not evaluated by colleagues and therefore should not be considered conclusive, guide clinical practice / health-related behavior or treated as established information.