{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:13:34Z","timestamp":1785420814336,"version":"3.56.0"},"reference-count":54,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T00:00:00Z","timestamp":1776816000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Science and Technology Council","award":["NSTC 114-2218-E-007-005"],"award-info":[{"award-number":["NSTC 114-2218-E-007-005"]}]},{"award":["NSTC 114-2218-E-007-005"],"award-info":[{"award-number":["NSTC 114-2218-E-007-005"]}],"id":[{"id":"https:\/\/ror.org\/02kv4zf79","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Asthma is a chronic respiratory disease characterized by airway hyperresponsiveness, obstruction, and persistent inflammation, arising from complex interactions among genetic, epigenetic, immune, and environmental factors. To elucidate the stage-specific molecular mechanisms underlying asthma progression, we constructed candidate genome-wide genetic and epigenetic networks (GWGENs) of human cells through large-scale biological database mining. Using a system order detection scheme, false-positive interactions were pruned to identify real GWGENs corresponding to three clinical stages of asthma: quiet, exacerbation, and follow-up. Core GWGENs were subsequently extracted from each real network using the principal network projection (PNP) method to highlight dominant regulatory structures and pathogenic pathways. Based on the inferred core networks, key stage-specific biomarkers were identified and further explored as potential drug targets. Drug\u2013target relationships were investigated by integrating gene expression perturbation profiles from the Connectivity Map (cMap), comprising microarray data for 14,207 genes across 1327 compounds. This network-guided analysis enabled the qualitative design of multi-molecule drug combinations tailored to each disease stage. Our results suggest that asthma onset is associated with reduced innate immunity, increased disease susceptibility, and impaired endothelial barrier recovery influenced by microenvironmental factors such as cigarette smoke and lipopolysaccharides, together with genetic and epigenetic alterations. During the exacerbation stage, enhanced differentiation of T cells toward the T helper 2 lineage contributes to airway inflammation and tissue injury. In the follow-up stage, T helper 1\u2013mediated responses are linked to mucus hypersecretion, airway obstruction, and sustained inflammation. Collectively, these findings demonstrate that a systems-level, network-based framework can uncover stage-specific pathogenic mechanisms of asthma and provide hypothesis-generating insights for network-informed drug repurposing strategies.<\/jats:p>","DOI":"10.3390\/ijms27093708","type":"journal-article","created":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T09:01:24Z","timestamp":1776848484000},"page":"3708","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Stage-Specific Reconstruction of Genome-Wide Genetic and Epigenetic Regulatory Networks Reveals Mechanistic Insights into Asthma Progression"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5883-4812","authenticated-orcid":false,"given":"Cheng-Wei","family":"Li","sequence":"first","affiliation":[{"name":"Department of Electrical Engineering, Chang Gung University, No. 259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui-En","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1644-6106","authenticated-orcid":false,"given":"Bor-Sen","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40733-016-0029-3","article-title":"Asthma costs and social impact","volume":"3","author":"Nunes","year":"2017","journal-title":"Asthma Res. Pract."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/1710-1492-10-27","article-title":"Epigenetic regulation of asthma and allergic disease","volume":"10","author":"Begin","year":"2014","journal-title":"Allergy Asthma Clin. Immunol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"4638949","DOI":"10.1155\/2016\/4638949","article-title":"Epigenetics: The New Frontier in the Landscape of Asthma","volume":"2016","author":"Chogtu","year":"2016","journal-title":"Scientifica"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1161\/CIRCULATIONAHA.110.956839","article-title":"Epigenetic modifications: Basic mechanisms and role in cardiovascular disease","volume":"123","author":"Handy","year":"2011","journal-title":"Circulation"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Maltby, S., Plank, M., Tay, H.L., Collison, A., and Foster, P.S. (2016). Targeting MicroRNA Function in Respiratory Diseases: Mini-Review. Front. Physiol., 7.","DOI":"10.3389\/fphys.2016.00021"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Aghaieabiane, N., and Koutis, I. (2021). A Novel Calibration Step in Gene Co-Expression Network Construction. Front. Bioinform., 1.","DOI":"10.3389\/fbinf.2021.704817"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Margolin, A.A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Dalla Favera, R., and Califano, A. (2006). ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform., 7.","DOI":"10.1186\/1471-2105-7-S1-S7"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"bbaf470","DOI":"10.1093\/bib\/bbaf470","article-title":"Machine learning methods for gene regulatory network inference","volume":"26","author":"Hegde","year":"2025","journal-title":"Brief. Bioinform."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/S0303-2647(98)00017-3","article-title":"Computation with the KEGG pathway database","volume":"47","author":"Ogata","year":"1998","journal-title":"Biosystems"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Lim, D.W., Choi, M.S., and Kim, S.M. (2023). Bioinformatics and Connectivity Map Analysis Suggest Viral Infection as a Critical Causative Factor of Hashimoto\u2019s Thyroiditis. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24021157"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Tessier, L., Cote, O., Clark, M.E., Viel, L., Diaz-Mendez, A., Anders, S., and Bienzle, D. (2017). Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma. BMC Genom., 18.","DOI":"10.1186\/s12864-017-4107-6"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1177\/1534735409352027","article-title":"Nr1d1, an important circadian pathway regulatory gene, is suppressed by cigarette smoke in murine lungs","volume":"8","author":"Vasu","year":"2009","journal-title":"Integr. Cancer Ther."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1016\/j.molonc.2012.11.003","article-title":"FLT3 signals via the adapter protein Grb10 and overexpression of Grb10 leads to aberrant cell proliferation in acute myeloid leukemia","volume":"7","author":"Kazi","year":"2013","journal-title":"Mol. Oncol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"24922","DOI":"10.1074\/jbc.M116.756791","article-title":"The TORC1-activated Proteins, p70S6K and GRB10, Regulate IL-4 Signaling and M2 Macrophage Polarization by Modulating Phosphorylation of Insulin Receptor Substrate-2","volume":"291","author":"Warren","year":"2016","journal-title":"J. Biol. Chem."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Afroz, S., Giddaluru, J., Vishwakarma, S., Naz, S., Khan, A.A., and Khan, N. (2017). A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. Front. Immunol., 8.","DOI":"10.3389\/fimmu.2017.00074"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1164\/rccm.200409-1223OC","article-title":"Positional identification of an asthma susceptibility gene on human chromosome 5q33","volume":"172","author":"Noguchi","year":"2005","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"801","DOI":"10.4049\/jimmunol.1402358","article-title":"Cutting Edge: Synchronization of IRF1, JunB, and C\/EBPbeta Activities during TLR3-TLR7 Cross-Talk Orchestrates Timely Cytokine Synergy in the Proinflammatory Response","volume":"195","author":"Liu","year":"2015","journal-title":"J. Immunol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1073\/pnas.0806383106","article-title":"MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium","volume":"106","author":"Schembri","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1016\/0091-6749(80)90123-2","article-title":"Alternation in both insulin release and its hypoglycemic effects in atopic bronchial asthma","volume":"66","author":"Szczeklik","year":"1980","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.jaci.2011.11.008","article-title":"Genetic and epigenetic influence on the response to environmental particulate matter","volume":"129","author":"Ji","year":"2012","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Gahring, L.C., Myers, E.J., Dunn, D.M., Weiss, R.B., and Rogers, S.W. (2017). Nicotinic alpha 7 receptor expression and modulation of the lung epithelial response to lipopolysaccharide. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0175367"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1016\/j.ajhg.2011.03.003","article-title":"Tobacco-smoking-related differential DNA methylation: 27K discovery and replication","volume":"88","author":"Breitling","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e198","DOI":"10.1038\/emm.2015.91","article-title":"The Wnt\/beta-catenin signaling pathway regulates the development of airway remodeling in patients with asthma","volume":"47","author":"Kwak","year":"2015","journal-title":"Exp. Mol. Med."