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pmid:41511918

Mechanisms of cellular senescence combined with molecular docking strategies: A biomarker study of potential therapeutic targets for allergic rhinitis.

Qingyong Chen · Han Zhang · Yue Wu · Jixin Liu · Dongqing Wang · Dezhong Sun · Zhipeng Chen · Liqiang Lin · Huaiqing Lv · Qiang Shao

PloS one · 2026 doi:10.1371/journal.pone.0338309

Paper

complete

Experiment

complete

Data

partial

Analysis

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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title
Mechanisms of cellular senescence combined with molecular docking strategies: A biomarker study of potential therapeutic targets for allergic rhinitis.
doi
10.1371/journal.pone.0338309
pmid
41511918
authors array · 10 items
[0]
Qingyong Chen
[1]
Han Zhang
[2]
Yue Wu
[3]
Jixin Liu
[4]
Dongqing Wang
[5]
Dezhong Sun
[6]
Zhipeng Chen
[7]
Liqiang Lin
[8]
Huaiqing Lv
[9]
Qiang Shao
journal
PloS one
year
2026
abstract
OBJECTIVE: Bioinformatics and molecular docking methods were used to screen potential biomarkers of cellular senescence in allergic rhinitis (Allergic rhinitis AR), which provided a theoretical basis for revealing the mechanism of AR and exploring new therapeutic approaches. METHODS: Four AR-related gene chips (GSE19187, GSE43523, GSE44037, and GSE51392) were downloaded from the gene expression database (GEO) for data pooling. Screening differential genes (DEGs) were taken to intersect with cellular senescence-related genes (SRGs) to obtain differential senescence genes (DESRGs). The differential senescence genes were subjected to Gene Ontology Database (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and GSEA enrichment analysis. Protein-protein interaction (PPI) networks were constructed through the STRING database, MCODE plugin weights were analyzed to identify important gene cluster modules, and Hub genes were screened using the CytoHubba plugin topological network algorithm. Hub gene protein interactions network (GeneMANIA) was constructed by the GeneMANIA database. Predict Hub gene construct mRNA-miNA-lncRNA interactions by miRanda, miRDB, miRWalk, TargetScan, and spongeScan databases; construct Hub gene transcription factor regulatory networks by TRRUST database; analyze Hub gene-drug interactions by DGIdb database and select commonly used drugs in the clinic for molecular docking validation. RESULTS: A total of 264 differential genes were screened in the training set with corrected P.adj < 0.05 and |log2FC| ≥ 1.2 as the filtering condition, and a total of 866 cellular senescence genes, and 20 differential senescence genes (DESRGs) were obtained by taking the intersection of the two. A total of 19 Hub genes were obtained after PPI analysis, which were CCL2, STAT1, TLR2, IGFBP3, TLR3, KLF4, IL1RN, IRF1, SERPINB2, DPP4, MME, NQO1, SAMHD1, XAF1, PHGDH, EIF4EBP1, CTH, HSPA2, AHR The gene-protein interaction network identified 19 Hub genes associated with 21 functional proteins. 5 of the Hub gene loci were associated with 29 miRNAs and 53 lncRNAs. The transcription factor regulatory network obtained 15 transcription factors capable of regulating Hub genes. The analysis of drug-gene interactions identified 489 drugs that target hub genes. For example, in the case of budesonide, the interacting genes STAT1, TLR2, TLR3, and AHR were selected for molecular docking. Similarly, for mometasone, the interacting genes TLR2 and CTH were chosen for molecular docking. CONCLUSION: Mining AR-related Hub senescence genes by bioinformatics analysis, constructing PPI network, ceRNA network, transcription factor regulatory network, gene-drug interaction network and molecular docking validation, we screened 19 CCL2, STAT1, TLR2, IGFBP3, TLR3, KLF4, IL1RN, IRF1, SERPINB2, DPP4, MME, NQO1, SAMHD1, XAF1, PHGDH, EIF4EBP1, CTH, HSPA2, and AHR are expected to be Hub genes for potential diagnostic and therapeutic biomarkers, which will provide targets and new insights for further in-depth explorations of AR cellular senescence-related mechanisms of action and therapy.
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Differential expression analysis was performed on the combined dataset using the R package “limma, dplyr, pheatmap, ggplot2”, and differential genes (DEGs) were screened with the filtering conditions of corrected P.adj < 0.05 and |log2FC| ≥ 1.2.
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sections[5] "2.2.1 Screening for differential senescence genes." paragraph 2
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Differential expression analysis was performed on the combined dataset using the R package “limma, dplyr, pheatmap, ggplot2”, and differential genes (DEGs) were screened with the filtering conditions of corrected P.adj < 0.05 and |log2FC| ≥ 1.2.
