Identification of Ferroptosis-Related Genes in Patients with Renal Ischemia-Reperfusion Injury.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40692585", "kind": "science-record", "revision": 4, "content_hash": "sha256:5f4212918ff84acfebb25cd90e1bf95d9927d527d9b983619036e9a7a50325ff", "created_at": "2026-11-01T20:30:47Z", "updated_at": "2026-11-01T22:56:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Ferroptosis-Related Genes in Patients with Renal Ischemia-Reperfusion Injury.", "doi": "10.2147/IJGM.S522363", "pmid": "40692585", "authors": ["Guangwei Jiang", "Jikuan Li", "Ruoyu Dong", "Yuyan Chen", "Xiaoyu Zhang", "Xiaoming Shi"], "journal": "International journal of general medicine", "year": 2025, "abstract": "Background: During acute kidney injury, hypoxic injury following reactive oxygen species (ROS) production due to reoxidation leads to severe inflammation and ferroptosis. Thus, the aim of the current research was to determine the ferroptosis-related biomarkers in IRI injury.\nMethods: GSE43974 dataset was analyzed to identify differentially expressed genes (DEGs) using bioinformatics analysis. The intersection of DEGs and ferroptosis-related genes was identified as differentially expressed ferroptosis-related genes (DEFRGs). Finally, a renal ischemia-reperfusion model was made using mice, and the model was identified by HE staining and markers of IRI, including BUN and Scr. Changes in the expression of hub gene in the model and sham groups were detected by RT-pcr.\nResults: A total of 3950 DEGs were identified between the IRI and control samples. Thereafter, 74 DEFRGs are obtained by taking the intersection of DEGs and ferroptosis-related genes. The GO analysis indicated that DEFRGs were mainly enriched in response to oxidative stress-related pathway. By MCODE, ATF3, ATF4, ATG3, ATG5, BECN1, DDIT3, HSPA5, NFE2L2, WIPI1, XBP1 were identified as hub genes. ATF3, DDIT3, ATF4, and ATG3 with AUC more than 0.7 were identified as biomarkers. It was confirmed by RT-pcr that the expression of hub genes ATF3, DDIT3, ATF4 was significantly elevated, and the expression of ATG3 was significantly reduced in the IRI model group. It was consistent with the expected results of data analysis in GEO.\nConclusion: In conclusion, our study identified 4 ferroptosis-related hub genes in the IRI and demonstrated that they are potential diagnostic biomarkers for IRI.", "claims": [{"id": "claim-method", "statement": "The R package limma was used for DEG analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40692585", "locator": "sections[4] \"Screening of DEGs\" paragraph 2", "quote": "The R package limma was used for DEG analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets for this study can be found in the GEO database. GSE43974, the original sequenced samples in GEO are tissue type samples. This paper has been uploaded to Research square as a preprint https://www.researchsquare.com/article/rs-2601585/v1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40692585", "locator": "sections[26] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets for this study can be found in the GEO database. GSE43974, the original sequenced samples in GEO are tissue type samples. This paper has been uploaded to Research square as a preprint https://www.researchsquare.com/article/rs-2601585/v1."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 3950 DEGs were identified between the IRI and control samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40692585", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 3950 DEGs were identified between the IRI and control samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 3950 DEGs were identified between the IRI and control samples.", "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:40692585"], "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:GSE43974"], "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:GSE43974"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40692585", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S522363", "sha256": "sha256:0438b1460d142ee5270405f69148d17b03f9c59b5fcc81a394007fb1830092d4", "bytes": 32681, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/IJGM.S522363", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12278950", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE43974", "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=GSE43974", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43974", "version": null, "note": "The datasets for this study can be found in the GEO database. GSE43974, the original sequenced samples in GEO are tissue type samples. This paper has been uploaded to Research square as a preprint https://www.researchsquare.com/article/rs-2601585/v1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets for this study can be found in the GEO database. GSE43974, the original sequenced samples in GEO are tissue type samples. 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The six SD rats (male) were grouped according to the randomi", "ng to the randomized numerical method (three rats in each group): sham operation group (Sham g", "rterial clamping of both renal pedicles. The rats in each group were anesthetized by intraperi"], "order_basis": "paper_text_order:1771", "id": "assay:1"}, {"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": ["The R package limma was used for DEG analysis."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}