Evidence of a dysregulated vitamin D endocrine system in SARS-CoV-2 infected patient’s lung cells

Although a defective vitamin D endocrine system has been widely suspected to be associated in SARS-CoV-2 pathobiology, the status of the vitamin D endocrine system and vitamin D-modulated genes in lung cells of patients infected with SARS-CoV-2 remains unknown. To understand the significance of the vitamin D endocrine system in SARS-CoV-2 pathobiology, computational approaches were applied to transcriptomic datasets from bronchoalveolar lavage fluid (BALF) cells of such patients or healthy individuals. Levels of vitamin D receptor, retinoid X receptor, and CYP27A1 in BALF cells of patients infected with SARS-CoV-2 were found to be reduced. Additionally, 107 differentially expressed, predominantly downregulated genes, as potentially modulated by vitamin D endocrine system, were identified in transcriptomic datasets from patient’s cells. Further analysis of differentially expressed genes provided eight novel genes with a conserved motif with vitamin D-responsive elements, implying the role of both direct and indirect mechanisms of gene expression by the dysregulated vitamin D endocrine system in SARS-CoV-2-infected cells. Protein–protein interaction network of differentially expressed vitamin D-modulated genes were enriched in the immune system, NF-κB/cytokine signaling, and cell cycle regulation as top predicted pathways that might be affected in the cells of such patients. In brief, the results presented here povide computational evidence to implicate a dysregulated vitamin D endocrine system in the pathobiology of SARS-CoV-2 infection.

www.nature.com/scientificreports/ from its nongenomic or cytoplasmic effects and/or genomic nuclear effects. They are caused by 1,25-dihydroxy vitamin D binding to the vitamin D receptor (VDR) or retinoid X receptor (RXR) complex within specific responsive DNA sequences in the target genes or through indirect mechanisms 9 . In addition to the status of vitamin D3/cholecalciferol, biosynthesis of 1,25-dihydroxy vitamin D is positively and negatively modulated by alpha-hydroxylases CYP27B1 and CYP24A1, respectively. Interestingly, these enzymes are under the control of fibroblast growth factor 23 (FGF23), a paracrine growth factor expressed in the lung, heart, and kidney 10 . Increased systemic levels of FGF23 are generally associated with general inflammation, cardiac hypertrophy, chronic kidney disease, and inflammation in lung airway 11 ; all these phenotypes are found to be closely associated in SARS-CoV-2 pathogenesis. In general, FGF23 acts through its receptors, FGFR1-4, in its coreceptor klothodependent or -independent manner. Other activities of FGF23 relevant to SARS-CoV-2 are as follows: participation in cardiac myocytes in stimulating the levels of fibrotic factors, cardiac fibrosis, and pathological cardiac remodeling 12 ; induction of proinflammatory cytokine IL-1beta 11 ; inhibition of ACE2 expression, angiotensin II (Ang II) induction, and blood pressure in kidney 13 ; and inhibition of M1 to M2 transitioning of macrophage and counteracting anti-inflammation response 14 . Additionally, FGF23 and CYP24A1 are components of a regulatory vitamin D feedback loop because both molecules are genomic targets of 1,25-dihydroxy vitamin D and are stimulated by it in a VDR-dependent manner 11,15,16 . In addition to vitamin D, FGF23 levels have been shown to be induced by obese growth factor leptin 16 , master regulator of hypoxia HIF1-alpha 17 , and proinflammatory TNF-alpha 17 . For example, leptin induces FGF23 expression and inhibits CYP27B1 expression 18 , implying a potential compromised status of 1,25-hydroxy vitamin D under conditions of obesity. Recent data suggest that increased levels of inflammatory cytokines in SARS-CoV2 infected patients with a reduced level of vitamin D 19 . Currently, we do not know the status of FGF23, and other core modifiers of the vitamin D endocrine system in lung cells of patients infected with SARS-CoV-2.
