ORIGINAL RESEARCH article

Front. Cell Dev. Biol., 19 June 2020

Sec. Molecular and Cellular Pathology

Volume 8 - 2020 | https://doi.org/10.3389/fcell.2020.00444

Decoding the Role of Sphingosine-1-Phosphate in Asthma and Other Respiratory System Diseases Using Next Generation Knowledge Discovery Platforms Coupled With Luminex Multiple Analyte Profiling Technology

  • 1. Department of Internal Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

  • 2. Department of Biology, Faculty of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia

  • 3. Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Makkah, Saudi Arabia

  • 4. Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

  • 5. Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

Abstract

Sphingosine-1-phosphate (S1P) is a pleiotropic sphingolipid derived by the phosphorylation of sphingosine either by sphingosine kinase 1 (SPHK1) or SPHK2. Importantly, S1P acts through five different types of G-protein coupled S1P receptors (S1PRs) in immune cells to elicit inflammation and other immunological processes by enhancing the production of various cytokines, chemokines, and growth factors. The airway inflammation in asthma and other respiratory diseases is augmented by the activation of immune cells and the induction of T-helper cell type 2 (Th2)-associated cytokines and chemokines. Therefore, studying the S1P mediated signaling in airway inflammation is crucial to formulate effective treatment and management strategies for asthma and other respiratory diseases. The central aim of this study is to characterize the molecular targets induced through the S1P/S1PR axis and dissect the therapeutic importance of this key axis in asthma, airway inflammation, and other related respiratory diseases. To achieve this, we have adopted both high throughput next-generation knowledge discovery platforms such as SwissTargetPrediction, WebGestalt, Open Targets Platform, and Ingenuity Pathway Analysis (Qiagen, United States) to delineate the molecular targets of S1P and further validated the upstream regulators of S1P signaling using cutting edge multiple analyte profiling (xMAP) technology (Luminex Corporation, United States) to define the importance of S1P signaling in asthma and other respiratory diseases in humans.

Introduction

Sphingosine-1-phosphate (S1P), a sphingolipid, is one of the essential modulators of various cellular processes such as differentiation, survival, growth, etc. (Aarthi et al., 2011). Sphingolipids are recently termed as “morphogenetic lipids” for their crucial role in embryonic stem cell differentiation, survival, and postnatal development (Wang et al., 2018). It was recently demonstrated that S1P plays an important role in allergic anaphylaxis and asthma (Schauberger et al., 2016; Kim, 2019). Asthma is a heterogeneous and complex disease typically characterized by bronchial hyperactivity, remodeling of lung tissues, and chronic bronchial inflammation (Mims, 2015). Importantly, asthma is predisposed by both genetic and environmental factors and the incidence of Asthma has been ever increasing in both children and adults around the globe (Beran et al., 2015; McGeachie et al., 2015). Approximately 1000 people die each day due to Asthma and there were 339.4 million people affected by asthma globally in 2016. This represents a 3.6% increase in age-standardized prevalence since 2006 (Global Asthma Network, 2018; Global Initiative for Asthma, 2018). Asthma affects individuals of all ages and all ethnicity and the economic burden of respiratory diseases to governments, healthcare systems, families, and patients are on the rise globally (Singh, 2005; Ellwood et al., 2017). Hence, creating new applied scientific knowledge in the area of asthma and related respiratory diseases has become a key priority around the globe (Ellwood et al., 2017; Koshak et al., 2017).

S1P is the ligand for G-protein coupled receptors (GPCRs) that belong to the Endothelial Differentiation Gene (EDG) family of proteins termed as S1P receptors (S1PRs) (van Koppen et al., 1996; Hla, 2001; Spiegel and Milstien, 2003; Aarthi et al., 2011). S1P can specifically stimulate distinct genetic events depending on the relative expression of S1PRs as well as downstream G-proteins (An et al., 1998; Aarthi et al., 2011; Manikandan et al., 2012). The intracellular S1P is transported through ATP binding cassette transporter, ABCC1 to the extracellular milieu (Mitra et al., 2006; Nieuwenhuis et al., 2009) and causes the chemotaxis of inflammatory cells that is a pre-requisite for T-lymphocyte exit from primary and secondary lymph organs (Aarthi et al., 2011). It was shown that the S1P/S1PR axis is important for the initiation of various pathophysiological processes that possibly leading to critical diseases such as cancer, inflammatory diseases, and disorders in humans and other higher eukaryotes (Aarthi et al., 2011). Recently, FDA has approved the first oral drug, named Gilenya (FTY720 or Fingolimod), a sphingosine analog for the treatment of relapse in Multiple Sclerosis (MS) (Aarthi et al., 2011). The sphingolipid metabolism was significantly affected in asthma and the S1P levels were increased and correlated with the severity of the disease (Mohammed and Harikumar, 2017; Saluja et al., 2017). The clinical phenotypes of asthma with distinct disease mechanisms are critically influenced by levels of sphingolipid metabolites such as S1P (McGeachie et al., 2015). It was shown that the changes in sphingolipid metabolism and airway hyperresponsiveness were positively correlated in patients suffering from dust mite allergy and the intravascular levels of both sphinganine-1-phosphate (SA1P) and S1P, were significantly associated with the severity of bronchial hyperreactivity (Kowal et al., 2019). The phenotypes of asthma may be distinct based on the levels of sphingolipid metabolites and the change in sphingolipids could represent a pathophysiological variation in bronchial hypersensitivity to allergens in asthmatics (McGeachie et al., 2015).

To address this important problem, we have designed this study to delineate the functions of S1P in the development of asthma and other respiratory diseases. Here, we have utilized both next-generation knowledge discovery platforms such as SwissTargetPrediction, WebGestalt, Open Targets Platform, and Ingenuity Pathway Analysis (Qiagen, United States) to delineate the molecular targets of S1P and validated the upstream regulators of S1P signaling using cutting edge multiple analyte profiling (xMAP) technology (Luminex Corporation, United States) (Bahlas et al., 2019; Pushparaj, 2019; Harakeh et al., 2020; Jafri et al., 2020).

Materials and Methods

SwissTargetPrediction Analysis

The in silico prediction of the molecular targets of S1P was performed using Swiss Target Prediction, a virtual screening web tool (Gfeller et al., 2013). Both canonical and isomeric SMILES of S1P were used as an input sequence as described before (Daina et al., 2019). In the SwissTargetPrediction web tool, the similarity principle is used to predict the targets by reverse screening strategy. In the SwissTargetPrediction web tool, the predictions are performed from analogous molecules in 2D and 3D, from 376342 experimentally active compounds that are significantly interacting with 3068 known macromolecular targets (Daina and Zoete, 2019).

