Exploration of the shared pathways and common biomarker in adamantinomatous craniopharyngioma and type 2 diabetes using integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38848397", "kind": "science-record", "revision": 4, "content_hash": "sha256:2b3d571c614c36d70e5befaa0e5e44f7b8c6ebe3a327e2a8245bebcb9ee5c7f8", "created_at": "2026-11-01T19:20:47Z", "updated_at": "2026-11-01T22:54:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of the shared pathways and common biomarker in adamantinomatous craniopharyngioma and type 2 diabetes using integrated bioinformatics analysis.", "doi": "10.1371/journal.pone.0304404", "pmid": "38848397", "authors": ["Yibo Han", "Yong Wang", "Shuo Li", "Kohji Sato", "Satoru Yamagishi"], "journal": "PloS one", "year": 2024, "abstract": "Craniopharyngiomas are rare tumors of the central nervous system that typically present with symptoms such as headache and visual impairment, and those reflecting endocrine abnormalities, which seriously affect the quality of life of patients. Patients with craniopharyngiomas are at higher cardiometabolic risk, defined as conditions favoring the development of type 2 diabetes and cardiovascular disease. However, the underlying common pathogenic mechanisms of craniopharyngiomas and type 2 diabetes are not clear. Especially due to the difficulty of conducting in vitro or in vivo experiments on craniopharyngioma, we thought the common pathway analysis between craniopharyngioma and type 2 diabetes based on bioinformatics is a powerful and feasible method. In the present study, using public datasets (GSE94349, GSE68015, GSE38642 and GSE41762) obtained from the GEO database, the gene expression associated with adamantinomatous craniopharyngioma, a subtype of craniopharyngioma, and type 2 diabetes were analyzed using a bioinformatic approach. We found 11 hub genes using a protein-protein interaction network analysis. Of these, seven (DKK1, MMP12, KRT14, PLAU, WNT5B, IKBKB, and FGF19) were also identified by least absolute shrinkage and selection operator analysis. Finally, single-gene validation and receptor operating characteristic analysis revealed that four of these genes (MMP12, PLAU, KRT14, and DKK1) may be involved in the common pathogenetic mechanism of adamantinomatous craniopharyngioma and type 2 diabetes. In addition, we have characterized the differences in immune cell infiltration that characterize these two diseases, providing a reference for further research.", "claims": [{"id": "claim-method", "statement": "DEGs were identified using the “limma” R package, with Log |FC| > 1 and p < 0.05 being considered to indicate statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38848397", "locator": "sections[6] \"Acquisition and analysis of DEGs\" paragraph 2", "quote": "DEGs were identified using the “limma” R package, with Log |FC| > 1 and p < 0.05 being considered to indicate statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets are obtained from public databases: GEO database", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38848397", "locator": "sections[10] \"All datasets are obtained from public databases: GEO database\" paragraph 1", "quote": "All datasets are obtained from public databases: GEO database"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Finally, single-gene validation and receptor operating characteristic analysis revealed that four of these genes (MMP12, PLAU, KRT14, and DKK1) may be involved in the common pathogenetic mechanism of adamantinomatous craniopharyngioma and type 2 diabetes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38848397", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Finally, single-gene validation and receptor operating characteristic analysis revealed that four of these genes (MMP12, PLAU, KRT14, and DKK1) may be involved in the common pathogenetic mechanism of adamantinomatous craniopharyngioma and type 2 diabetes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Finally, single-gene validation and receptor operating characteristic analysis revealed that four of these genes (MMP12, PLAU, KRT14, and DKK1) may be involved in the common pathogenetic mechanism of adamantinomatous craniopharyngioma and type 2 diabetes.", "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:38848397"], "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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