TNF Signaling Pathway Is the Key Pathway Regulated by Disitamab Vedotin in Bladder Cancer Cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40699768", "kind": "science-record", "revision": 4, "content_hash": "sha256:b65eb0701fbc0a7550ea62d475785d47726fbb6c75b8b1a0fcd114ded2ea2099", "created_at": "2026-11-01T20:30:48Z", "updated_at": "2026-11-01T22:56:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "TNF Signaling Pathway Is the Key Pathway Regulated by Disitamab Vedotin in Bladder Cancer Cells.", "doi": "10.3390/cimb47050369", "pmid": "40699768", "authors": ["Xingxing Tang", "Jia Liu", "Qiang Zhao", "Yudong Cao", "Xiao Yang", "Peng Du", "Yong Yang"], "journal": "Current issues in molecular biology", "year": 2025, "abstract": "Disitamab Vedotin has shown good therapeutic efficacy against bladder cancer. Although its mechanism is clear, the regulation of gene expression in bladder cancer cells by Disitamab Vedotin is not fully understood. We searched the GEO database and identified the GSE237789 dataset, in which researchers treated the bladder cancer cell line SW780 with Disitamab Vedotin and performed high-throughput transcriptome sequencing. Compared with the control SW780 cells, the expression levels of the vast majority of genes (16,223/16,390, 98.98%) in Disitamab Vedotin-treated SW780 cells remained unchanged. Only one hundred fifty-nine genes (0.97%) were upregulated, and eight genes (0.05%) were downregulated. Enrichment analysis results showed that the related differentially expressed genes (DEGs) were mainly enriched in the TNF signaling pathway, NF-κB signaling pathway, and other pathways. Protein-protein interaction analysis revealed that 10 genes, TNF, IL1B, IL1A, CXCL8, CXCL1, CCL2, MMP9, ICAM1, CXCL10, and CCL20, had the highest connectivity, and all of these genes belong to the TNF signaling pathway. These results suggest that the TNF signaling pathway is the key pathway regulated by Disitamab Vedotin in bladder cancer cells, which may represent a stress response of bladder cancer cells to Disitamab Vedotin.", "claims": [{"id": "claim-method", "statement": "We analyzed the DEGs between the RC48 group and the control group in the GSE237789 dataset using R (version 4.4.2) and the limma package (version 3.62.2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40699768", "locator": "sections[4] \"2.2. Identification of Differentially Expressed Genes (DEGs)\" paragraph 2", "quote": "We analyzed the DEGs between the RC48 group and the control group in the GSE237789 dataset using R (version 4.4.2) and the limma package (version 3.62.2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the datasets generated in this study are available on reasonable request to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40699768", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "All the datasets generated in this study are available on reasonable request to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The TNF signaling pathway was identified as the key pathway regulated by Disitamab Vedotin in bladder cancer cells, with 10 hub genes having the highest connectivity in the PPI network.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40699768", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These results suggest that the TNF signaling pathway is the key pathway regulated by Disitamab Vedotin in bladder cancer cells, which may represent a stress response of bladder cancer cells to Disitamab Vedotin."}, {"asset": "source:pmid:40699768", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Protein–protein interaction analysis revealed that 10 genes, TNF, IL1B, IL1A, CXCL8, CXCL1, CCL2, MMP9, ICAM1, CXCL10, and CCL20, had the highest connectivity, and all of these genes belong to the TNF signaling pathway."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The TNF signaling pathway was identified as the key pathway regulated by Disitamab Vedotin in bladder cancer cells, with 10 hub genes having the highest connectivity in the PPI network.", "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:40699768"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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