Deciphering oxidative stress contributions in vestibular schwannoma: A bioinformatics approach to novel therapeutic pathways.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41231782", "kind": "science-record", "revision": 4, "content_hash": "sha256:0570461ad3305efc9c35cb176e39f6b61be0432a1c970f036ea5c942402c743d", "created_at": "2026-11-01T20:31:16Z", "updated_at": "2026-11-01T22:57:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Deciphering oxidative stress contributions in vestibular schwannoma: A bioinformatics approach to novel therapeutic pathways.", "doi": "10.1371/journal.pone.0336451", "pmid": "41231782", "authors": ["Yubin Xue", "Mingyue Wang", "Hongwei Ma"], "journal": "PloS one", "year": 2025, "abstract": "BACKGROUND: Vestibular schwannoma (VS) is a benign tumor originating from Schwann cells, and its molecular pathogenesis remains poorly understood. Increasing evidence suggests oxidative stress (OS) plays a critical role in tumor development, but its involvement in VS is largely unexplored.\nMETHODS: We analyzed two GEO transcriptomic datasets (GSE54934 and GSE56597) to identify oxidative stress-related differentially expressed genes (OSRDEGs). Functional enrichment, protein-protein interaction (PPI) network construction, hub gene identification, and immune infiltration analyses were performed to uncover potential molecular mechanisms.\nRESULTS: Fifteen OSRDEGs were identified, and nine hub genes (IL6, CYBB, CAV1, EGFR, SELE, IL18, CDKN2A, ADIPOQ, CDH2) were screened. Enrichment analysis indicated that these genes are mainly involved in apoptosis, reactive oxygen species regulation, and immune-related pathways. Moreover, immune infiltration analysis revealed significant differences in CD8 + T cells and macrophage populations between VS and control tissues.\nCONCLUSIONS: Our study suggests that oxidative stress may contribute to VS progression by influencing immune responses and signaling pathways. These findings provide new insights into the molecular basis of VS and may guide future experimental and therapeutic investigations.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed using the limma package [18], with the criteria set at |logFC| > 1.5 and adjusted p-value < 0.05. Genes with logFC > 1.5 were considered upregulated, and those with logFC <−1.5 were considered downregulated. The Benjamini-Hochberg method was applied to control the false discovery rate.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41231782", "locator": "sections[4] \"2.2 Identification of VS-associated oxidative stress-related differentially expressed genes (OSRDEGs)\" paragraph 2", "quote": "Differential expression analysis was performed using the limma package [18], with the criteria set at |logFC| > 1.5 and adjusted p-value < 0.05. Genes with logFC > 1.5 were considered upregulated, and those with logFC <−1.5 were considered downregulated. The Benjamini-Hochberg method was applied to control the false discovery rate."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The minimal dataset underlying this study is openly available at Zenodo (DOI: https://doi.org/10.5281/zenodo.17163233). Code Availability All author-generated analysis code used in this study is archived together with the dataset at Zenodo (DOI: https://doi.org/10.5281/zenodo.17163233).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41231782", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "The minimal dataset underlying this study is openly available at Zenodo (DOI: https://doi.org/10.5281/zenodo.17163233). Code Availability All author-generated analysis code used in this study is archived together with the dataset at Zenodo (DOI: https://doi.org/10.5281/zenodo.17163233)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 15 oxidative stress-related differentially expressed genes and screened nine oxidative stress-related hub genes in vestibular schwannoma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41231782", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Fifteen OSRDEGs were identified, and nine hub genes (IL6, CYBB, CAV1, EGFR, SELE, IL18, CDKN2A, ADIPOQ, CDH2) were screened."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 15 oxidative stress-related differentially expressed genes and screened nine oxidative stress-related hub genes in vestibular schwannoma.", "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:41231782"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE54934"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE54934"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41231782", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0336451", "sha256": "sha256:d67aab96d894faea294f6823dc24eb7570408a246672bcb3bc39f37832efe7c1", "bytes": 53871, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0336451", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12614553", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE54934", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54934", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54934", "version": null, "note": "The minimal dataset underlying this study is openly available at Zenodo (DOI: https://doi.org/10.5281/zenodo.17163233). 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Genes with logFC > 1.5 were considered upregulated, and those with logFC <−1.5 were considered downregulated. The Benjamini-Hochberg method was applied to control the false discovery rate."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman rank correlation"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-5", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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METHODS: We analyzed two GEO transcriptomic datasets (GSE54934 and GSE56597) to identify"], "order_basis": "paper_text_order:401", "id": "assay:1"}, {"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": ["ated that these genes are mainly involved in apoptosis, reactive oxygen species regulation, and imm"], "order_basis": "paper_text_order:927", "id": "assay:2"}, {"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": ["Differential expression analysis was performed using the limma package [18], with the criteria set at |logFC| > 1.5 and adjusted p-value < 0.05. 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