For productive infection, many viruses use the host machinery to antagonize the host defense mechanism while using survival pathways to abort apoptosis for ensuring a successful completion of their replication and generation of progeny virions. In this context, previous work suggest that during the host-RNA-virus interaction, pathogen replication and its propagation are profoundly influenced by human p21-activated kinases (PAKs) 20 , which are the established modifiers of cytoskeleton remodeling, inflammation, thrombosis, cell survival, and gene expression or repression, in addition to its oncogenic role in cancer development progression [21][22][23][24][25] . However, to the best of our knowledge, no published data exist about the effect of SARS-CoV-2 on PAK mRNA expression levels in the context of the vitamin D endocrine system. Current data suggest a mechanistic role of PAK-dependent actin polymerization in vitamin D-mediated stimulation of FGF23 expression 26 ; vitamin D signaling stimulates actin depolymerization in endometrial cancer by inhibiting RAC1 and PAK1 expression 27 ; the vitamin D endocrine system uses PAK1 in protecting murine fibroblasts from vitamin E-succinate-triggered apoptosis; and dependency of cholecalciferol-mediated NF-kB transactivation on PAK1 activity 28 . These examples of regulatory crosstalk between vitamin D and PAKs suggest that the cellular effects of vitamin D in the context of SARS-CoV-2 pathobiology might not be merely affected by the biosynthesis of cholecalciferol but also by the status of FGF23, vitamin D metabolic enzymes, and PAK signaling. However, the status of vitamin D endocrine system in the pathobiology of SARS-CoV-2 infection remains unknown.
To better understand the significance of vitamin D in SARS-CoV-2 pathobiology, we applied computational approaches to study the expression levels of core components and modifiers of the vitamin D endocrine system and to understand its potential relationship with the status of the PAK pathway in SARS-CoV-2-infected individuals.

Status of the vitamin D endocrine system in viral infection model systems.
To better understand the significance of the vitamin D endocrine system in the pathobiology of SARS-CoV-2 infection, we first examined the expression levels of core components of the vitamin D endocrine system in various models of viral infection using the Signaling Pathways Project Datasets (SPPD), a collection of transcriptomic datasets initially biocurated by the Nuclear Receptor Signaling Atlas Organization 29 . As illustrated in Fig. 1, we found evidence of both down-and upregulation of molecules belonging to the vitamin D endocrine system. In general, we noticed a preferential downregulation of the vitamin D endocrine system in majority of the studies compiled in SPPD. We believe that the noted variability in the levels of molecules among various independent biological studies is a common observation and might arise because of differences in the nature and preparation of test samples as well as experimental conditions and reagents used in the different studies. Specifically, we observed reduced expression of vitamin D coreceptors RXRA, CYP27A1, CYP24A1, and FGFR1-4 in most of the SARS virusderived datasets. However, most of the SPPD datasets lacked information of the vitamin D endocrine system in the SARS-CoV-2 infection model system, except for CYP27B1 upregulation. In general, these observations are consistent with the notion of a general reduced expression of several, but not all, components of the vitamin D endocrine system caused by viruses.

Suppression of the vitamin D endocrine system in lung cells of patients infected with SARS-CoV-2.
To assess the status of the vitamin D endocrine system in lung cells of patients infected with SARS-CoV-2, we next evaluated the levels of core molecules of the vitamin D endocrine system in three separate RNA sequencing-based transcriptomic datasets of bronchoalveolar lavage fluid (BALF) cells from patients with confirmed SARS-CoV-2 infection and in control healthy subjects [30][31][32][33] , as well as in A549, NHBE, and Calu3 human lung cell lines expressing infected SARS-CoV-2 31 . Our analysis indicated an association between SARS-CoV-2 infection and reduced expression of VDR and its mandatory binding partner RXR and reduced expression of CYP27A1 in two of the three human transcriptomic studies and increased expression of CYP24A1 and  Table S1). In contrast to the levels of core components of the vitamin D endocrine system in BALF cells from SARS-CoV-2-infected patients, infection associated SARS-CoV-2 overexpression in three lung cancer cells did not alter the expression of most components of the vitamin D endocrine system. However, SARS-CoV-2 overexpression in A549 and Calu3 cells downregulated FGFR1-4 levels ( Fig. 2b, Supplementary Table S1). These observations suggest that data from cell lines infected with ectopic overexpression by infection of SARS-CoV-2 may not always be compatible with patient-derived primary cultured cells to understand the significance of the vitamin D endocrine system in SARS-CoV-2-infected patients. Therefore, we focused on transcriptomic data from the patients in subsequent analyses.

Vitamin D-modulated genes overlap with differentially expressed genes in lung cells of patients infected with SARS-CoV-2.