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The transcriptome data analyzed in this study are publicly available from the NCBI GEO database (https://www.ncbi.nlm.nih.govgeo/) under accession numbers GSE19187, GSE43523, GSE44037, and GSE51392. Gene set enrichment analysis (GSEA) was performed using the c2.cp.kegg.Hs.symbols.gmt gene set from MSigDB (http://www.gsea-msigdb.orggseaindex.jsp). Protein–protein interaction (PPI) networks were constructed using the STRING database (https://cn.string-db.org/), and hub gene PPI networks were generated via the GeneMANIA database (http://genemania.org/). Transcription factor regulatory networks were obtained from the 2nd edition of the TRRUST database (https://www.grnpedia.orgtrrust/). Drug–hub gene interactions were predicted using the DGIdb database (https://dgidb.org/), and key chemical structures of clinically used AR treatment drugs were retrieved from PubChem (https://pubchem.ncbi.nlm.nih.gov/). Three-dimensional structures of core hub gene target proteins with drug enrichment were downloaded from the PDB database (https://www.rcsb.org/), and molecular docking was performed using the online tool CB-Dock2 (https://cadd.labshare.cncb-dock2). For further inquiries, please contact the corresponding author.
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sections[28] "Data Availability" paragraph 2
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The transcriptome data analyzed in this study are publicly available from the NCBI GEO database (https://www.ncbi.nlm.nih.govgeo/) under accession numbers GSE19187, GSE43523, GSE44037, and GSE51392. Gene set enrichment analysis (GSEA) was performed using the c2.cp.kegg.Hs.symbols.gmt gene set from MSigDB (http://www.gsea-msigdb.orggseaindex.jsp). Protein–protein interaction (PPI) networks were constructed using the STRING database (https://cn.string-db.org/), and hub gene PPI networks were generated via the GeneMANIA database (http://genemania.org/). Transcription factor regulatory networks were obtained from the 2nd edition of the TRRUST database (https://www.grnpedia.orgtrrust/). Drug–hub gene interactions were predicted using the DGIdb database (https://dgidb.org/), and key chemical structures of clinically used AR treatment drugs were retrieved from PubChem (https://pubchem.ncbi.nlm.nih.gov/). Three-dimensional structures of core hub gene target proteins with drug enrichment were downloaded from the PDB database (https://www.rcsb.org/), and molecular docking was performed using the online tool CB-Dock2 (https://cadd.labshare.cncb-dock2). For further inquiries, please contact the corresponding author.
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The analysis identified 19 overlapping hub genes associated with cellular senescence in allergic rhinitis.
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sections[19] "3.4 PPI network, key modules, and Hub gene screening results" paragraph 2
quote
through the CytoHubba plugin’s will ClusteringCoefficient, Stress, Betweenness, Radiality, Closeness, EcCentricity, BottleNeck, Degree, MNC, DMNC, and MCC calculated by a total of 11 algorithms to identify the extracted intersecting genes as Hub genes, and finally identified 19 overlapping Hub genes (CCL2, STAT1, TLR2, IGFBP3, TLR3, KLF4, IL1RN, IRF1, SERPINB2, DPP4, MME, NQO1, SAMHD1, XAF1, PHGDH, EIF4EBP1, CTH, HSPA2, AHR) as shown in Fig 7c.
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The analysis identified 19 overlapping hub genes associated with cellular senescence in allergic rhinitis.
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title
Expression data from airway epithelial cells stimulated with Poly(I:C) from patients with asthma, rhinitis, and healthy controls
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Differential expression analysis was performed on the combined dataset using the R package “limma, dplyr, pheatmap, ggplot2”, and differential genes (DEGs) were screened with the filtering conditions of corrected P.adj < 0.05 and |log2FC| ≥ 1.2.
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The transcriptome data analyzed in this study are publicly available from the NCBI GEO database (https://www.ncbi.nlm.nih.govgeo/) under accession numbers GSE19187, GSE43523, GSE44037, and GSE51392. Gene set enrichment analysis (GSEA) was performed using the c2.cp.kegg.Hs.symbols.gmt gene set from MSigDB (http://www.gsea-msigdb.orggseaindex.jsp). Protein–protein interaction (PPI) networks were constructed using the STRING database (https://cn.string-db.org/), and hub gene PPI networks were generated via the GeneMANIA database (http://genemania.org/). Transcription factor regulatory networks were obtained from the 2nd edition of the TRRUST database (https://www.grnpedia.orgtrrust/). Drug–hub gene interactions were predicted using the DGIdb database (https://dgidb.org/), and key chemical structures of clinically used AR treatment drugs were retrieved from PubChem (https://pubchem.ncbi.nlm.nih.gov/). Three-dimensional structures of core hub gene target proteins with drug enrichment were downloaded from the PDB database (https://www.rcsb.org/), and molecular docking was performed using the online tool CB-Dock2 (https://cadd.labshare.cncb-dock2). For further inquiries, please contact the corresponding author.