WebGestalt Analysis of S1P Targets

The Over Representation Analysis (ORA) of the molecular targets of S1P derived using Swiss Target Prediction was used in the WebGestalt tool (wGSEA) (Zhang et al., 2005; Wang et al., 2013, 2017; Liao et al., 2019). Using wGSEA gene lists obtained from large scale -omics studies were categorized based on biological, molecular, and cellular functions. wGSEA is a freely available open-source platform1 that enables a more broad, effective, flexible, and interactive functional enrichment study (Liao et al., 2019). The latest version of the wGSEA recognizes 155175 functional categories, 342 gene identifiers, and 12 organisms including many user-defined functional databases (Liao et al., 2019).

To functionally characterize the S1P-induced molecular profile, we analyzed the molecular targets of S1P obtained by Swiss Target Prediction using ORA (Liao et al., 209). Here, the enrichment method was chosen as ORA, the selected organism was Homo sapiens, and gene ontology (Molecular Function, Biological Function, and Cellular Function) was selected for each type of analysis. The reference list for each analysis included all mapped Entrez gene IDs from the selected platform genome. The parameters for the enrichment analysis included the minimum number of IDs in the category (5), the maximum number of IDs in the category (2000), the Benjamini Hochberg (BH) method (P < 0.05) for computing the False Discovery Rate (FDR) (P < 0.05), and the significance Level (Top 10).

Open Targets Platforms Analysis

The Open Targets Platform was used to find the S1P molecular targets associated with respiratory diseases (Koscielny et al., 2017; Carvalho-Silva et al., 2019; Zhang et al., 2019). The evidence from scientific literature, animal models, genomics, transcriptomics, genetics, and drugs are used in the Open Targets Platform to score and rank target-disease associations and aid target prioritization (Carvalho-Silva et al., 2019; Zhang et al., 2019). The query list with 93 molecular targets of S1P was used to find the respiratory diseases significantly (P < 0.05) regulated by the S1P signaling and its associated molecular networks.

Ingenuity Pathway Analysis

Ingenuity pathway analysis (IPA) software has a cutting edge up to date next generation knowledge base consists of clarified scientific information from publications, databases, and other relevant resources (Jafri et al., 2020). Here, we applied the IPA software (Qiagen, United States) to functionally annotate the gene clusters and identified biologically significant pathways regulated by S1P. The molecular target of S1P was subjected to Core Analysis in the IPA to delineate biologically relevant canonical pathways as well as novel molecular signatures, using the right-tailed Fisher Exact Test and Benjamini Hochberg Correction (BHC) for multiple testing (P < 0.05), affecting the respiratory diseases through S1P/SPHK pathway to deduce unique disease-causing gene clusters.

Luminex xMAP Assay for Biomarkers of Asthma

The blood samples were collected from healthy volunteers and asthma patients and both groups were age, and sex-matched. Healthy non-atopic individuals (n = 12) were used as control and the asthma patients (n = 12) were with moderate to severe disease state, non-smokers, and without any other co-morbid conditions such as chronic obstructive pulmonary disease (COPD), other types of pulmonary diseases and disorders, diabetes, cancer, autoimmune diseases, etc. The institutional ethical approval was obtained before collecting the samples and the study was approved by the Scientific Research Committee, Deanship of Scientific Research (DSR), King Abdulaziz University (KAU), Jeddah. The peripheral blood isolated was kept at room temperature for clotting and then centrifuged at 3000 rpm for 10 min for the separation of serum and the aliquots were stored at −80°C till the xMAP assays were done (Bahlas et al., 2019). The evaluation of cytokines and growth factors filtered using the next-generation knowledge discovery platforms was done in both healthy controls and asthma patients using a multi-cytokine/chemokine (30-plex) magnetic-bead based fluorescence assay and the results were obtained based on the standard curves generated using the 30plex standards (16 plex and 14 plex vials) supplied with the xMAP kit (Catalog No: LHC6003M) (Novex, Invitrogen, United States) using MAGPIX multiplex platform as described before (Bahlas et al., 2019; Pushparaj, 2019; Harakeh et al., 2020; Jafri et al., 2020; Pushparaj, 2020). Serum samples were also used to evaluate the concentration of S1P in both healthy controls and asthma patients using a competitive ELISA method as described before (Milara et al., 2012). The absorbance was measured at 450 nm using SpectraMax i3 Multi-Mode Reader with MiniMax Imaging Cytometer (Molecular Devices, United States).

Statistical Analyses

The raw xMAP data was analyzed by the xPONENT analysis software (Version 4.2) (Luminex Corporation, Austin, TX, United States) to determine the absolute concentration of cytokines and growth factors in both healthy control and asthma groups (Bahlas et al., 2019; Harakeh et al., 2020; Jafri et al., 2020). The statistical significance was further computed by using GraphPad Prism Version 8.3 (GraphPad Software, San Diego, CA, United States). P ≤ 0.05 was considered to be statistically significant based on the Student’s t-test (Two Tail). The values were represented as mean ± SD. Furthermore, an F-test to compare the variances and simple correlation analysis of S1P levels against cytokines and chemokines in the serum of asthma patients was also performed using GraphPad Prism (Version 8.3) software.

Results

In silico Prediction of the Molecular Targets of S1P Using SwissTargetPrediction

In the present study, the SwissTargetPrediction was performed for S1P (C18H38NO5P) using both Canonical [CCCCCCCCCCCCCC = CC(C(COP(= O)(O)O)N)O] and Isomeric (CCCCCCCCCCCCC/C = C/[C@H]([C@H](COP(= O) (O)O)N)O) Simplified Molecular Input Line Entry System (SMILES) codes (Supplementary Figure S1) computed by OEChem (Version 2.1.5), have shown that it interacts with 64 and 93 molecules respectively (Tables 1A,B) with the highest percentage of binding (46.7 and 53.3%, respectively) with Family A GPCRs (Figure 1).