Vitamin D mediates its biological effects via upregulating or downregulating the expression of cellular genes responsible for various biological processes. Vitamin D modifies the expression of cellular genes either through a direct mechanism involving predicted or validated VDR motifs in the target genes and/or through indirect pathways 34,35 . Further, we assessed whether noted downregulation of the vitamin D endocrine system in SARS-CoV-2 might also be accompanied by misregulation of vitamin D-modulated genes, and eventually, resultant functions of such gene products. Thus, as illustrated in Fig. 3a, we found a widespread overlap of vitamin D-modulated genes with differentially expressed genes in three transcriptomic datasets from cells of patients infected with SARS-CoV-2. Upon cross-comparing vitamin D-modulated genes that overlapped in SARS-CoV-2 transcriptomic datasets used here, we recognized 43 differentially expressed vitamin D-modulated genes that shared vitamin D dataset and three transcriptomic datasets from lung cells of patients infected with SARS-CoV-2 (Fig. 3b). Enrichment analysis of 43 vitamin D-modulated genes in samples collected from COVID patients suggested that many of these genes were downregulated in SARS-CoV-2-infected lung cells 31 and CD14 + monocytes 36 . The associated primary pathways included neutrophil degranulation, regulation of multiorganism processes, and positive regulation of apoptosis 37 (Fig. 3c,d). They could potentially influence a whole range of functions in SAR-CoV-2-infected lung cells in a vitamin D-sensitive manner (Supplementary Tables S2, S3). The expression of  Figure S1). Expression profiling of these 43 genes indicated that 12 vitamin D-modulated genes (HTT, KCNAB2, EHMT1, RGS3, HEXA, NLRP1, GGA3, MYO1G, ARRB1, PSMD3,  MGAT1, and EIF3D) were downregulated in 3 SAR-CoV-2 datasets, 9 genes (SIRPB1, CD4, CTSC, LIPA, PDE4DIP, ITSN1, SSH2, IER2, and HCFC1R1) in 2 datasets, and 3 genes (SECTM1, FOXN3, and GADD45B) in 1 SARS-CoV-2 transcriptomic dataset (Fig. 3e). additionally, Fig. 3e shows the levels of downregulation of 12 genes that overlapped with vitamin D-modulated genes in cells of patients infected with SARS-CoV-2. Protein-protein interaction network analysis of these 12 genes (shown by green circles, Fig. 3f, right) indicated that several of such downregulated genes, such as ARRB1, RGS3, GGA3, HEXA, EIF3D, and PSMD3, are functionally related to the immune system (functional enrichment analysis of network genes using Reactome with a rank of 56, p value 1.31e−21, Supplementary Table S4). Significance of downregulation of these shared 12 genes is judged by the nature of their functions. For example, functions associated with the following genes are expected to be compromised in SARS-CoV-2-infected lung cells: (1) EIF3D, a component of the protein translational complex; reduction in the levels of this component inhibits CD8 + T cell activity and promotes HIV progression 38 , (2) NLRP1, a component of inflammasome with role in innate immunity 39 , and (3) RGS3, a G protein signaling component with role in T-lymphocyte motility during T helper 2 (Th2)-driven inflammation in airway cells 40 . Among the 43 differentially expressed genes, 19 genes (SLPI, CCL2, STEAP4, FGL2, MARCKS, TMEM71, MXD1, DAPP1, IFITM2, OAS1, SELL, CSTA, CIR1, TIMP1, DYNLT1, IRF2, YWHAE, SCLT1, and NOP10) were upregulated in 3 SARS-CoV-2 datasets; 3 genes (GADD45B, FOXN3, and SECTM1) were upregulated in 2 datasets, and 10 genes (HCFC1R1, IER2, SIRPB1, CD4, CTSC, LIPA, PDE4DIP, ITSN1, and SSH2) were upregulated in 1 dataset (Fig. 3e). Protein-protein interaction network analysis revealed that the upregulated genes were strongly correlated with the immune system. Surprisingly, Reactome pathway enrichment analysis of network of 19 up-regulated genes identified the immune system, cytokine signaling, and adaptive and innate immunity as first four primary enriched gene sets (Fig. 3f, Supplementary Table S5). We found that many of the differentially expressed genes (that overlapped with vitamin D-modulated genes) in the cells of patients infected with SARS-CoV-2 having a role in antiviral responses were induced