Characteristic genes and immune landscape of interstitial cystitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40435311", "kind": "science-record", "revision": 2, "content_hash": "sha256:d721119de94a311d30624fcf7846ce5212d68857375bb1a74f5a85e3ff8f6fcd", "created_at": "2026-11-01T20:30:34Z", "updated_at": "2026-11-01T21:35:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characteristic genes and immune landscape of interstitial cystitis.", "doi": "10.1371/journal.pone.0320249", "pmid": "40435311", "authors": ["Junhao Wang", "Yan Zhou", "Jie Hu", "Jianpeng Han", "Jianyong Feng", "Kuo Guo", "Wenbin Chen", "Yanrui Yun", "Yongzhang Li"], "journal": "PloS one", "year": 2025, "abstract": "BACKGROUND: Interstitial cystitis (IC) was still a disease with the exclusive diagnosis and lacked an effective gold standard. It was of great significance to find diagnostic markers for IC. Our study was aimed to screen characteristic genes via machine learning algorithms, characterize the immune landscape of IC, and show correlations between characteristic genes and immune cell subtypes.\nMETHODS: RNA sequencing data sets on IC were downloaded from Gene Expression Omnibus (GEO) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. Three machine learning algorithms were applied for identification of characteristic gene for IC. Single sample Gene Set Enrichment Analysis (ssGSEA) was applied to figure out the immune cell infiltration (ICI) of IC and normal tissue samples. Correlation analysis was performed via Spearman test. Receiver operator characteristic curve (ROC) was used to evaluate diagnostic efficacy of key genes.\nRESULTS: CCL18, MMP10 and WIF1 were identified as characteristic gene via machine learning algorithms. MMP10 and CCL18 were with higher expression in IC tissues compared with normal bladder tissues, while WIF1 had lower expressionin IC tissues (P < 0.05). These three genes had good diagnostic efficacy for IC. Compared with normal bladder tissues, 18 immune cell subtypes were up-regulated in interstitial cystitis tissues (P < 0.05). MMP10 and CCL18 were positively correlated to immune scores in IC, while WIF1 was negatively correlated to immune scores (P > 0.05).\nCONCLUSION: We screened the feature genes, CCL18, MMP10 and WIF1, among the differentially expressed genes (DEGs) by three different machine learning algorithms. They showed good diagnostic performance in both training and testing cohorts and were potential diagnostic markers for IC. We paint the immune landscape of IC. In IC tissue, immune cell subtypes infiltrated extensively. Most immune cell subtypes were up-regulated in IC tissue, including mast cells, activated CD4 T cells, and regulatory T cells that suppress immune responses. MMP10 and CCL18 had positive correlation to ICI, while WIF was negatively correlated with ICI. MMP10 and CCL18 may be the driving factors of immune response or their expression levels may be increased by immune response. The effect of characteristic genes of IC on immune cell subtypes still needed to be further explored.", "claims": [{"id": "claim-method", "statement": "Receiver operator characteristic curve (ROC) was conducted to evaluate diagnostic efficacy of key genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40435311", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Receiver operator characteristic curve (ROC) was conducted to evaluate diagnostic efficacy of key genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40435311", "locator": "sections[3] \"Data sets download\" paragraph 2", "quote": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In the training cohort, MMP10 (AUC = 0.938, 95 CI%(0.796, 1.000), p < 0.05), CCL18 (AUC = 0.944, 95 CI%(0.840, 1.000), p < 0.05), WIF1 (AUC = 0.883, 95 CI%(0.728, 0.981), p < 0.05) had good diagnostic efficacy for IC (Fig 4G-4I).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "In the training cohort, MMP10 (AUC = 0.938, 95 CI%(0.796, 1.000), p < 0.05), CCL18 (AUC = 0.944, 95 CI%(0.840, 1.000), p < 0.05), WIF1 (AUC = 0.883, 95 CI%(0.728, 0.981), p < 0.05) had good diagnostic efficacy for IC (Fig 4G-4I)."}, "evidence": [{"asset": "source:pmid:40435311", "locator": "sections[11] \"Expression level and diagnostic efficacy of key genes in training cohort and test cohort\" paragraph 2", "quote": "In the training cohort, MMP10 (AUC = 0.938, 95 CI%(0.796, 1.000), p < 0.05), CCL18 (AUC = 0.944, 95 CI%(0.840, 1.000), p < 0.05), WIF1 (AUC = 0.883, 95 CI%(0.728, 0.981), p < 0.05) had good diagnostic efficacy for IC (Fig 4G-4I)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In the training cohort, MMP10 (AUC = 0.938, 95 CI%(0.796, 1.000), p < 0.05), CCL18 (AUC = 0.944, 95 CI%(0.840, 1.000), p < 0.05), WIF1 (AUC = 0.883, 95 CI%(0.728, 0.981), p < 0.05) had good diagnostic efficacy for IC (Fig 4G-4I).", "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:40435311"], "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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METHODS: RNA sequencing data sets on IC were downloaded from Gene Ex"], "order_basis": "paper_text_order:425", "id": "assay:1"}]}