Identification and validation of CDC20 and ITCH as ubiquitination related biomarker in idiopathic pulmonary fibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40170095", "kind": "science-record", "revision": 4, "content_hash": "sha256:a1f9be395bf7ec66b7f70943f8ef217791758c683fabc3da18c49f1c47894eb2", "created_at": "2026-11-01T20:30:21Z", "updated_at": "2026-11-01T22:56:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of CDC20 and ITCH as ubiquitination related biomarker in idiopathic pulmonary fibrosis.", "doi": "10.1186/s41065-025-00401-y", "pmid": "40170095", "authors": ["Shulei Sun", "Yubao Wang", "Jing Feng"], "journal": "Hereditas", "year": 2025, "abstract": "PURPOSE: Ubiquitination plays a crucial role in various diseases. This study aims to explore the potential ubiquitination related genes in IPF.\nMETHODS: The gene microarray dataset GSE24206 was obtained from GEO database. Subsequently, through differential expression analysis and molecular signatures database, we obtained 1734 differentially expressed genes and 742 ubiquitination related genes. Through the venn diagram analysis, we obtained 53 differentially expressed ubiquitination related genes. Then, gene-ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, protein-protein interactions (PPI) and gene set enrichment analysis (GSEA) were applied for the differentially expressed ubiquitination related genes. Finally, the expression of CDC20 and ITCH in IPF patients and cells were validated by qPCR and western blot assay.\nRESULTS: A total of 53 differentially expressed ubiquitination related genes (36 up-regulated genes and 17 down-regulated genes) were identified between 17 IPF patients and 6 healthy controls. GO and KEGG enrichment analysis of ubiquitination related genes mainly involved in regulation of protein ubiquitination, regulation of post-translational protein modification and ubiquitin mediated proteolysis. The PPI results demonstrated that these ubiquitination related genes interacted with each other. The GSEA analysis results for some of the hub genes mainly involved epithelial mesenchymal transition, inflammatory response, hypoxia, and apoptosis. The experiment expression level of CDC20 and ITCH in IPF patients and IPF cells were consistent with the bioinformatics analysis results.\nCONCLUSION: We identified 53 potential ubiquitination related genes of IPF through bioinformatics analysis. CDC20 and ITCH and other ubiquitination related genes may influence the development of IPF through epithelial mesenchymal transition and inflammatory response. Our research findings provide insights into the mechanisms of fibrosis and may provide evidence for potential therapeutic targets for fibrosis.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) between IPF group and control group were analyzed using “limma” in R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40170095", "locator": "sections[4] \"Differentially expressed analysis of ubiquitination related genes\" paragraph 2", "quote": "Differentially expressed genes (DEGs) between IPF group and control group were analyzed using “limma” in R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. 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The datasets GSE24206 for this study can be found here: https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 53 differentially expressed ubiquitination related genes (36 up-regulated genes and 17 down-regulated genes) were identified between 17 IPF patients and 6 healthy controls.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40170095", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 53 differentially expressed ubiquitination related genes (36 up-regulated genes and 17 down-regulated genes) were identified between 17 IPF patients and 6 healthy controls."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 53 differentially expressed ubiquitination related genes (36 up-regulated genes and 17 down-regulated genes) were identified between 17 IPF patients and 6 healthy controls.", "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:40170095"], "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: The gene microarray dataset GSE24206 was obtained from GEO datab"], "order_basis": "paper_text_order:235", "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": ["in IPF patients and cells were validated by qPCR and western blot assay. RESULTS: A total of", "cells (PBMCs). The reverse transcription and qPCR procedures were conducted following the manu", "al reference gene. Primer sequences used for qPCR Statistical analysis The statistics analyses", "ose these two genes for further exploration. qPCR was used to detect the mRNA expression of CD"], "order_basis": "paper_text_order:936", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["atients and cells were validated by qPCR and western blot assay. RESULTS: A total of 53 differentially", "t the mRNA expression of CDC20 and ITCH. (C) Western blot assay was used to detect the protein express"], "order_basis": "paper_text_order:944", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["nsition, inflammatory response, hypoxia, and apoptosis. The experiment expression level of CDC20 an"], "order_basis": "paper_text_order:1604", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) between IPF group and control group were analyzed using “limma” in R software."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}