Bioinformatics Approach for Identifying Novel Biomarkers and Their Signaling Pathways Involved in Interstitial Cystitis/Bladder Pain Syndrome with Hunner Lesion.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32575815", "kind": "science-record", "revision": 8, "content_hash": "sha256:894a352733c20c95810283bc97b28521bf39222b6bdde4c6b50de39f050d7689", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T22:01:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Approach for Identifying Novel Biomarkers and Their Signaling Pathways Involved in Interstitial Cystitis/Bladder Pain Syndrome with Hunner Lesion.", "doi": "10.3390/jcm9061935", "pmid": "32575815", "authors": ["Subbroto Kumar Saha", "Tak-Il Jeon", "Soo Bin Jang", "Se Jong Kim", "Kyung Min Lim", "Yu Jin Choi", "Hyeong Gon Kim", "Aram Kim", "Ssang-Goo Cho"], "journal": "Journal of clinical medicine", "year": 2020, "abstract": "The complexity of interstitial cystitis/bladder pain syndrome (IC/BPS) has led to considerable uncertainty in terms of diagnosis and prevalence of the condition. Here, we try to identify the IC/BPS-associated genes through an integrated analysis of Gene Expression Omnibus (GEO) datasets and confirm experimentally to predict the pathologic diagnosis of IC/BPS. Data mining analysis of GEO datasets (GSE621, GSE11783, GSE28242, and GSE57560) revealed a total of 53 (51 upregulated and two downregulated) common differentially expressed genes (DEGs) in IC/BPS. A protein-protein interaction (PPI) network was then constructed with the 53 common DEGs using Cytoscape v3.7.2, and subsequently, six hub genes (CD5, CD38, ITGAL, IL7R, KLRB1, and IL7R) were identified using cytoHubba v0.1 that were upregulated in IC/BPS. Enrichment analysis of common DEGs revealed that hematopoietic cell lineage, immune system, and T-cell receptor (TCR) signaling in naïve CD4+ T cell signaling pathways were prominently involved with the common 51 upregulated DEGs. The two common downregulated DEGs may enrich linoleic acid metabolism and synthesis of epoxy (EET) and dihydroxyeicosatrienoic acid (DHET) signaling pathways in IC/BPS. Moreover, our RT-PCR data confirmed that the expression of the five hub genes (CD38, ITGAL, IL7R, KLRB1, and IL7R) was significantly augmented in IC/BPS patients' samples when compared with their normal counterparts. In this study, we systematically predict the significant biomarkers and possible signaling pathways involved in IC/BPS, confirming the differential expression of the hub genes in tissue samples from patients with IC/BPS. Thus, the hub genes might be used as potential diagnostic biomarkers of IC/BPS.", "claims": [{"id": "claim-method", "statement": "These results were compared between the IC/BPS and normal group, and statistical significance was calculated using a two-tailed unpaired t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32575815", "locator": "sections[9] \"2.7. Statistical Analysis\" paragraph 2", "quote": "These results were compared between the IC/BPS and normal group, and statistical significance was calculated using a two-tailed unpaired t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset GSE621 contained human cDNA gene array analysis of cell lines treated with/without antiproliferative factor (APF) (n = 16), IC/BPS (n = 6), and normal (n = 6) tissue samples using GPL262 platform. In our study, we included DEGs only from IC/BPS vs. normal tissue samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32575815", "locator": "sections[3] \"2.1. Identification of Differentially Expressed Genes (DEGs) from Gene Expression Omnibus (GEO) Datasets of IC/BPS\" paragraph 2", "quote": "The dataset GSE621 contained human cDNA gene array analysis of cell lines treated with/without antiproliferative factor (APF) (n = 16), IC/BPS (n = 6), and normal (n = 6) tissue samples using GPL262 platform. In our study, we included DEGs only from IC/BPS vs. normal tissue samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32575815"], "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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Thus, the hub genes might be used as", "ient Symptom/Bother score (PUF). We enrolled patients with >13 points on the PUF, >24 points on the IC-", "1. The bladder tissue samples obtained from patients were immediately processed for examination. After", "or Hunner lesions were performed. The IC/BPS patient-derived specimens (IC/BPS 1–7) were obtained from Hu"], "order_basis": "paper_text_order:1750", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nd IC/BPS patients are shown in Table 3. Our RT-qPCR data showed that all six hub genes were upre", "IC/BPS patients are shown in Table 3. Our RT-qPCR data showed that all six hub genes were upre"], "order_basis": "paper_text_order:12007", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}