during viral infection. Interestingly, a subset of differentially expressed 19 genes in lung cells of patients infected with SARS-CoV-2 included genes that have been implicated in the action of interferons, development of antiviral response, and regulation of innate immune responses in individuals and cells infected with viruses [41][42][43][44][45][46][47] . Examples of such upregulated genes included 2′-5′-oligoadenylate synthetase 1 (OAS1), an interferon-responsive gene [48][49][50] , interferon regulatory factor 2 (IRF2), interferon-induced transmembrane protein 2 (IFITM2), secretory leukocyte peptidase inhibitor (SLP1), max dimerization protein 1 (MXD1), tissue inhibitor of metalloproteinase-1 (TIMP1), PH domain-containing adaptor Bam32/DAPP1, and T helper type 1 (Th1)/monocyte-associated chemokine CCL2, which have been shown to also participate in SARS-CoV-2-AEC2 signaling in lung cells 51 . In fact, upregulation of OAS1 and IFITM2 has been recently noticed as a common feature in patients infected with SARS-CoV-2 41 , and certain variants of OAS1 have been predicted to influence SARS-CoV-2 infection 52 . These observations suggest that the noticed reduced expression of the vitamin D endocrine system in lung cells of patients infected with SARS-CoV-2 could be associated with both down-and upregulation of cellular genes because vitamin D is known to regulate gene expression both positively and negatively. These observations suggested codysregulation of the vitamin D endocrine system with molecules with roles in Th1 response and immune regulation pathways in a subset of patients infected with SARS-CoV-2.
Exploring a potential relationship between SARS-CoV-2 and PAKs. The PAK family of cellular kinases has been found to be activated by pathogens, including RNA viruses such as influenza and HIV 53,54 . Over the years, PAKs have been implicated in various stages of virus entry and replication and in supporting the cell survival phenotype during certain viral infections 20 . To understand the significance of the PAK pathway in SARS-CoV-2 pathobiology, we first examined the status of PAKs in SPPD. We found that the levels of PAK1 and PAK4 mRNAs are generally upregulated in model systems pertaining to middle east respiratory syndrome coronavirus (MERSCOV), whereas PAK2 and PAK3 are downregulated in MERSCOV models (Fig. 4a).
Further, we examined the levels PAK1-4 in transcriptomic analyses in lung cells of patients infected with SARS-CoV-2. We noticed PAK1 mRNA upregulation in datasets of all three patients infected with SARS-CoV-2. No significant alteration was observed in the differential expression of PAK2, PAK3 and PAK4 in samples collected from patients infected with SARS-CoV-2 compared with the healthy controls (Fig. 4b). In addition to PAK kinases, cell survival is known to be profoundly regulated by AKT kinases 55,56 . However, as opposed to PAKs, we noticed a reduction in AKT levels in SARS-CoV-2-infected cells (Fig. 4b). These observations suggested an association between the levels of PAK1 mRNA and SARS-CoV-2 infection. However, the current literature provides no clues about the role of PAK expression in the pathobiology of SARS-CoV-2 infection. Because we observed a compromised vitamin D endocrine system and increased PAK1 expression in the SARS-CoV-2 transcriptome, we further searched for genes that might be common effectors of vitamin D and PAK pathways. Figure 5a shows that indeed there is a widespread overlap of genes common to vitamin D-and PAK-regulated genes. Our analysis identified 563 differentially expressed genes common to vitamin D-and PAK-regulated datasets (Fig. 5b). The expression levels of the two sets of genes are depicted in the heatmap (Fig. 5c). We next searched 563 differentially expressed genes for vitamin D-modulated genes that might be downregulated or upregulated in SARS-CoV-2 transcriptome, presumably because of a compromised vitamin D endocrine system or gene expression due to derepression. We believe that such genes might be the shared effectors of vitamin D and PAK pathways in lung cells of patients infected with SARS-CoV-2, and hence, they might be involved in SARS-CoV-2 pathobiology.