TABLE 1A

TargetCommon nameUniprot IDChEMBL IDTarget classProbabilityKnown actives (3D/2D)
Sphingosine 1-phosphate receptor Edg-8S1PR5Q9H228CHEMBL2274Family A G protein-coupled receptor0.84360691442/1
Sphingosine 1-phosphate receptor Edg-6S1PR4O95977CHEMBL3230Family A G protein-coupled receptor0.84360691440/1
Sphingosine 1-phosphate receptor Edg-3S1PR3Q99500CHEMBL3892Family A G protein-coupled receptor0.84360691495/2
Sphingosine 1-phosphate receptor Edg-1S1PR1P21453CHEMBL4333Family A G protein-coupled receptor0.843606914123/2
Sphingosine 1-phosphate receptor Edg-5S1PR2O95136CHEMBL2955Family A G protein-coupled receptor0.78347412910/1
Lysophosphatidic acid receptor Edg-7LPAR3Q9UBY5CHEMBL3250Family A G protein-coupled receptor0.09723998912/10
Farnesyl diphosphate synthaseFDPSP14324CHEMBL1782Transferase011/0
Sphingosine kinase 2SPHK2Q9NRA0CHEMBL3023Enzyme00/2
Sphingosine kinase 1SPHK1Q9NYA1CHEMBL4394Enzyme00/3
Lysophosphatidic acid receptor Edg-2LPAR1Q92633CHEMBL3819Family A G protein-coupled receptor010/5
Squalene synthetase (by homology)FDFT1P37268CHEMBL3338Enzyme01/0
Endothelin-converting enzyme 1ECE1P42892CHEMBL4791Protease06/0
Toll-like receptor (TLR7/TLR9)TLR7Q9NYK1CHEMBL5936Toll-like and Il-1 receptors01/0
Glutathione S-transferase Mu 1GSTM1P09488CHEMBL2081Enzyme01/0
Glutathione S-transferase A1GSTA1P08263CHEMBL3409Enzyme02/0
Glyoxalase IGLO1Q04760CHEMBL2424Enzyme04/0
2′-deoxynucleoside 5′-phosphate N-hydrolase 1DNPH1O43598CHEMBL3351218Hydrolase01/0
Cysteinyl leukotriene receptor 1CYSLTR1Q9Y271CHEMBL1798Family A G protein-coupled receptor01/0
Leukotriene A4 hydrolaseLTA4HP09960CHEMBL4618Protease03/0
GABA transporter 1 (by homology)SLC6A1P30531CHEMBL1903Electrochemical transporter02/0
Serine/threonine-protein kinase PIM1PIM1P11309CHEMBL2147Kinase04/0
Serine/threonine-protein kinase PIM2PIM2Q9P1W9CHEMBL4523Kinase03/0
Serine/threonine-protein kinase PIM3PIM3Q86V86CHEMBL5407Kinase03/0
Tyrosine-protein kinase SRCSRCP12931CHEMBL267Kinase03/0
Folylpoly-gamma-glutamate synthetaseFPGSQ05932CHEMBL3171Enzyme02/0
DNA (cytosine-5)-methyltransferase 3BDNMT3BQ9UBC3CHEMBL6095Reader04/0
Cholesteryl ester transfer proteinCETPP11597CHEMBL3572Other ion channel00/1
Dipeptidyl peptidase ICTSCP53634CHEMBL2252Protease09/0
Tyrosine-protein kinase ZAP-70ZAP70P43403CHEMBL2803Kinase01/0
Histone-lysine N-methyltransferase, H3 lysine-79 specificDOT1LQ8TEK3CHEMBL1795117Writer04/0
Glutathione S-transferase PiGSTP1P09211CHEMBL3902Enzyme01/0
Lysine-specific demethylase 4AKDM4AO75164CHEMBL5896Eraser01/0
Acyl coenzyme A:cholesterol acyltransferase 1SOAT1P35610CHEMBL2782Enzyme03/0
Diacylglycerol O-acyltransferase 1DGAT1O75907CHEMBL6009Enzyme03/0
Cathepsin KCTSKP43235CHEMBL268Protease01/0
Glutamate receptor ionotropic kainate 2GRIK2Q13002CHEMBL3683Ligand-gated ion channel01/0
Lysine-specific demethylase 5AKDM5AP29375CHEMBL2424504Eraser01/0
Dihydrofolate reductaseDHFRP00374CHEMBL202Oxidoreductase02/0
Nitric-oxide synthase, brainNOS1P29475CHEMBL3568Enzyme01/0
Receptor protein-tyrosine kinase erbB-2ERBB2P04626CHEMBL1824Kinase01/0
Adenosine A2a receptorADORA2AP29274CHEMBL251Family A G protein-coupled receptor01/0
Prostanoid EP1 receptorPTGER1P34995CHEMBL1811Family A G protein-coupled receptor01/0
Prostanoid FP receptorPTGFRP43088CHEMBL1987Family A G protein-coupled receptor01/0
Tryptophan 5-hydroxylase 1TPH1P17752CHEMBL5689Enzyme01/0
Protein farnesyltransferaseFNTA FNTBP49354 P49356CHEMBL2094108Enzyme00/10
Glutamate receptor ionotropic kainate 1GRIK1P39086CHEMBL1918Ligand-gated ion channel00/1
Muscarinic acetylcholine receptor M4CHRM4P08173CHEMBL1821Family A G protein-coupled receptor00/1
Glucocorticoid receptorNR3C1P04150CHEMBL2034Nuclear receptor00/1
Muscarinic acetylcholine receptor M5CHRM5P08912CHEMBL2035Family A G protein-coupled receptor00/1
Muscarinic acetylcholine receptor M1CHRM1P11229CHEMBL216Family A G protein-coupled receptor00/1
Histamine H1 receptorHRH1P35367CHEMBL231Family A G protein-coupled receptor00/1
Muscarinic acetylcholine receptor M3CHRM3P20309CHEMBL245Family A G protein-coupled receptor00/1
Serine/threonine-protein kinase AKTAKT1P31749CHEMBL4282Kinase00/1
Geranylgeranyl pyrophosphate synthetaseGGPS1O95749CHEMBL4769Enzyme09/4
Lysophosphatidic acid receptor 6LPAR6P43657CHEMBL2331058Family A G protein-coupled receptor02/1
Lysophosphatidic acid receptor Edg-4LPAR2Q9HBW0CHEMBL3724Family A G protein-coupled receptor03/1
Lysophosphatidic acid receptor 5LPAR5Q9H1C0CHEMBL5700Family A G protein-coupled receptor02/1
Lysophosphatidic acid receptor 4LPAR4Q99677CHEMBL5968Family A G protein-coupled receptor02/1
AutotaxinENPP2Q13822CHEMBL3691Enzyme08/1
Vanilloid receptorTRPV1Q8NER1CHEMBL4794Voltage-gated ion channel01/1
Putative P2Y purinoceptor 10P2RY10O00398CHEMBL3562166Family A G protein-coupled receptor01/15
Probable G-protein coupled receptor 34GPR34Q9UPC5CHEMBL3562165Family A G protein-coupled receptor01/6
Probable G-protein coupled receptor 174GPR174Q9BXC1CHEMBL3562167Family A G protein-coupled receptor01/7

SwissTargePrediction of the molecular targets of S1P (Canonical SMILES) in Homo sapiens.

