Unraveling the role of PBK in glioblastoma: from molecular mechanisms to therapeutic targets.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39649886", "kind": "science-record", "revision": 4, "content_hash": "sha256:f64e7e99755b6e4e89beca0257b0ab60b1b5cad415f4710a27d92ed1e16f6573", "created_at": "2026-11-01T20:29:56Z", "updated_at": "2026-11-01T22:55:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Unraveling the role of PBK in glioblastoma: from molecular mechanisms to therapeutic targets.", "doi": "10.1097/MS9.0000000000002708", "pmid": "39649886", "authors": ["Yizheng Zhang", "Mingyuan Luan"], "journal": "Annals of medicine and surgery (2012)", "year": 2024, "abstract": "Background: This study investigates the gene expression characteristics of glioma-initiating cells (GIC), an important subgroup of glioblastoma (GBM), after knockdown of PBK (PDZ-binding kinase). Differentially expressed genes (DEGs) between PBK knockdown GIC and control groups were screened through bioinformatics methods. The authors analyzed the mechanisms and roles of these DEGs in GBM tumorigenesis and patient prognosis.\nMethods: Microarray data (GSE53800) were obtained from the Gene Expression Omnibus (GEO) database, selecting 18 GIC cell line samples with or without PBK knockdown. Each control and knockdown group contained three samples. DEGs were screened using R software. GO enrichment analysis, KEGG pathway analysis, PPI network analysis, and hub gene identification were conducted to explore DEG mechanisms. Western blot analysis was also performed to detect EIF4E protein expression, one of the key hub genes, after PBK knockdown in the HS683 glioma cell line.\nResults: A total of 175 upregulated and 145 downregulated genes were identified. GO analysis showed that DEGs were mainly enriched in the positive regulation of cell proliferation, cell adhesion, and angiogenesis. KEGG pathway analysis revealed that DEGs were mainly involved in neuroactive ligand-receptor interactions, calcium signaling, and HIF-1 signaling pathways. Western blot results indicated that EIF4E was downregulated after PBK knockdown.\nConclusion: A group of genes, such as EIF4E, were closely associated with PBK expression and functions. These findings may provide insight into the molecular mechanism of PBK in GBM.", "claims": [{"id": "claim-method", "statement": "Background correction, homogenization, and DEG screening were conducted using the limma package in R software (3.5.0, https://www.r-project.org). Statistical data were analyzed using t-tests and Bayesian tests, with a |log2FC| > 1 and adjusted P-value <0.05 as the screening threshold.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39649886", "locator": "sections[3] \"Data processing and differential gene screening\" paragraph 2", "quote": "Background correction, homogenization, and DEG screening were conducted using the limma package in R software (3.5.0, https://www.r-project.org). Statistical data were analyzed using t-tests and Bayesian tests, with a |log2FC| > 1 and adjusted P-value <0.05 as the screening threshold."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors are willing to provide raw data if needed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39649886", "locator": "sections[24] \"Data availability statement\" paragraph 2", "quote": "The authors are willing to provide raw data if needed."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 175 upregulated genes and 145 downregulated genes between PBK-knockdown and control glioma-initiating-cell samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39649886", "locator": "sections[11] \"Identification of DEGs between PBK knockdown and PBK NS glioma-initiating cells\" paragraph 2", "quote": "We identified 175 upregulated genes (Fig. 1E) and 145 downregulated genes (Fig. 1F)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 175 upregulated genes and 145 downregulated genes between PBK-knockdown and control glioma-initiating-cell 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:39649886"], "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:GSE53800"], "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:GSE53800"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39649886", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MS9.0000000000002708", "sha256": "sha256:f74af78d1cd31e52b1f3171336f84f3db6842334281dce8bc2cac4751ec26531", "bytes": 18454, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MS9.0000000000002708", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11623866", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE53800", "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=GSE53800", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53800", "version": null, "note": "The authors are willing to provide raw data if needed.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The authors are willing to provide raw data if needed.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1301012", "GSM1301013", "GSM1301014", "GSM1301015", "GSM1301016", "GSM1301017", "GSM1301018", "GSM1301019", "GSM1301020", "GSM1301021", "GSM1301022", "GSM1301023", "GSM1301024", "GSM1301025", "GSM1301026", "GSM1301027", "GSM1301028", "GSM1301029", "GSM1301030", "GSM1301031", "GSM1301032", "GSM1301033", "GSM1301034", "GSM1301035", "GSM1301036", "GSM1301037", "GSM1301038", "GSM1301039", "GSM1301040", "GSM1301041", "GSM1301042", "GSM1301043", "GSM1301044", "GSM1301045", "GSM1301046", "GSM1301047"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Targeting PBK/TOPK decreases growth and survival of glioblastoma stem cells in vitro and attenuates tumor growth in vivo", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE53800 not downloaded", "asset:data:geo:GSE53800 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Background correction, homogenization, and DEG screening were conducted using the limma package in R software (3.5.0, https://www.r-project.org). 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