We focused on vitamin D-modulated genes that were downregulated in two out of three SARS-CoV-2 transcriptomic studies. Our analysis identified 40 such downregulated genes out of 563 differentially expressed genes, shared between vitamin D and PAK pathways, in SARS-CoV-2-infected lung cells (Fig. 5b). Similarly, there are 24 upregulated genes (shared between vitamin D and PAK pathways) in SARS-CoV-2-infected lung cells (Fig. 5b). These observations suggest that the evident dysregulated vitamin D endocrine system in SARS-CoV-2-infected  www.nature.com/scientificreports/ tein interaction network analysis of 43 genes revealed that many of these genes are functionally related to NF-κB pathway and cytokine signaling, DNA damage checkpoint and response (rank 2 and 3), and apoptosis (rank 4) (Fig. 6a). Similarly, protein-protein interaction network analysis of 40 downregulated genes, which were shared targets of vitamin D and PAK pathways, in SARS-CoV-2-infected lung cells indicated that genes in the top four rank orders belong to different aspects of regulation of immune response (Fig. 6b). In contrast to the aforementioned downregulated genes, protein-protein interaction network analysis of 24 upregulated genes, which were shared targets of vitamin D and PAK pathways, suggested cell cycle regulation and gene expression as the top functional targets (Fig. 6c). These observations raised the possibility that the evident downregulation of vitamin D and upregulation of PAK1 in SARS-CoV-2-infected cells is likely to have a significant influence upon NF-κB pathway, cytokine signalling and immune regulation. The critical role of genes important for promoting the G1-S progression as well as key components of the cell survival that could impact the pathobiology of SARS-CoV-2 is also evident in the analysis. Further studies are warranted to delineate the mechanism underlying these findings with a broad implication in the pathobiology of SARS-CoV-2.  (Fig. 7a,b). These observations suggest that a defective vitamin D endocrine system could impact the levels of differential expression of vitamin D-modulated genes in SARS-CoV-2-infected lung cells via both direct mechanisms involving the VDR motif in the target genes and indirect mechanisms.

Discussion
In brief, the present study was conducted to assess the status of the vitamin D endocrine system in patients infected with SARS-CoV-2 using public transcriptomic datasets and computational approaches. Results presented support the notion of a potential association between SARS-CoV-2 infection and reduced expression of several components of the vitamin D endocrine system. As expected, the dysregulated vitamin D endocrine system in the lung cells of patients infected with SARS-CoV-2 was accompanied by dysregulation (both down-and upregulation) of cellular genes of vitamin D-modulated genes, including molecules involved in Th1 response and immune regulation. Another novel notable observation is the upregulation of PAK1 expression (but not another family of survival AKT kinases) in the same SARS-CoV-2 sample sets with a reduced expression of vitamin D endocrine system components, suggesting a potential correlative relationship between these two phenomena. Consistent with this hypothesis, we noticed that indeed a subset of differentially expressed genes in lung cells of patients infected with SARS-CoV-2 is also the shared target of PAK-and vitamin D-modulated genes and such genes were coinfluenced by not only a defective vitamin D endocrine system but also PAK1 upregulation associated with SARS-CoV-2-infection; thus, they are involved in SARS-CoV-2 pathobiology. Future studies are required to define the precise levels of crosstalk between PAK1 and vitamin D endocrine system and to determine whether PAK1 plays a role in the dysregulated vitamin D endocrine system. As vitamin D modulates the expression of several cellular genes through a direct mechanism involving VDR motifs in the putative target genes as well as through indirect mechanisms, we observed that most differentially expressed genes, common to vitamin D and/or PAK-modulated genes, in SARS-CoV-2-infected lung cells lacked the VDR motif in target gene promoters. Hence, they were expected to be regulated by indirect mechanisms in SARS-CoV-2-infected cells by vitamin D. However, our analysis did discover, at least, eight new vitamin D target genes with a conserved VDR motif within − 1000 and − 100 from TSS in gene promoters as differentially expressed genes in SARS-CoV-2-infected lung cells. This raised the possibility of direct mechanisms of regulation of such vitamin D-modulated genes by the dysregulated vitamin D endocrine system.
To highlight the potential significance of a subset of eight newly recognized VDR-containing target genes in SARS-CoV-2 pathobiology, we here briefly discuss the potential connection between six differentially expressed genes in SARS-CoV-2-infected lung cells; however, ZNF589 and HTT remained novel in the context of viral infection.