TABLE 1B

TargetCommon nameUniprot IDChEMBL IDTarget classProbabilityKnown actives (3D/2D)
Sphingosine 1-phosphate receptor Edg-8S1PR5Q9H228CHEMBL2274Family A G protein-coupled receptor148/1
Sphingosine 1-phosphate receptor Edg-5S1PR2O95136CHEMBL2955Family A G protein-coupled receptor110/1
Sphingosine 1-phosphate receptor Edg-6S1PR4O95977CHEMBL3230Family A G protein-coupled receptor142/1
Sphingosine 1-phosphate receptor Edg-3S1PR3Q99500CHEMBL3892Family A G protein-coupled receptor199/2
Sphingosine 1-phosphate receptor Edg-1S1PR1P21453CHEMBL4333Family A G protein-coupled receptor1141/2
Lysophosphatidic acid receptor Edg-7LPAR3Q9UBY5CHEMBL3250Family A G protein-coupled receptor0.0972399894/10
Endothelin-converting enzyme 1ECE1P42892CHEMBL4791Protease07/0
Sphingosine kinase 2SPHK2Q9NRA0CHEMBL3023Enzyme00/2
Sphingosine kinase 1SPHK1Q9NYA1CHEMBL4394Enzyme00/3
Lysophosphatidic acid receptor Edg-2LPAR1Q92633CHEMBL3819Family A G protein-coupled receptor03/5
Farnesyl diphosphate synthaseFDPSP14324CHEMBL1782Transferase011/0
Glyoxalase IGLO1Q04760CHEMBL2424Enzyme06/0
NAD-dependent deacetylase sirtuin 1SIRT1Q96EB6CHEMBL4506Eraser04/0
Cysteinyl leukotriene receptor 1CYSLTR1Q9Y271CHEMBL1798Family A G protein-coupled receptor01/0
Glutathione S-transferase Mu 1GSTM1P09488CHEMBL2081Enzyme02/0
Angiotensin-converting enzymeACEP12821CHEMBL1808Protease07/0
NeprilysinMMEP08473CHEMBL1944Protease08/0
Indoleamine 2,3-dioxygenaseIDO1P14902CHEMBL4685Enzyme03/0
Disks large homolog 4DLG4P78352CHEMBL5666Unclassified protein04/0
DNA (cytosine-5)-methyltransferase 3BDNMT3BQ9UBC3CHEMBL6095Reader04/0
Glutathione S-transferase A1GSTA1P08263CHEMBL3409Enzyme02/0
Carbonic anhydrase IICA2P00918CHEMBL205Lyase022/0
Carbonic anhydrase ICA1P00915CHEMBL261Lyase020/0
Carbonic anhydrase XIICA12O43570CHEMBL3242Lyase06/0
Carbonic anhydrase IXCA9Q16790CHEMBL3594Lyase06/0
Squalene synthetase (by homology)FDFT1P37268CHEMBL3338Enzyme06/0
Thrombin and coagulation factor XF10P00742CHEMBL244Protease03/0
Dipeptidyl peptidase ICTSCP53634CHEMBL2252Protease07/0
Glutamate receptor ionotropic kainate 2GRIK2Q13002CHEMBL3683Ligand-gated ion channel02/0
Serine/threonine-protein kinase PIM1PIM1P11309CHEMBL2147Kinase04/0
Glutathione S-transferase PiGSTP1P09211CHEMBL3902Enzyme03/0
Serine/threonine-protein kinase PIM2PIM2Q9P1W9CHEMBL4523Kinase03/0
Serine/threonine-protein kinase PIM3PIM3Q86V86CHEMBL5407Kinase03/0
Leukotriene A4 hydrolaseLTA4HP09960CHEMBL4618Protease07/0
Cholesteryl ester transfer proteinCETPP11597CHEMBL3572Other ion channel00/1
Caspase-1CASP1P29466CHEMBL4801Protease02/0
Tryptophan 5-hydroxylase 1TPH1P17752CHEMBL5689Enzyme01/0
Histone-lysine N-methyltransferase, H3 lysine-79 specificDOT1LQ8TEK3CHEMBL1795117Writer02/0
Calcium sensing receptorCASRP41180CHEMBL1878Family C G protein-coupled receptor03/0
EZH2/SUZ12/EED/RBBP7/RBBP4EZH2Q15910CHEMBL2189110Writer01/0
2′-deoxynucleoside 5′-phosphate N-hydrolase 1DNPH1O43598CHEMBL3351218Hydrolase02/0
Transmembrane protease serine 11DTMPRSS11DO60235CHEMBL1795138Protease01/0
ThrombinF2P00734CHEMBL204Protease01/0
Glycogen synthase kinase-3 betaGSK3BP49841CHEMBL262Kinase01/0
MatriptaseST14Q9Y5Y6CHEMBL3018Protease01/0
Matrix metalloproteinase 2MMP2P08253CHEMBL333Protease01/0
Matrix metalloproteinase 12MMP12P39900CHEMBL4393Protease01/0
Matrix metalloproteinase 8MMP8P22894CHEMBL4588Protease01/0
Glutamate receptor ionotropic kainate 3GRIK3Q13003CHEMBL3684Ligand-gated ion channel01/0
GABA transporter 1 (by homology)SLC6A1P30531CHEMBL1903Electrochemical transporter02/0
Integrin alpha-V/beta-3ITGAV ITGB3P06756 P05106CHEMBL1907598Membrane receptor01/0
Cathepsin KCTSKP43235CHEMBL268Protease01/0
Tyrosine-protein kinase ZAP-70ZAP70P43403CHEMBL2803Kinase01/0
Caspase-3CASP3P42574CHEMBL2334Protease01/0
Aminopeptidase NANPEPP15144CHEMBL1907Protease01/0
Integrin alpha-5/beta-1ITGB1 ITGA5P05556 P08648CHEMBL2095226Membrane receptor01/0
C3a anaphylatoxin chemotactic receptorC3AR1Q16581CHEMBL4761Family A G protein-coupled receptor01/0
Endoplasmic reticulum aminopeptidase 2ERAP2Q6P179CHEMBL5043Protease01/0
Endoplasmic reticulum aminopeptidase 1ERAP1Q9NZ08CHEMBL5939Protease01/0
Prostanoid EP4 receptor (by homology)PTGER4P35408CHEMBL1836Family A G protein-coupled receptor01/0
Protein farnesyltransferaseFNTA FNTBP49354 P49356CHEMBL2094108Enzyme00/10
Muscarinic acetylcholine receptor M4CHRM4P08173CHEMBL1821Family A G protein-coupled receptor00/1
Glucocorticoid receptorNR3C1P04150CHEMBL2034Nuclear receptor00/1
Muscarinic acetylcholine receptor M5CHRM5P08912CHEMBL2035Family A G protein-coupled receptor00/1
Muscarinic acetylcholine receptor M1CHRM1P11229CHEMBL216Family A G protein-coupled receptor00/1
Histamine H1 receptorHRH1P35367CHEMBL231Family A G protein-coupled receptor00/1
Muscarinic acetylcholine receptor M3CHRM3P20309CHEMBL245Family A G protein-coupled receptor00/1
Serine/threonine-protein kinase AKTAKT1P31749CHEMBL4282Kinase00/1
Geranylgeranyl pyrophosphate synthetaseGGPS1O95749CHEMBL4769Enzyme012/4
Lysophosphatidic acid receptor 6LPAR6P43657CHEMBL2331058Family A G protein-coupled receptor02/1
Lysophosphatidic acid receptor Edg-4LPAR2Q9HBW0CHEMBL3724Family A G protein-coupled receptor03/1
Lysophosphatidic acid receptor 5LPAR5Q9H1C0CHEMBL5700Family A G protein-coupled receptor02/1
Lysophosphatidic acid receptor 4LPAR4Q99677CHEMBL5968Family A G protein-coupled receptor02/1
Putative P2Y purinoceptor 10P2RY10O00398CHEMBL3562166Family A G protein-coupled receptor03/15
Probable G-protein coupled receptor 34GPR34Q9UPC5CHEMBL3562165Family A G protein-coupled receptor03/6
AutotaxinENPP2Q13822CHEMBL3691Enzyme05/1
Vanilloid receptorTRPV1Q8NER1CHEMBL4794Voltage-gated ion channel01/1
Probable G-protein coupled receptor 174GPR174Q9BXC1CHEMBL3562167Family A G protein-coupled receptor02/7
Glutamate receptor ionotropic kainate 1GRIK1P39086CHEMBL1918Ligand-gated ion channel01/1
EnteropeptidaseTMPRSS15P98073CHEMBL1741195Protease02/0
Trypsin IPRSS1P07477CHEMBL209Protease02/0
Vascular endothelial growth factor receptor 2KDRP35968CHEMBL279Kinase01/0
Carbonic anhydrase IVCA4P22748CHEMBL3729Lyase010/0
Thymidylate synthase (by homology)TYMSP04818CHEMBL1952Transferase03/0
Acyl coenzyme A:cholesterol acyltransferase 1SOAT1P35610CHEMBL2782Enzyme04/0
Diacylglycerol O-acyltransferase 1DGAT1O75907CHEMBL6009Enzyme05/0
Metastin receptorKISS1RQ969F8CHEMBL5413Family A G protein-coupled receptor02/0
Dihydrofolate reductaseDHFRP00374CHEMBL202Oxidoreductase01/0
Integrin alpha-IIb/beta-3ITGA2B ITGB3P08514 P05106CHEMBL2093869Membrane receptor01/0
Growth factor receptor-bound protein 2GRB2P62993CHEMBL3663Other cytosolic protein01/0
MAP kinase ERK2 (by homology)MAPK1P28482CHEMBL4040Kinase01/0
MAP kinase p38 alpha (by homology)MAPK14Q16539CHEMBL260Kinase01/0
Folylpoly-gamma-glutamate synthetase (by homology)FPGSQ05932CHEMBL3171Enzyme01/0

