Screening for biomarkers of tuberous sclerosis complex-associated epilepsy: a bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39144436", "kind": "science-record", "revision": 3, "content_hash": "sha256:d86298eabedf63f62c7bd3aaee7a043437424c59ec0c3de8fc658bb35ea9f837", "created_at": "2026-11-01T20:29:15Z", "updated_at": "2026-11-01T22:12:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening for biomarkers of tuberous sclerosis complex-associated epilepsy: a bioinformatics analysis.", "doi": "10.21037/tp-24-211", "pmid": "39144436", "authors": ["Yongsheng Sun", "Haonan Ji", "Liqin Xu", "Ruiyin Gu", "Pasquale Striano", "Gavin P Winston", "Bin Li", "Hui Zhou"], "journal": "Translational pediatrics", "year": 2024, "abstract": "Background: The optimal biomarkers for early diagnosis, treatment, and prognosis of tuberous sclerosis complex (TSC)-associated epilepsy are not yet clear. This study identifies the crucial genes involved in the pathophysiology of TSC-associated epilepsy via a bioinformatics analysis. These genes may serve as novel therapeutic targets.\nMethods: Gene chip data sets (GSE62019 and GSE16969) comprising the data of patients with TSC-associated epilepsy and healthy control participants were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in the GEO database were identified using the GEO2R gene expression analysis tool. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Gene Ontology function, and protein-protein interaction (PPI) network analyses were then conducted. The results were analyzed using R language, and are presented in volcano plots, Venn diagrams, heatmaps, and enrichment pathway bubble charts. A gene set enrichment analysis (GSEA), was conducted to examine the KEGG pathways and crucial genes linked to TSC-associated epilepsy. The potential genes were compared with the genes listed in the Online Mendelian Inheritance in Man (OMIM) database and analyzed against the literature to determine their clinical significance. Finally, the expression of the key genes in the TSC-associated epilepsy mice cerebral cortex was examined through immunohistochemical staining.\nResults: The intersection of the GSE62019 and GSE16969 data sets revealed 151 commonly upregulated DEGs. The KEGG enrichment analysis indicated that these DEGs affected the occurrence and development of TSC-associated epilepsy by modulating complement and coagulation cascades, glycosaminoglycans in cancer, and extracellular matrix-receptor interactions. Four high-scoring clusters emerged, and podoplanin (PDPN) was identified as a key gene through the construction of a PPI network of the common DEGs using the Cytoscape software. A GSEA of the DEGs revealed that the common DEG PDPN was enriched in both data sets in pathways related to platelet activation, aggregation, and the glycoprotein VI (GPVI)-mediated activation cascade. Immunohistochemical staining revealed a significant elevation in PDPN expression in the cerebral cortex of mice with TSC-associated epilepsy. Conversely, the control group mice did not display any significantly positive neurons.\nConclusions: The discovery of these crucial genes and signaling pathways extends understanding of the molecular processes underlying the development of TSC-associated epilepsy. Additionally, our findings may provide a theoretical basis for research into targeted clinical treatments.", "claims": [{"id": "claim-method", "statement": "A t-test was employed to determine the P value for the DEG analysis, with the false discovery rate adjustment applied to the P values.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39144436", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "A t-test was employed to determine the P value for the DEG analysis, with the false discovery rate adjustment applied to the P values."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Available at https://tp.amegroups.com/article/view/10.21037/tp-24-211/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39144436", "locator": "sections[23] \"Data Sharing Statement\" paragraph 2", "quote": "Available at https://tp.amegroups.com/article/view/10.21037/tp-24-211/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Intersection of the GSE62019 and GSE16969 datasets identified 151 commonly upregulated DEGs associated with TSC-associated epilepsy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39144436", "locator": "sections[12] \"Identification of the DEGs associated with TSC-associated epilepsy\" paragraph 2", "quote": "By intersecting the upregulated DEGs from both data sets, we constructed a Venn diagram and identified 151 upregulated DEGs (Figure 1B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Intersection of the GSE62019 and GSE16969 datasets identified 151 commonly upregulated DEGs associated with TSC-associated epilepsy.", "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:39144436"], "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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