Intersectin-1 (ITSN1). Cytoskeleton remodeling and interactions, including dynamics of actin polymerization-depolymerization, which is a process also regulated by PAK signaling 21 , plays a role in the early steps of endocytosis during viral infection and phagocytosis 60,61 . One such regulator is the guanine nucleotide exchange factor ITSN1 with an established role in vaccinia infection-associated actin polymerization and Fc-gamma receptor-mediated phagocytosis 62 . In the context of SARS-CoV-2 infection, actin remodeling represents a central event in inflammatory responses in the lungs 63 and might be involved in virus entry 64 . Further, components of actin remodeling have emerged as important interactors of membranous ACE2 65 , which is the primary receptor for SARS-CoV-2. Likewise, Fc-gamma-mediated phagocytosis, a process known to be regulated by ITSN1, plays an important role in immune responses during SARS-CoV-2 infection 66   shown to be important in the regulation of DNA damage response and senescence 67 . Relevance of the presence of a conserved VDR motif in the promoter region of GADD45B and its differential expression in SARS-CoV-2-infected lung cells (as shown in this study) lies in a recent finding presenting the differential expression of GADD45B as well as other genes belonging to mitochondrial functions in patients with chronic obstructive pulmonary disease (COPD) 68 . Further, as older patients with COPD are more susceptible to SARS-CoV-2 infection 69 , GADD45B might be involved in SARS-CoV-2 pathobiology in patients with COPD.
Phosphodiesterase 4D-interacting protein (PDE4DIP). PDE4DIP is an understudied enzyme that hydrolyzes the 3′ cyclic phosphate linkages in 3′,5′-cAMP and cGMP and 3′,5′-cAMP and participate in cellular signaling and other processes 70 . PDE4DIP has recently been suggested to be a differentially expressed genes in lung cells in COPD 71 . As no precedence of vitamin D regulation of PDE4DIP exists, our present finding indicates the possibility of a regulatory relationship between vitamin D and cyclin AMP or GMP signaling in SARS-CoV-2 pathobiology in lung cells.
ST3 beta-galactoside alpha-2,3-sialyltransferase 1 (ST3GAL1). ST3GAL1 is an enzyme with sialyltransferase activity. It participates in transferring sialic acid to substrates with galactose as the acceptor and is involved in glycosylation 21 . Glycosylation is fundamental to the regulation of numerous cellular processes, including vitamin D-binding proteins 72 . As certain genetic variants of ST3GAL1 have been shown to be associated with an increased probability of severity in patients with influenza A(H1N1)pdm09 infection 73 , the dysregulated vitamin D endocrine system in SARS-CoV-2-infected patients might be accompanied by misglycosylation of certain proteins, which in turn may impact SARS-CoV-2 pathobiology in lung cells.
Jagged-1 (JAG1). Activation of Notch receptors by Notch ligands, including JAG1, and resulting signaling events have been shown to be involved in cell-to-cell communication. In addition, JAGs/Notch signaling influences diverse aspects of cytokine biology, inflammation, dendritic cell biology, T-cell development, B-cell repertoire, and innate immunity [74][75][76][77] . Further, Notch signaling has been suggested to be downstream of IL6, which is a proinflammatory cytokine with a role in the inflammatory storm, in the lung and heart 78 . In the context of viral infection, JAG1/Notch 1 signaling participates in the development of Th2 response in bronchial epithelial cells following infection with respiratory syncytial infection 79 . Interestingly, experimental downregulation of JAG1has been shown to promote Th1 response while suppressing Th2 differentiation, a situation similar to that observed in SARS-CoV-2-infected lung cells in this study 79 . This situation is also somewhat similar to that of SARS-CoV-2-specific CD4 + T cells and is shown to be Th1 type 80 . These observations and the finding in this study that JAG1 could be a vitamin D-regulated gene suggest that a dysregulated vitamin D endocrine system might influence cellular immunity via the JAG1 pathway.
