Integrative analysis of TBI data reveals Lgmn as a key player in immune cell-mediated ferroptosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38057699", "kind": "science-record", "revision": 3, "content_hash": "sha256:687cbef450e6790d649d24b8336ceee40ed0bad7f8f0fef5ee4d06f1e38dff13", "created_at": "2026-11-01T19:03:00Z", "updated_at": "2026-11-01T22:10:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative analysis of TBI data reveals Lgmn as a key player in immune cell-mediated ferroptosis.", "doi": "10.1186/s12864-023-09842-z", "pmid": "38057699", "authors": ["Liyan Yan", "Xiaonan Han", "Mingkang Zhang", "Yikun Fu", "Fei Yang", "Qian Li", "Tian Cheng"], "journal": "BMC genomics", "year": 2023, "abstract": "BACKGROUND: Traumatic brain injury (TBI) is a central nervous system disease caused by external trauma, which has complex pathological and physiological mechanisms. The aim of this study was to explore the correlation between immune cell infiltration and ferroptosis post-TBI.\nMETHODS: This study utilized the GEO database to download TBI data and performed differentially expressed genes (DEGs) and ferroptosis-related differentially expressed genes (FRDEGs) analysis. DEGs were further analyzed for enrichment using the DAVID 6.8. Immunoinfiltration cell analysis was performed using the ssGSEA package and the Timer2.0 tool. The WGCNA analysis was then used to explore the gene modules in the data set associated with differential expression of immune cell infiltration and to identify the hub genes. The tidyverse package and corrplot package were used to calculate the correlations between hub genes and immune cell infiltration and ferroptosis-marker genes. The miRDB and TargetScan databases were used to predict complementary miRNAs for the Hub genes selected from the WGCNA analysis, and the DIANA-LncBasev3 tool was used to identify target lncRNAs for the miRNAs, constructing an mRNA-miRNA-lncRNA regulatory network.\nRESULTS: A total of 320 DEGs and 21 FRDEGs were identified in GSE128543. GO and KEGG analyses showed that the DEGs after TBI were primarily associated with inflammation and immune response. Xcell and ssGSEA immune infiltration cell analysis showed significant infiltration of T cell CD4+ central memory, T cell CD4+ Th2, B cell memory, B cell naive, monocyte, macrophage, and myeloid dendritic cell activated. The WGCNA analysis identified two modules associated with differentially expressed immune cells and identified Lgmn as a hub gene associated with immune infiltrating cells. Lgmn showed significant correlation with immune cells and ferroptosis-marker genes, including Gpx4, Hspb1, Nfe2l2, Ptgs2, Fth1, and Tfrc. Finally, an mRNA-miRNA-lncRNA regulatory network was constructed using Lgmn.\nCONCLUSION: Our results indicate that there is a certain correlation between ferroptosis and immune infiltrating cells in brain tissue after TBI, and that Lgmn plays an important role in this process.", "claims": [{"id": "claim-method", "statement": "In order to gain a deeper understanding of the roles and interactions of different types of immune cells in TBI, we used WGCNA analysis to cluster genes into different gene modules.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38057699", "locator": "sections[15] \"Construction of WGCNA network and identification of immune-related modules and hub genes\" paragraph 2", "quote": "In order to gain a deeper understanding of the roles and interactions of different types of immune cells in TBI, we used WGCNA analysis to cluster genes into different gene modules."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. The datasets GSE128543 for this study can be found here: https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38057699", "locator": "sections[23] \"Data Availability\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. The datasets GSE128543 for this study can be found here: https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our results indicate that there is a certain correlation between ferroptosis and immune infiltrating cells in brain tissue after TBI, and that Lgmn plays an important role in this process.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38057699", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our results indicate that there is a certain correlation between ferroptosis and immune infiltrating cells in brain tissue after TBI, and that Lgmn plays an important role in this process."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Our results indicate that there is a certain correlation between ferroptosis and immune infiltrating cells in brain tissue after TBI, and that Lgmn plays an important role in this process.", "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:38057699"], "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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