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1002\/ajmg.b.31031","article-title":"The effect of smoking on MAOA promoter methylation in DNA prepared from lymphoblasts and whole blood","volume":"153B","author":"Philibert","year":"2010","journal-title":"Am. J. Med. Genet. Part B Neuropsychiatr. Genet."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Pejanovic, N., Hochrainer, K., Liu, T., Aerne, B.L., Soares, M.P., and Anrather, J. (2012). Regulation of nuclear factor kappaB (NF-kappaB) transcriptional activity via p65 acetylation by the chaperonin containing TCP1 (CCT). PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0042020"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1016\/j.jaci.2010.08.040","article-title":"Human basophils express amphiregulin in response to T cell-derived IL-3","volume":"126","author":"Qi","year":"2010","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1172\/JCI8204","article-title":"Th2 cells and GATA-3 in asthma: New insights into the regulation of airway inflammation","volume":"104","author":"Ray","year":"1999","journal-title":"J. Clin. Investig."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Shi, Y., Xu, X., Tan, Y., Mao, S., Fang, S., and Gu, W. (2014). A Liver-X-Receptor Ligand, T0901317, Attenuates IgE Production and Airway Remodeling in Chronic Asthma Model of Mice. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0092668"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Moustakas, A., and Heldin, C.-H. (2016). Mechanisms of TGF\u03b2-Induced Epithelial\u2013Mesenchymal Transition. J. Clin. Med., 5.","DOI":"10.3390\/jcm5070063"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1002\/mc.22802","article-title":"Nickel exposure induces persistent mesenchymal phenotype in human lung epithelial cells through epigenetic activation of ZEB1","volume":"57","author":"Jose","year":"2018","journal-title":"Mol. Carcinog."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Karpurapu, M., Ranjan, R., Deng, J., Chung, S., Lee, Y.G., Xiao, L., Nirujogi, T.S., Jacobson, J.R., Park, G.Y., and Christman, J.W. (2014). Kruppel like factor 4 promoter undergoes active demethylation during monocyte\/macrophage differentiation. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0093362"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.it.2016.12.002","article-title":"Negative Regulation of Type 2 Immunity","volume":"38","author":"Ghosh","year":"2017","journal-title":"Trends Immunol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.3892\/ijo.2017.3876","article-title":"miR-21 and KLF4 jointly augment epithelialmesenchymal transition via the Akt\/ERK1\/2 pathway","volume":"50","author":"Liu","year":"2017","journal-title":"Int. J. Oncol."},{"key":"ref_34","first-page":"3014","article-title":"Exploring of the molecular mechanism of rhinitis via bioinformatics methods","volume":"17","author":"Song","year":"2018","journal-title":"Mol. Med. Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1002\/gepi.21675","article-title":"Genome-wide association analysis of imputed rare variants: Application to seven common complex diseases","volume":"36","author":"Magi","year":"2012","journal-title":"Genet. Epidemiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.ebiom.2017.03.033","article-title":"A Comprehensive Evaluation of Nasal and Bronchial Cytokines and Chemokines Following Experimental Rhinovirus Infection in Allergic Asthma: Increased Interferons (IFN-gamma and IFN-lambda) and Type 2 Inflammation (IL-5 and IL-13)","volume":"19","author":"Hansel","year":"2017","journal-title":"EBioMedicine"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2304","DOI":"10.1038\/jid.2010.128","article-title":"Eotaxins and CCR3 interaction regulates the Th2 environment of cutaneous T-cell lymphoma","volume":"130","author":"Miyagaki","year":"2010","journal-title":"J. Investig. Dermatol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1038\/mi.2015.94","article-title":"A CCL24-dependent pathway augments eosinophilic airway inflammation in house dust mite-challenged Cd163(-\/-) mice","volume":"9","author":"Dai","year":"2016","journal-title":"Mucosal Immunol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1038\/ni1362","article-title":"Detection of pathogenic intestinal bacteria by Toll-like receptor 5 on intestinal CD11c+ lamina propria cells","volume":"7","author":"Uematsu","year":"2006","journal-title":"Nat. Immunol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Wright, W.R., Parzych, K., Crawford, D., Mein, C., Mitchell, J.A., and Paul-Clark, M.J. (2012). Inflammatory Transcriptome Profiling of Human Monocytes Exposed Acutely to Cigarette Smoke. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0030120"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"4924","DOI":"10.4049\/jimmunol.1401362","article-title":"CCL7 and IRF-7 Mediate Hallmark Inflammatory and IFN Responses following Rhinovirus 1B Infection","volume":"194","author":"Girkin","year":"2015","journal-title":"J. Immunol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/bjh.13317","article-title":"Haematopoietic and immune defects associated with GATA2 mutation","volume":"169","author":"Collin","year":"2015","journal-title":"Br. J. Haematol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/j.clim.2010.01.003","article-title":"Monocytes differentiated with IL-15 support Th17 and Th1 responses to wheat gliadin: Implications for celiac disease","volume":"135","author":"Harris","year":"2010","journal-title":"Clin. Immunol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"33","DOI":"10.4049\/jimmunol.1200470","article-title":"TRAF4 restricts IL-17-mediated pathology and signaling processes","volume":"189","author":"Zepp","year":"2012","journal-title":"J. Immunol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.3390\/biom5031266","article-title":"NF-kappaB Signaling in Chronic Inflammatory Airway Disease","volume":"5","author":"Schuliga","year":"2015","journal-title":"Biomolecules"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Baud, V., and Collares, D. (2016). Post-Translational Modifications of RelB NF-kappaB Subunit and Associated Functions. Cells, 5.","DOI":"10.3390\/cells5020022"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1038\/onc.2016.309","article-title":"Non-canonical NFkappaB mutations reinforce pro-survival TNF response in multiple myeloma through an autoregulatory RelB:p50 NFkappaB pathway","volume":"36","author":"Roy","year":"2017","journal-title":"Oncogene"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/s12974-016-0528-4","article-title":"Systemic pro-inflammatory response facilitates the development of cerebral edema during short hypoxia","volume":"13","author":"Song","year":"2016","journal-title":"J. Neuroinflamm."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1164\/rccm.201011-1882OC","article-title":"Early alveolar epithelial dysfunction promotes lung inflammation in a mouse model of Hermansky-Pudlak syndrome","volume":"184","author":"Bates","year":"2011","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"29752","DOI":"10.1074\/jbc.M300489200","article-title":"Suppressor of cytokine signaling 3 regulates proliferation and activation of T-helper cells","volume":"278","author":"Yu","year":"2003","journal-title":"J. Biol. Chem."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"48270","DOI":"10.1074\/jbc.M207986200","article-title":"Transcriptional activation of the MUC2 gene by p53","volume":"277","author":"Ookawa","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"L348","DOI":"10.1152\/ajplung.00099.2015","article-title":"IFN-\u03b3-induced JAK\/STAT, but not NF-\u03baB, signaling pathway is insensitive to glucocorticoid in airway epithelial cells","volume":"309","author":"Bouazza","year":"2015","journal-title":"Am. J. Physiol.-Lung Cell. Mol. Physiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"635","DOI":"10.3390\/cells2040635","article-title":"Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering","volume":"2","author":"Chen","year":"2013","journal-title":"Cells"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1126\/science.1132939","article-title":"The Connectivity Map: Using gene-expression signatures to connect small molecules, genes, and disease","volume":"313","author":"Lamb","year":"2006","journal-title":"Science"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/9\/3708\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T04:36:58Z","timestamp":1777005418000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/9\/3708"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,22]]},"references-count":54,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["ijms27093708"],"URL":"https:\/\/doi.org\/10.3390\/ijms27093708","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,22]]}}}