Myristoylated alanine-rich C kinase substrate (MARCKS). MARCKS, a substrate of protein kinase C and actin-interacting protein, is present in the plasma membrane. It modulates vascular contractility and regulates Ca 2+ and phosphatidylinositol 4,5-bisphosphate signaling 81 . Upon activation by PKC signaling, MARCKS translocates from the plasma membrane to the cytoplasm and regulates many cellular processes depending on actin remodeling, such as membrane trafficking and phagocytosis. MARCKS has been shown to be involved in lung diseases, including COPD and asthma 82 , probably because of its ability to regulate mucin secretion and inflammation 83 . Activation of PKC, either directly or through secreted cytokines, is generally viewed a common event during viral infections, including human immunodeficiency virus in promonocytic cells, respiratory syncytial virus in bronchial epithelial cells 84,85 , and hepatitis B virus transactivator HBx 86 . Additionally, Ang II has been shown to activate PKC-β, and in turn, cellular redistribution of MARCKS in neurons 87 . Vitamin D3 metabolites are known activators of PKC, and vitamin D deficiency is associated with a dysregulated subcellular distribution of PKC isoforms in rat colonocytes 88 . The aforementioned observations suggest that a defective vitamin D endocrine system might be associated with a misregulated subcellular distribution of MARCKS in lung cells and could be involved in SARS-CoV-2 pathobiology. In brief, this study provides insights about a potentially causal association between a compromised vitamin D endocrine system at multiple levels and SARS-CoV-2 infections in patients, and consequently, dysregulation of pathways downstream to vitamin D. These preliminary results now set the stage for experimental validation of the observations and postulations made using computational approaches. Additionally, this study also sets the stage for conducting a larger study to determine whether a compromised vitamin D endocrine systemmight influence the susceptibility of lung cells to SARS-CoV-2 and/or the consequence of SARS-CoV-2 infection.

Methods
Gene expression profiling in viral infection models. Relative transcript abundance for individual genes were analyzed using Ominer tool from The Signaling Pathways Project 89,90 . Single gene target was analyszed under transcriptomics category. An FDR cut-off of 5E-02 was applied for the analysis, expression profiles for viral infection models were extracted and represented in the article. www.nature.com/scientificreports/ pital of Wuhan University 32 . Second study reports that BALF cell transcriptome indicates robust innate immune responses in SARS-CoV-2 patients 30 and the remaining studies provided the transcriptomic data of SARS-CoV-2 deceased patients, the data has accessed from Gene Expression Omnibus under the accession GSE147507.

SARS-COV-2 lung cell line transcriptome.
The transcriptome data of primary human lung epithelium (NHBE), transformed lung alveolar (A549), transformed lung-derived Calu-3 cells mock treated or infected with SARS-CoV-2 (USA-WA1/2020), data was accessed from Gene Expression Omnibus under the accession GSE147507 31 . In a multi sampled study, samples were selected only for SARS-COV-2 cell line and differential expression analysis was performed with respect to corresponding control cell line.
PAK silenced transcriptome data. The gene expression profiles of MCF10A.B2 cells (MCF10A cells expressing a chemically activatable form of Her2) stably expressing a Tet inducible shRNA directed against Pak1 gene was accessed from Gene Expression Omnibus under the accession GSE71283 91 . Differentially expressed genes were obtained using GEO2R, an interactive web tool available with Gene Expression Omnibus. GEO2R uses GEOquery and limma R packages from the Bioconductor project to identify differentially expressed genes.
Differential expression analysis and data. Differential expression data available as supplementary data were collected from two studies, The first study 32 called differentially expressed genes using DESeq2 package (v1.26.0) 92 and the second study 30 used the limma package 93 (v3.42.2) from BioconductorDifferential expression analysis was performed using BioJupies 94 for the gene count data provided under the accession GSE147507, BioJupies 94 determines differentially expressed genes using the limma package v3. 42.2(ref). Differentially expressed genes for the cell lines infected with SARS-COV-2 with respect to corresponding control was obtained, and genes were considered for analysis form all the samples if they show a fold-change of at least 1.5 and also satisfy p value < 0.05.

Functional enrichment analysis.
We have performed Gene Enrichment analysis for the 43 genes identified in common with Vitamin D regulated genes and PAK regulated genes using Metascape 37 . Gene symbols are used as input to perform the enrichment and analysis species as Homo Sapiens. An express enrichment analysis was performed for given gene list with default parameters. The analysis involves enrichment for multiple pathways, data sets and COVID. All genes in the genome have been used as the enrichment background. Terms with a p value < 0.01, a minimum count of 3, and an enrichment factor > 1.5. The top-level Gene Ontology biological processes results and Summary of enrichment analysis in COVID were exported.
Protein-protein interaction network and enrichment analysis. Generic protein-protein interactions of gene sets (official gene symbol) were obtained from using IMEx Interactome 95 and default confidence score cutoff (900) and the Corresponding gene cluster was analysed for biological pathway involvement using functional explorer based on Reactome database 96 . Protein-protein interaction network visualization for the set of genes were performed using Network Analyst 3.0 tool 97-99 .