SwissTargePrediction of the molecular targets of S1P (Isomeric SMILES) in Homo sapiens.

FIGURE 1

Over Representation Analysis (ORA) of the Molecular Targets of S1P Using WebGestalt

All the 93 molecular targets of S1P obtained using isomeric SMILES were used as input molecules in WebGestalt Open Source Tool to perform the ORA. GO Slim Summary for S1P Molecular Targets in Humans showing Biological Process, Cellular Component, and Molecular Function category in the red, blue, and green bar, respectively. The height of the bar represents the number of IDs in the user list and also in the category (Figure 2). The query list had 93 targets of S1P in which 89 were mapped to 89 unique Entrez gene IDs unambiguously, and the remaining 4 could not be mapped to any Entrez gene ID. Therefore, the GO Slim summary was established upon the 89 distinctive Entrez gene IDs (Figure 2). The reference list was mapped to 61506 Entrez gene IDs and 16671 IDs were annotated to the selected functional categories that were used as the reference for the enrichment analysis. The GO Biological Processes such as sphingolipid mediated signaling pathway, S1P receptor signaling pathway, chemical homeostasis, positive regulation of cytosolic calcium ion concentration, and cellular calcium ion homeostasis, and phospholipase C-activating G protein-coupled receptor signaling pathway were significantly regulated (P < 0.01; Q < 0.01) in ORA (Table 2). The GO Molecular Functions such as the bioactive lipid receptor activity, S1P receptor activity, transmembrane signaling receptor activity, molecular transducer activity, G protein-coupled receptor activity, etc. were significantly regulated (P < 0.01; Q < 0.01) in the ORA (Table 3). The molecules involved in the bioactive receptor activity (GO:0045125) comprise of GPR174, LPAR1, LPAR2, LPAR3, LPAR4, S1PR1, S1PR2, S1PR3, S1PR4, S1PR5, SPHK1, and SPHK2 (Table 4).

FIGURE 2

TABLE 2

Gene setDescriptionSizeExpectRatioP-valueFDR
GO:0003376Sphingosine-1-phosphate receptor signaling pathway100.053402131.081.1546e-141.0497e-10
GO:0090520Sphingolipid mediated signaling pathway110.058742119.163.1530e-141.4332e-10
GO:0007200Phospholipase C-activating G protein-coupled receptor signaling pathway960.5126623.4071.0836e-133.2836e-10
GO:0050801Ion homeostasis7764.14406.03281.6986e-133.8606e-10
GO:0007186G protein-coupled receptor signaling pathway12906.88894.50002.6357e-134.5957e-10
GO:0048878Chemical homeostasis11195.97574.85303.0331e-134.5957e-10
GO:0051482Positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway310.1655548.3253.4222e-124.4444e-9
GO:0007204Positive regulation of cytosolic calcium ion concentration3011.60749.95394.6408e-125.2737e-9
GO:0006874Cellular calcium ion homeostasis4392.34447.67801.4333e-111.4478e-8

The biological processes regulated by the molecular targets of S1P in Homo sapiens.

TABLE 3

Gene setDescriptionSizeExpectRatioP-valueFDR
GO:0045125Bioactive lipid receptor activity140.074741160.5600
GO:0038036Sphingosine-1-phosphate receptor activity80.042709163.907.7716e-167.2936e-13
GO:0004930G protein-coupled receptor activity8064.30296.27485.4401e-153.4037e-12
GO:0038023Signaling receptor activity14297.62894.45681.5210e-147.1373e-12
GO:0004888Transmembrane signaling receptor activity12116.46514.79504.7962e-141.5594e-11
GO:0060089Molecular transducer activity14887.94394.28004.9849e-141.5594e-11
GO:0004175Endopeptidase activity4362.32767.73321.2733e-113.4142e-9
GO:0070011Peptidase activity, acting on L-amino acid peptides6103.25666.14155.0832e-111.1927e-8
GO:0008233Peptidase activity6343.38475.90901.0096e-102.1055e-8
GO:0008236Serine-type peptidase activity2041.089111.0198.4807e-101.5918e-7

The molecular processes regulated by the molecular targets of S1P in Homo sapiens.

