Identification of cuproptosis-related genes in chronic apical periodontitis based on bulk and single-cell RNA sequencing analyses and experimental validation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40909264", "kind": "science-record", "revision": 3, "content_hash": "sha256:a59d879154ec8f1b5e9002b27f8f996135ccd95647940c52cbee75df4c8677ab", "created_at": "2026-11-01T20:31:01Z", "updated_at": "2026-11-01T22:14:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of cuproptosis-related genes in chronic apical periodontitis based on bulk and single-cell RNA sequencing analyses and experimental validation.", "doi": "10.3389/fimmu.2025.1559220", "pmid": "40909264", "authors": ["Caiyi Zhang", "Jie Zhao", "Keqing Pan", "Lingshuang Liu", "Mengyu Jiao", "Changqing Yuan", "Chunyan Wan"], "journal": "Frontiers in immunology", "year": 2025, "abstract": "Background: Chronic apical periodontitis (CAP) is a prevalent oral inflammatory disease, yet the complex mechanisms underlying its etiology remain unclear. A recently identified cell death pathway known as cuproptosis may be linked to this condition.\nMethods: Differentially expressed cuproptosis-related genes (DE-CRGs) were identified by integrating human CAP dataset (GSE237398) with health control (HC) dataset (GSE223924) from the Gene Expression Omnibus (GEO) database. Subsequently, single-cell RNA sequencing (scRNA-seq) data from clinical samples with CAP (n=3) and HC (n=3) from the GSE171213 dataset were analyzed to assess variations across different cell clusters. The association of CRGs with macrophages and fibroblasts in periodontitis was then explored. Fibroblasts and macrophages were selected for further analysis, which included subset classification, cell-chat analysis, and functional enrichment analysis. Additionally, Receiver Operating Characteristic (ROC) curves were employed to evaluate the discriminatory ability of gene features. Changes in DE-CRGs within the whole periodontitis tissue were confirmed through quantitative real-time PCR (qRT-PCR) and immumohistochemical staining (IHC).\nResults: Eight CAP-related DE-CRGs were identified through bulk mRNA sequencing. Numerous interactions among these CRGs were observed, highlighting the complexity of protein-protein interactions. ROC curve analysis demonstrated strong diagnostic potential for these genes. ScRNA-seq sequencing revealed significant alterations in CRGs within fibroblasts and macrophages, along with close intercellular communication between these cell clusters. qRT-PCR and IHC analysis of clinical samples further confirmed DE-CRGs expression in CAP.\nConclusion: These findings suggest that CRGs are closely associated with the COL4A1-Fibro and APOE-Macro intercellular interactions, which may facilitate the occurrence and progression of cuproptosis in chronic apical periodontitis.", "claims": [{"id": "claim-method", "statement": "To evaluate the diagnostic performance of the predictive model, a Receiver Operating Characteristic (ROC) curve was generated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40909264", "locator": "sections[7] \"Construction of the prognostic model\" paragraph 2", "quote": "To evaluate the diagnostic performance of the predictive model, a Receiver Operating Characteristic (ROC) curve was generated."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. 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The names of the repository/repositories and accession number(s) can be found below: PRJNA1213680 (SRA)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The results indicated that CRGs demonstrated strong diagnostic performance in the training set except DLST, GCSH or LIAS (AUC > 0.8, Figure 7K ).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40909264", "locator": "sections[25] \"Construction of the prognostic model with CRGs\" paragraph 2", "quote": "The results indicated that CRGs demonstrated strong diagnostic performance in the training set except DLST, GCSH or LIAS (AUC > 0.8, Figure 7K )."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The results indicated that CRGs demonstrated strong diagnostic performance in the training set except DLST, GCSH or LIAS (AUC > 0.8, Figure 7K ).", "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:40909264"], "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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Subsequently, single-cell RNA sequencing (scRNA-seq) data from clinical samples with", "e. Subsequently, single-cell RNA sequencing (scRNA-seq) data from clinical samples with CAP (n=3) a", "strong diagnostic potential for these genes. ScRNA-seq sequencing revealed significant alterations"], "order_basis": "paper_text_order:49", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["periodontitis based on bulk and single-cell RNA sequencing analyses and experimental validation.", "us (GEO) database. Subsequently, single-cell RNA sequencing (scRNA-seq) data from clinical samples with"], "order_basis": "paper_text_order:62", "id": "assay:2"}, {"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": ["s tissue were confirmed through quantitative real-time PCR (qRT-PCR) and immumohistochemical staining (", "howed significant differential expression in qPCR analysis, as well as NFE2L2 and SLC25A3, who", "nal areas for both proteins, consistent with qPCR findings. The positive signals were predomin"], "order_basis": "paper_text_order:1268", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["(qRT-PCR) and immumohistochemical staining (IHC). Results: Eight CAP-related DE-CRGs were id", "ion between these cell clusters. qRT-PCR and IHC analysis of clinical samples further confirm", "dicted downregulation of NFE2L2 and SLC25A3, immunohistochemical results demonstrated significantly increased", "(n = 5) and CAP tissue (n = 5) evaluated by IHC. 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