Identification and verification of autophagy-related gene signatures and their association with immune infiltration and drug responsiveness in epilepsy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39911741", "kind": "science-record", "revision": 4, "content_hash": "sha256:4cc467917f93a9db56f879713860ee76796c3b2611f1c8c765f32c531250d3da", "created_at": "2026-11-01T20:30:10Z", "updated_at": "2026-11-01T22:56:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and verification of autophagy-related gene signatures and their association with immune infiltration and drug responsiveness in epilepsy.", "doi": "10.3389/fneur.2024.1503632", "pmid": "39911741", "authors": ["Han-Han He", "Xiao-Ge Zhang", "Fen-Fang Chen"], "journal": "Frontiers in neurology", "year": 2024, "abstract": "Background: Epilepsy, a common neurological disorder, is characterized by susceptibility to recurrent seizures. Increasing evidence suggests that autophagy plays a crucial role in the initiation and progression of epilepsy. However, the precise mechanisms by which autophagy deficiencies involved in epileptogenesis are still not fully understood.\nMethods: Two datasets of epilepsy (GSE143272 and GSE256068) were downloaded from the Gene Expression Omnibus (GEO) database. Differential expression genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA) were employed to screen for autophagy related differential expression genes (ARDEGs) in GSE143272 database. Subsequently, protein-protein interaction, transcription factors and miRNAs networks were constructed. Additionally, the functional enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied. The hub ARDEGs were identified through CytoHubba, followed by the LASSO analysis. The Immune Cell Abundance Identifier (ImmuCellAI) was used to estimate peripheral immune cells abundance of epilepsy. Furthermore, the expression level of hub ARDEGs were detected in patients treated with different epilepsy monotherapies to explore the role of autophagy in the responsiveness of antiepileptic drug therapy. Finally, the expression level of hub ARDEGs were further validated in hippocampus of GSE256068 to enhance the reliability of the results.\nResults: Twenty ARDEGs in epilepsy were screened out by integrating DEGs and WGCNA analysis. KEGG enrichment analysis showed that the ARDEGs in epilepsy were not only involved in the autophagy, but also apoptosis, the NOD-like receptor signaling pathway, the neurotrophin signaling pathway, etc. Four hub ARDEGs (PIK3R1, TRIM21, TRIM22, and ITPR3) were screened through integrating CytoHubba plug and LASSO analysis. The immune infiltration analysis showed that there was a significantly increased abundance of macrophages and a decreased abundance of CD4 and CD8 T cells, including Tr1, nTreg, Tfh, CD8 naïve, cytotoxic T cells and effector memory T cells in the epilepsy group. Furthermore, the hub ARDEGs were significantly correlated with the abundance of differential immune cells. In expression level validation and anti-epileptic drug responsiveness analysis, PIK3R1 and ITPR3 had significant differences in the hippocampus of patients with epilepsy. PIK3R1 expression level was found to be related with carbamazepine resistance.\nConclusion: This study elucidated the autophagy-related gene signatures in epilepsy and clarified their association with immune infiltration and anti-epileptic drug responsiveness, providing a novel target for future therapeutic interventions and disease markers in epilepsy.", "claims": [{"id": "claim-method", "statement": "The DEGs between epilepsy and HC samples was analyzed by the “Limma” package in R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39911741", "locator": "sections[4] \"Differential expression genes identification between epilepsy patients and HCs\" paragraph 2", "quote": "The DEGs between epilepsy and HC samples was analyzed by the “Limma” package in R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39911741", "locator": "sections[24] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Twenty ARDEGs in epilepsy were screened out by integrating DEGs and WGCNA analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39911741", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Twenty ARDEGs in epilepsy were screened out by integrating DEGs and WGCNA analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Twenty ARDEGs in epilepsy were screened out by integrating DEGs and WGCNA analysis.", "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:39911741"], "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:GSE143272"], "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:GSE143272"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39911741", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fneur.2024.1503632", "sha256": 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