TABLE 4

Gene symbolGene NameEntrez Gene ID
GPR174G protein-coupled receptor 17484636
LPAR1Lysophosphatidic acid receptor 11902
LPAR2Lysophosphatidic acid receptor 29170
LPAR3Lysophosphatidic acid receptor 323566
LPAR4Lysophosphatidic acid receptor 42846
S1PR1Sphingosine-1-phosphate receptor 11901
S1PR2Sphingosine-1-phosphate receptor 29294
S1PR3Sphingosine-1-phosphate receptor 31903
S1PR4Sphingosine-1-phosphate receptor 48698
S1PR5Sphingosine-1-phosphate receptor 553637
SPHK1Sphingosine kinase 18877
SPHK2sphingosine kinase 256848

The genes involved in the bioactive receptor activity (GO:0045125) regulated by S1P in Homo sapiens.

Identification of S1P-Induced Molecular Targets in Asthma and Other Respiratory Diseases

Then, we used the Open Targets Platform to find the S1P molecular targets associated with respiratory diseases. Our findings showed that about 109 types of respiratory diseases were significantly (P < 0.05) affected by the molecular targets of S1P. The top 15 respiratory diseases significantly (P < 0.01; Q < 0.01) induced by S1P and its molecular targets were lung disease, respiratory system disease, respiratory system neoplasm, bronchial disease, lung carcinoma, asthma, interstitial lung disease, COPD, Rare genetic respiratory disease, idiopathic pulmonary fibrosis, pulmonary fibrosis, acute lung injury, pneumonia, whooping cough, and non-small cell lung adenocarcinoma (Table 5).

TABLE 5

Disease full nameRelevance (p-value)Number of associated targetsTherapeutic areaHighest associated targets (max 10)
Lung disease6.00E-4282Respiratory system diseaseKDR TYMS CHRM3 MMP8 NR3C1 CHRM1 AKT1 CA4 ACE MMP2…
Respiratory system disease2.00E-3984Respiratory system diseaseKDR TYMS CHRM3 MMP8 HRH1 NR3C1 CHRM1 AKT1 CA4 MMP2…
Respiratory system neoplasm2.00E-3877Neoplasm, respiratory system diseaseKDR TYMS NR3C1 AKT1 MMP2 DHFR FDPS GRB2 MMP8 MMP12…
Bronchial disease2.00E-3858Respiratory system diseaseNR3C1 CYSLTR1 HRH1 CHRM1 CHRM3 DHFR GSTM1 MAPK14 CASP1 S1PR2…
Lung carcinoma5.00E-3878Neoplasm, respiratory system diseaseKDR TYMS NR3C1 AKT1 MMP2 DHFR FDPS GRB2 MMP12 IDO1…
Asthma1.00E-3555Respiratory system diseaseNR3C1 CYSLTR1 HRH1 CHRM3 CHRM1 DHFR GSTM1 MAPK14 CASP1 S1PR2…
Interstitial lung disease3.00E-3243Respiratory system diseaseNR3C1 KDR MMP8 CTSK EZH2 SOAT1 CYSLTR1 SIRT1 CASP3 MMP12…
Chronic obstructive pulmonary disease8.00E-3248Respiratory system diseaseCHRM3 MMP8 ACE NR3C1 CA1 CHRM1 CA12 CA4 CA2 MMP12…
Rare genetic respiratory disease3.00E-3144Genetic disorder, respiratory system diseaseMMP8 FDPS NR3C1 CHRM3 SIRT1 PRSS1 EZH2 CTSK HRH1 KISS1R…
Idiopathic pulmonary fibrosis2.00E-2939Neoplasm, respiratory system diseaseNR3C1 KDR MMP8 CTSK EZH2 SOAT1 CASP3 MMP2 ANPEP TYMS…
Pulmonary fibrosis7.00E-2937Neoplasm, respiratory system diseaseNR3C1 KDR MMP8 CTSK EZH2 SOAT1 CASP3 MMP12 ANPEP MMP2…
Acute lung injury9.00E-2832Respiratory system diseaseMAPK14 MMP8 MMP2 GSK3B IDO1 S1PR1 SIRT1 CASP1 CASP3 SOAT1…
Pneumonia2.00E-2737Infectious disease, respiratory system diseaseMMP8 NR3C1 CHRM3 CHRM1 MMP12 ACE DHFR SOAT1 F2 MMP2…
Whooping cough3.00E-2732Infectious disease, respiratory system diseaseCASP1 CASP3 AKT1 CA1 S1PR4 S1PR1 MAPK1 HRH1 MMP2 TRPV1…
Non-small cell lung adenocarcinoma3.00E-2642Neoplasm, respiratory system diseaseSIRT1 EZH2 CASR GSK3B TYMS MMP2 IDO1 KDR CASP3 CA9…

Top 15 respiratory diseases associated with the molecular targets of S1P.

Ingenuity Pathway Analysis of the Differentially Regulated Gene Networks by S1P/S1PR Axis in Respiratory Diseases

Next, we utilized the IPA to deduce the canonical pathways, upstream regulators, causal functions, diseases, and bio functions, and non-directional unique networks significantly impacted by the S1P mediated signaling molecules. The IPA core analysis of the molecular targets of S1P revealed that the canonical pathways such as eNOS signaling, S1P signaling, GPCRs signaling, ceramide signaling, G a12/13 signaling, human embryonic stem cell pluripotency, and endocannabinoid cancer inhibition pathway (Figure 3) were potentially regulated (P < 0.05). About 263 molecules play a significant role (P < 0.05) as upstream regulators of the molecular targets of S1P (Supplementary Table S1). Furthermore, we have filtered the upstream regulators based on the molecule types such as cytokines, and growth factors using the IPA. The cytokines such as Interleukin-13 (IL-13), Interferon-gamma (IFN-γ), IFN-β1, Tumor Necrosis Factor-alpha (TNF-α), Interleukin-4 (IL-4), Interleukin-5 (IL-5), Interleukin-1 (IL-1β), Interleukin-21 (IL-21), Tissue Inhibitor of Metalloproteinases-1 (TIMP-1) that has cytokine-like activity, and cytokine-inducing Corticotropin-Releasing Hormone (CRH) were found to be the upstream regulators of the S1P signaling. The growth factors such as Hepatocyte Growth Factor (HGF), Vascular Endothelial Growth Factors (VEGF), Colony Stimulating Factor 1 (CSF1) or Macrophage Colony-Stimulating Factor (M-CSF), Colony Stimulating Factor-2 (CSF2) or Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF), VEGF-A, VEGF-B, VEGF-D, Fibroblast Growth Factor 16 (FGF16), Insulin-like Growth Factor (IGF), and Transforming Growth Factor-beta 1 (TGF-β1) were identified as the upstream regulators of S1P signaling (Table 6).