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Differential expression analysis was performed on the combined dataset using the R package “limma, dplyr, pheatmap, ggplot2”, and differential genes (DEGs) were screened with the filtering conditions of corrected P.adj < 0.05 and |log2FC| ≥ 1.2.
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{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41511918", "kind": "science-record", "revision": 4, "content_hash": "sha256:053934e1eed801623c484321c1362f3e31c35a998aaafd40f3271b11cbbceda5", "created_at": "2026-11-01T20:31:29Z", "updated_at": "2026-11-01T22:57:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Mechanisms of cellular senescence combined with molecular docking strategies: A biomarker study of potential therapeutic targets for allergic rhinitis.", "doi": "10.1371/journal.pone.0338309", "pmid": "41511918", "authors": ["Qingyong Chen", "Han Zhang", "Yue Wu", "Jixin Liu", "Dongqing Wang", "Dezhong Sun", "Zhipeng Chen", "Liqiang Lin", "Huaiqing Lv", "Qiang Shao"], "journal": "PloS one", "year": 2026, "abstract": "OBJECTIVE: Bioinformatics and molecular docking methods were used to screen potential biomarkers of cellular senescence in allergic rhinitis (Allergic rhinitis AR), which provided a theoretical basis for revealing the mechanism of AR and exploring new therapeutic approaches.\nMETHODS: Four AR-related gene chips (GSE19187, GSE43523, GSE44037, and GSE51392) were downloaded from the gene expression database (GEO) for data pooling. Screening differential genes (DEGs) were taken to intersect with cellular senescence-related genes (SRGs) to obtain differential senescence genes (DESRGs). The differential senescence genes were subjected to Gene Ontology Database (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and GSEA enrichment analysis. Protein-protein interaction (PPI) networks were constructed through the STRING database, MCODE plugin weights were analyzed to identify important gene cluster modules, and Hub genes were screened using the CytoHubba plugin topological network algorithm. Hub gene protein interactions network (GeneMANIA) was constructed by the GeneMANIA database. Predict Hub gene construct mRNA-miNA-lncRNA interactions by miRanda, miRDB, miRWalk, TargetScan, and spongeScan databases; construct Hub gene transcription factor regulatory networks by TRRUST database; analyze Hub gene-drug interactions by DGIdb database and select commonly used drugs in the clinic for molecular docking validation.\nRESULTS: A total of 264 differential genes were screened in the training set with corrected P.adj < 0.05 and |log2FC| ≥ 1.2 as the filtering condition, and a total of 866 cellular senescence genes, and 20 differential senescence genes (DESRGs) were obtained by taking the intersection of the two. A total of 19 Hub genes were obtained after PPI analysis, which were CCL2, STAT1, TLR2, IGFBP3, TLR3, KLF4, IL1RN, IRF1, SERPINB2, DPP4, MME, NQO1, SAMHD1, XAF1, PHGDH, EIF4EBP1, CTH, HSPA2, AHR The gene-protein interaction network identified 19 Hub genes associated with 21 functional proteins. 5 of the Hub gene loci were associated with 29 miRNAs and 53 lncRNAs. The transcription factor regulatory network obtained 15 transcription factors capable of regulating Hub genes. The analysis of drug-gene interactions identified 489 drugs that target hub genes. For example, in the case of budesonide, the interacting genes STAT1, TLR2, TLR3, and AHR were selected for molecular docking. Similarly, for mometasone, the interacting genes TLR2 and CTH were chosen for molecular docking.\nCONCLUSION: Mining AR-related Hub senescence genes by bioinformatics analysis, constructing PPI network, ceRNA network, transcription factor regulatory network, gene-drug interaction network and molecular docking validation, we screened 19 CCL2, STAT1, TLR2, IGFBP3, TLR3, KLF4, IL1RN, IRF1, SERPINB2, DPP4, MME, NQO1, SAMHD1, XAF1, PHGDH, EIF4EBP1, CTH, HSPA2, and AHR are expected to be Hub genes for potential diagnostic and therapeutic biomarkers, which will provide targets and new insights for further in-depth explorations of AR cellular senescence-related mechanisms of action and therapy.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed on the combined dataset using the R package “limma, dplyr, pheatmap, ggplot2”, and differential genes (DEGs) were screened with the filtering conditions of corrected P.adj < 0.05 and |log2FC| ≥ 1.2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41511918", "locator": "sections[5] \"2.2.1 Screening for differential senescence genes.