FIGURE 3

TABLE 6

Upstream regulatorMolecule typep-value of overlapTarget molecules in dataset
HGFGrowth factor0.000000328AKT1, CA9, CTSK, MAPK14, MMP2, MMP8, ST14
IL13Cytokine0.0000174C3AR1, CASP1, CTSC, CYSLTR1, ENPP2, LTA4H, ST14
IFNGCytokine0.000145ACE, CASP1, CASP3, ERAP2, IDO1, MMP2, PIM1, SOAT1
IFNB1Cytokine0.000528CASP1, CASP3, IDO1
VEGFAGrowth factor0.000775KDR, MMP12, MMP2
TNFCytokine0.00118CTSC, GSTA1, IDO1, MMP12, MMP2, MMP8, NR3C1, SOAT1
IL4Cytokine0.00132CYSLTR1, IDO1, PIM1, ST14
VEGFBGrowth factor0.0044MMP12
CSF1Growth factor0.00767CTSK, MMP12
LIFCytokine0.0131ERAP1
CSF2Growth factor0.0133CASP3, CTSC, PIM1
CRHCytokine0.0175TPH1
FGF16Growth factor0.0175MMP2
VEGFDGrowth factor0.0175MMP12
TGFB1Growth factor0.0195KDR, MAPK1, MMP12, MMP2, SPHK1
IL5Cytokine0.0197CTSC, PIM1
IL1BCytokine0.0236GSTA1, KDR, MMP12, MMP8
IL21Cytokine0.0296IDO1, MMP2
TIMP1Cytokine0.0389MME
IGF2Growth factor0.0389MMP12

Upstream regulators of the S1P molecular targets – Focus on cytokines and growth Factors.

Validation of Biomarkers in Asthma Using Luminex xMAP Technology

Besides, we have used the Luminex xMAP assay to validate the cytokines and growth factors that were upstream of the S1P signaling in asthma. Here, we have analyzed the levels of cytokines such as IL-13, IFN-γ, TNF-α, IL-4, IL-5, and IL-1β (Figure 4) and growth factors such as HGF, VEGF, and CSF2 or GM-CSF along with the estimation of serum S1P concentration in asthma patients compared with the healthy controls (Figure 5). The clinical and laboratory characteristics of asthma patients and healthy controls were given in Table 7. The upstream regulator cytokines of S1P signaling such as IL-13, IFN-γ, TNF-α, IL-4, IL-5, and IL-1β were significantly (P < 0.01) increased in the serum of asthma patients compared the healthy controls. Similarly, the growth factors that were found to be upstream of S1P signaling such as HGF, VEGF, and CSF2 were significantly (P < 0.01) increased in the serum of asthma patients compared to the healthy controls. The S1P levels were significantly increased in the serum of asthma patients compared to the healthy controls. All the cytokines and growth factors analyzed by the Luminex xMAP assay were positively correlated with the S1P levels in the serum of asthmatics (Supplementary Table S2).

FIGURE 4

FIGURE 5

TABLE 7

Clinical ParametersHealthy (n = 12)Asthma (n = 12)
Age (Years)34 (23 – 48)33 (22 – 45)
Disease Duration (Years)NA8.5 (5 – 10)
Serum IgE (IU/L)22 (14 – 65)365 (79 – 621)
WBC Count (109/L)6.75 (5.2 – 7.3)7.1 (5.7 – 8.1)
Eosinophils (percentage)0.14 (0.11 – 0.19)5.5 (3 – 10)
FEV1(Liter)NA2.3 (1.9 – 2.9)

Clinical and laboratory parameters in healthy control and asthma patients.

NA, either data not available or not applicable. The table shows data as medians with the range indicated in the parentheses.

Discussion

In the present study, to decode the biological and molecular functions of bioactive lipid molecule, S1P in the development of asthma and other respiratory diseases, we have applied both next-generation knowledge discovery platforms such as SwissTargetPrediction, WebGestalt, Open Targets Platform, and IPA and validated the key upstream regulators of S1P signaling using Luminex xMAP technology. Currently, knowledge discovery and big data analytical platforms are swiftly transforming the Biomedical Research landscape (Cirillo and Valencia, 2019; Paczkowska et al., 2020). All the chemical or biochemical compounds with pharmacological or pathological actions influencing diagnosis, treatment, or recuperation, and prevention of a disease can be used in next-generation knowledge discovery platforms using a unique SMILES code (Weininger, 1988; Ratnawati et al., 2018). SMILES, postulated by David Weininger, is a chemical annotation method that symbolizes a simple molecule structure (Weininger, 1988; Ratnawati et al., 2018). Here, we have used the isomeric SMILES of S1P to deduce its downstream molecular targets using the SwissTargetPrediction server (Gfeller et al., 2013; Daina and Zoete, 2019; Daina et al., 2019).

Several studies have shown that S1P augments airway hyperactivity, bronchoconstriction, and airway remodeling in asthma and other related respiratory diseases (Roviezzo et al., 2010; Petrache and Berdyshev, 2016; Liu et al., 2018) and the S1P receptors are differentially expressed in the lymphoid tissues, dendritic cells, and the lung (Aarthi et al., 2011). S1P is an effective biologically active paracrine mediator that regulates various cellular functions such as apoptosis, cell growth, cell proliferation, immune regulation, etc. (Le Stunff et al., 2004; Aarthi et al., 2011). Here, we have further identified that biological processes such as S1PR signaling pathway, sphingolipid mediated signaling pathway, chemical homeostasis, positive regulation of cytosolic calcium ion concentration, and cellular calcium ion homeostasis were regulated by S1P. Importantly, the interaction of S1P with the five types of S1PRs and four types of LPARs on the plasma membrane triggers an intracellular cascade of reactions leading to the biosynthesis of various pro-inflammatory mediators that contribute to the pathogenicity in asthma. Also, the S1P regulates various molecular functions that are essential for the pathogenesis of asthma and respiratory diseases such as the bioactive lipid receptor activity, S1P receptor activity, G protein-coupled receptor activity, signaling receptor activity, transmembrane signaling receptor activity, molecular transducer activity, endopeptidase activity, peptidase activity acting on L-amino acid peptides, peptidase activity, and serine-type peptidase activity. We found that the S1P signaling was associated with more than 100 types of respiratory diseases such as lung disease, respiratory system disease, respiratory system neoplasm, bronchial disease, lung carcinoma, asthma, interstitial lung disease, COPD, rare genetic respiratory disease, idiopathic pulmonary fibrosis, pulmonary fibrosis, acute lung injury, pneumonia, whooping cough, non-small cell lung adenocarcinoma, etc., Besides, the S1P levels were found to be increased in the bronchoalveolar lavage fluids of allergic asthma patients and were also positively associated with augmented airway inflammation (Ammit et al., 2001; Kim, 2019). Altered sphingolipid metabolism according to the phenotype and genotype of asthma was deduced using metabolic studies in asthma patients (McGeachie et al., 2015; Kim, 2019). Similarly, the sphingolipid metabolism was found to be disturbed in aspirin-exacerbated respiratory disease (AERD), a serious type of adult-onset eosinophilic asthma (Trinh et al., 2016; Reinke et al., 2017).

In the present study, we have found several upstream regulators of S1P signaling including various cytokines such as IL-13, IFN-γ, IFN-β1, TNF-α, IL-4, IL-5, IL-1β, IL-21, TIMP-1, and CRH, and growth factors such as HGF, VEGF, CSF1, CSF2, VEGF-A, VEGF-B, VEGF-D, FGF16, IGF, and TGFβ1. Using multiplex xMAP technology, we have further validated that the levels of the upstream cytokines of S1P signaling such as IL-13, IFN-γ, TNF-α, IL-4, IL-5, and IL-1β were increased in the serum of asthma patients. Similarly, the growth factors such as HGF, VEGF, and CSF2 were increased in the serum of asthmatic patients. To further decode the association of the upstream cytokines and growth factors with S1P, we have estimated the S1P concentration in the serum of asthmatics. The levels of cytokines and growth factors analyzed using xMAP technology positively correlated with the S1P levels in the serum of asthmatics which further vouch for the significance of S1P signaling in the pathogenicity of asthma.

Asthma is a chronic disease and the incidence is ever-increasing around the globe (Al-Moamary et al., 2019). Most of the asthmatics have disease exacerbation caused by the Th2 type of immune cells compared to other types such as T-helper type 1 (Th1) and T-helper type 17 (Th17) and other immune cells such as mast cells, eosinophils, and bronchial smooth muscles, myofibroblasts and epithelial cells (Manikandan et al., 2012). The Th2 associated cytokines play a vital role in the development of allergy and airway remodeling in asthma (Komai-Koma et al., 2012). The asthmatics studied here had more eosinophils in their blood and the levels of Th2 serum cytokines such as IL-4, IL-5, and IL-13 were increased compared to the healthy controls. Here, most of the cytokines and growth factors examined were associated positively with an increase in the serum S1P. The sphingosine kinases regulate the expression of Th2, Th1, Th17, chemokines, and an array of other pro-inflammatory factors by catalyzing the conversion of sphingosine into S1P (Nayak et al., 2010; Aarthi et al., 2011). Many asthmatics have an uncontrolled disease state even though they are under a treatment regimen which could be due to the increased production of S1P (Aarthi et al., 2011) and a recent study found that ceramide/S1P rheostat was indeed dysregulated in uncontrolled asthma (Kim et al., 2020). Hence, it is prudent that the ceramide/S1P production may be targeted in controlling the airway inflammation in asthma (Kim et al., 2020). Importantly, the in silico results obtained using our next generation knowledge discovery pipeline coupled with xMAP assay also showed a potential association of S1P in asthma and other respiratory diseases which is detrimental for the patients due to its ability to trigger an array of cytokines, chemokines, and growth factors. More importantly, an increase in the upstream regulator Th2 cytokines such as IL-4, IL-5, and IL-13 is potentially harmful to asthmatics and play an underlying role in the disease pathogenesis. Similarly, the growth factors such as VEGF, CSF2, and HGF were found to be increased in asthmatics and may also be responsible for making the disease chronically worse. A recent study showed that the inhibition of S1P receptors potentially augments the inhibition of VEGF (Fischl et al., 2019). The S1P/S1PR signaling was regulated through the activation of SPHK1 and SPHK 2 to produce S1P by the phosphorylation of sphingosine (Nayak et al., 2010; Aarthi et al., 2011) and the airway hyperresponsiveness and inflammation was potentially reduced by SPHK inhibitors and FTY720, a synthetic analog of S1P and S1PR agonist (Aarthi et al., 2011) and other S1PR modulators (Marciniak et al., 2018), in animal models of allergic asthma (Sawicka et al., 2003; Idzko et al., 2006; Price et al., 2013).

We conclude that the S1P and its associated signaling molecules, either upstream or downstream, are pharmacological targets of great significance for the development of novel drugs for asthma and other related respiratory diseases in humans. However, one of the critical limitations of this study is the less number of samples used for the validation of biomarkers in the serum associated with S1P signaling in asthma. In future, we will be collecting more samples from patients suffering from atopic and non-atopic asthma and other respiratory diseases and disorders with varying severity that undergo different treatment regimens, for further validation of upstream regulator molecules associated with S1P signaling along with the key cytokines, chemokines, and growth factors that play a crucial role in the pathogenesis of an array of respiratory diseases and disorders.

Statements

Data availability statement

The datasets generated for this study are available on request to the corresponding author.

Ethics statement

The studies involving human participants were reviewed and approved by our institutional ethical committee, and the study was accepted by the Scientific Research Committee, Deanship of Scientific Research (DSR), King Abdulaziz University (KAU), Jeddah. The patients/participants provided their written informed consent to participate in this study.

Author contributions

All authors designed and conducted the experiments, analyzed the data, wrote the manuscript, and contributed to the editing of the manuscript and the scientific discussions. SB, LD, and PP proposed the research idea.

Funding

This work was approved and funded by the Deanship of Scientific Research (DSR), the King Abdulaziz University, Jeddah, the Kingdom of Saudi Arabia (KSA) through Grant Number G-608-140-37.

Acknowledgments

We acknowledge with thanks the Deanship of Scientific Research (DSR), King Abdulaziz University, for their excellent technical support.

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The handling editor declared a past co-authorship with one of the authors PP.

Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fcell.2020.00444/full#supplementary-material

FIGURE S1

The flow diagram illustrates the essential steps in the in silico experiments using next-generation knowledge discovery platforms to uncover the molecular targets of S1P and their association with various respiratory diseases and disorders and the subsequent validation of disease-specific biomarkers and their relationship with S1P in Asthma.

TABLE S1

The list of 263 upstream regulators identified based on the IPA core analysis of the molecular targets of S1P.

TABLE S2

Simple linear regression analysis of S1P with upstream regulatory cytokines and growth factors in asthma patients.

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Summary

Keywords

asthma, respiratory diseases, sphingosine-1-phosphate, SwissTargetPrediction, WebGestalt, open targets platform, ingenuity pathway analysis, Luminex xMAP technology

Citation

Bahlas S, Damiati LA, Al-Hazmi AS and Pushparaj PN (2020) Decoding the Role of Sphingosine-1-Phosphate in Asthma and Other Respiratory System Diseases Using Next Generation Knowledge Discovery Platforms Coupled With Luminex Multiple Analyte Profiling Technology. Front. Cell Dev. Biol. 8:444. doi: 10.3389/fcell.2020.00444

Received

12 February 2020

Accepted

12 May 2020

Published

19 June 2020

Volume

8 - 2020

Edited by

Ahmed Rebai, Centre of Biotechnology of Sfax, Tunisia

Reviewed by

Shafiq Ur Rehman, Gyeongsang National University, South Korea; Ikram Ullah, International Islamic University, Islamabad, Pakistan

Updates

Copyright

*Correspondence: Sami Bahlas,

This article was submitted to Molecular Medicine, a section of the journal Frontiers in Cell and Developmental Biology

Disclaimer

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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