\" paragraph 2", "quote": "Differential expression analysis was performed on the combined dataset using the R package “limma, dplyr, pheatmap, ggplot2”, and differential genes (DEGs) were screened with the filtering conditions of corrected P.adj < 0.05 and |log2FC| ≥ 1.2."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The transcriptome data analyzed in this study are publicly available from the NCBI GEO database (https://www.ncbi.nlm.nih.govgeo/) under accession numbers GSE19187, GSE43523, GSE44037, and GSE51392. Gene set enrichment analysis (GSEA) was performed using the c2.cp.kegg.Hs.symbols.gmt gene set from MSigDB (http://www.gsea-msigdb.orggseaindex.jsp). Protein–protein interaction (PPI) networks were constructed using the STRING database (https://cn.string-db.org/), and hub gene PPI networks were generated via the GeneMANIA database (http://genemania.org/). Transcription factor regulatory networks were obtained from the 2nd edition of the TRRUST database (https://www.grnpedia.orgtrrust/). Drug–hub gene interactions were predicted using the DGIdb database (https://dgidb.org/), and key chemical structures of clinically used AR treatment drugs were retrieved from PubChem (https://pubchem.ncbi.nlm.nih.gov/). Three-dimensional structures of core hub gene target proteins with drug enrichment were downloaded from the PDB database (https://www.rcsb.org/), and molecular docking was performed using the online tool CB-Dock2 (https://cadd.labshare.cncb-dock2). For further inquiries, please contact the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41511918", "locator": "sections[28] \"Data Availability\" paragraph 2", "quote": "The transcriptome data analyzed in this study are publicly available from the NCBI GEO database (https://www.ncbi.nlm.nih.govgeo/) under accession numbers GSE19187, GSE43523, GSE44037, and GSE51392. Gene set enrichment analysis (GSEA) was performed using the c2.cp.kegg.Hs.symbols.gmt gene set from MSigDB (http://www.gsea-msigdb.orggseaindex.jsp). Protein–protein interaction (PPI) networks were constructed using the STRING database (https://cn.string-db.org/), and hub gene PPI networks were generated via the GeneMANIA database (http://genemania.org/). Transcription factor regulatory networks were obtained from the 2nd edition of the TRRUST database (https://www.grnpedia.orgtrrust/). Drug–hub gene interactions were predicted using the DGIdb database (https://dgidb.org/), and key chemical structures of clinically used AR treatment drugs were retrieved from PubChem (https://pubchem.ncbi.nlm.nih.gov/). Three-dimensional structures of core hub gene target proteins with drug enrichment were downloaded from the PDB database (https://www.rcsb.org/), and molecular docking was performed using the online tool CB-Dock2 (https://cadd.labshare.cncb-dock2). For further inquiries, please contact the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 19 overlapping hub genes associated with cellular senescence in allergic rhinitis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41511918", "locator": "sections[19] \"3.4 PPI network, key modules, and Hub gene screening results\" paragraph 2", "quote": "through the CytoHubba plugin’s will ClusteringCoefficient, Stress, Betweenness, Radiality, Closeness, EcCentricity, BottleNeck, Degree, MNC, DMNC, and MCC calculated by a total of 11 algorithms to identify the extracted intersecting genes as Hub genes, and finally identified 19 overlapping Hub genes (CCL2, STAT1, TLR2, IGFBP3, TLR3, KLF4, IL1RN, IRF1, SERPINB2, DPP4, MME, NQO1, SAMHD1, XAF1, PHGDH, EIF4EBP1, CTH, HSPA2, AHR) as shown in Fig 7c."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 19 overlapping hub genes associated with cellular senescence in allergic rhinitis.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41511918"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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Gene set enrichment analysis (GSEA) was performed using the c2.cp.kegg.Hs.symbols.gmt gene set from MSigDB (http://www.gsea-msigdb.orggseaindex.jsp). Protein–protein interaction (PPI) networks were constructed using the STRING database (https://cn.string-db.org/), and hub gene PPI networks were generated via the GeneMANIA database (http://genemania.org/). Transcription factor regulatory networks were obtained from the 2nd edition of the TRRUST database (https://www.grnpedia.orgtrrust/). Drug–hub gene interactions were predicted using the DGIdb database (https://dgidb.org/), and key chemical structures of clinically used AR treatment drugs were retrieved from PubChem (https://pubchem.ncbi.nlm.nih.gov/). Three-dimensional structures of core hub gene target proteins with drug enrichment were downloaded from the PDB database (https://www.rcsb.org/), and molecular docking was performed using the online tool CB-Dock2 (https://cadd.labshare.cncb-dock2). 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