Identification and Verification of Key Genes Associated with Temozolomide Resistance in Glioblastoma Based on Comprehensive Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40225293", "kind": "science-record", "revision": 4, "content_hash": "sha256:4d03c6f878e590bc32dc674a90a92d134d3aedfd872eb67b667b0111fec0d176", "created_at": "2026-11-01T20:30:23Z", "updated_at": "2026-11-01T22:56:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Verification of Key Genes Associated with Temozolomide Resistance in Glioblastoma Based on Comprehensive Bioinformatics Analysis.", "doi": "10.30498/ijb.2024.448826.3892", "pmid": "40225293", "authors": ["Jun Hu", "Jingyan Yang", "Na Hu", "Zongting Shi", "Tiemin Hu", "Baohong Mi", "Hong Wang", "Weiheng Chen"], "journal": "Iranian journal of biotechnology", "year": 2024, "abstract": "Background: Glioblastoma (GBM) is the most aggressive form of brain cancer, with poor prognosis despite treatments like temozolomide (TMZ). Resistance to TMZ is a significant clinical challenge, and understanding the genes involved is crucial for developing new therapies and prognostic markers. This study aims to identify key genes associated with TMZ resistance in GBM, which could serve as valuable biomarkers for predicting patient outcomes and potential targets for treatment.\nObjectives: This study aimed to identify genes involved in TMZ resistance in GBM and to assess the value of these genes in GBM treatment and prognosis evaluation.\nMaterials and Methods: Bioinformatics analysis of Gene Expression Omnibus (GEO) datasets (GSE113510 and GSE199689) and The Chinese Glioblastoma Genome Atlas (CGGA) database was performed to identify differentially expressed genes (DEGs) between GBM cell lines with and without TMZ resistance. Subsequently, the key modules associated with GBM patient prognosis were identified by weighted gene coexpression network analysis (WGCNA). Furthermore, hub genes related to TMZ resistance were accurately screened and confirmed using three machine learning algorithms. In addition, immune cell infiltration analysis, TF-miRNA coregulatory network analysis, drug sensitivity prediction, and gene set enrichment analysis (GSEA) were also performed for temozolomide resistance-specific genes. Finally, the expression levels of key genes were validated in our constructed TMZ-resistant cell lines by real-time quantitative polymerase chain reaction (RT-qPCR) and Western blotting (WB).\nResults: Integrated analysis of the GEO and CGGA datasets revealed 769 differentially expressed genes (DEGs), comprising 350 downregulated and 419 upregulated genes, between GBM patients and normal controls. Among these DEGs, three key genes, namely, PITX1, TNFRSF11B, and IGFBP2, exhibited significant differences in expression between groups and were prioritized via machine learning algorithms. The expression levels of these genes were found to be closely related to adverse clinical features and immune cell infiltration levels in GBM patients. These genes were also found to participate in several biological pathways and processes. RT‒qPCR and WB confirmed the differential expression of these genes in vitro, indicating that they play vital roles in GBM patients with TMZ resistance.\nConclusions: PITX1, TNFRSF11B, and IGFBP2 are key genes associated with the prognosis of GBM patients with TMZ resistance. The differential expression of these genes correlates with adverse outcomes in GBM patients, suggesting that they are valuable biomarkers for predicting patient prognosis and that they could serve as diagnostic biomarkers or treatment targets.", "claims": [{"id": "claim-method", "statement": "After normalization and comparison of gene expression levels between the TMZ-sensitive and TMZ-resistant groups, DEGs were screened using the R package “limma” with the cutoff criteria |log2-fold change| >1 and adjusted p value < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40225293", "locator": "sections[5] \"3.2. Identification of DEGs\" paragraph 2", "quote": "After normalization and comparison of gene expression levels between the TMZ-sensitive and TMZ-resistant groups, DEGs were screened using the R package “limma” with the cutoff criteria |log2-fold change| >1 and adjusted p value < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The study’s datasets are accessible online via the following GEO accession numbers: GSE113510 and GSE199689, available at NCBI’s Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40225293", "locator": "sections[28] \"ack\" paragraph 1", "quote": "The study’s datasets are accessible online via the following GEO accession numbers: GSE113510 and GSE199689, available at NCBI’s Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Integrated analysis of the GEO and CGGA datasets revealed 769 differentially expressed genes (DEGs), comprising 350 downregulated and 419 upregulated genes, between GBM patients and normal controls.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40225293", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Integrated analysis of the GEO and CGGA datasets revealed 769 differentially expressed genes (DEGs), comprising 350 downregulated and 419 upregulated genes, between GBM patients and normal controls."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Integrated analysis of the GEO and CGGA datasets revealed 769 differentially expressed genes (DEGs), comprising 350 downregulated and 419 upregulated genes, between GBM patients and normal controls.", "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:40225293"], "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:GSE113510"], "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": {"fold_change": "e cutoff criteria |log2-fold change| >1 and adjusted p valu"}, "inputs": ["data:geo:GSE113510"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40225293", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.30498/ijb.2024.448826.3892", "sha256": "sha256:0d78d7075bdbae298a9bb7f6dcc8e33ed49bad232adac97c27fdf2ade58c0150", "bytes": 38892, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.30498/ijb.2024.448826.3892", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11993235", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE113510", "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=GSE113510", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE113510", "version": null, "note": "The study’s datasets are accessible online via the following GEO accession numbers: GSE113510 and GSE199689, available at NCBI’s Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The study’s datasets are accessible online via the following GEO accession numbers: GSE113510 and GSE199689, available at NCBI’s Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3108207", "GSM3108208", "GSM3108209", "GSM3108210", "GSM3108211", "GSM3108212"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "21047", "taxon": "Homo sapiens", "title": "The different expression of long non-coding RNAs and messenger RNAs in temozolomide-resistant glioblastoma cells and parental glioblastoma cells", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE199689", "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=GSE199689", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE199689", "version": null, "note": "The study’s datasets are accessible online via the following GEO accession numbers: GSE113510 and GSE199689, available at NCBI’s Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The study’s datasets are accessible online via the following GEO accession numbers: GSE113510 and GSE199689, available at NCBI’s Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5981753", "GSM5981754", "GSM5981755", "GSM5981756", "GSM5981757", "GSM5981758"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "16956", "taxon": "Homo sapiens", "title": "LncRNA and mRNA expression data from TMZ-resistant cell line", "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:GSE113510 not downloaded", "asset:data:geo:GSE113510 licence not read", "asset:data:geo:GSE199689 not downloaded", "asset:data:geo:GSE199689 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": {"fold_change": "e cutoff criteria |log2-fold change| >1 and adjusted p valu"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "After normalization and comparison of gene expression levels between the TMZ-sensitive and TMZ-resistant groups, DEGs were screened using the R package “limma” with the cutoff criteria |log2-fold change| >1 and adjusted p value < 0.05."}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE113510", "GSE199689"], "resolved_accessions": ["GSE113510", "GSE199689"], "statements": ["The study’s datasets are accessible online via the following GEO accession numbers: GSE113510 and GSE199689, available at NCBI’s Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo)."], "basis": "The paper names GSE113510, GSE199689 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40225293", "data:geo:GSE113510"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE113510"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:50:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10971, "completion_tokens": 1568, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40225293", "type": "paper", "label": "pmid:40225293"}, {"id": "source:pmid:40225293", "type": "manuscript", "label": "PMID 40225293 full text"}, {"id": "data:geo:GSE113510", "type": "dataset", "label": "GEO GSE113510"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40225293", "type": "paper", "label": "pmid:40225293"}, {"id": "source:pmid:40225293", "type": "manuscript", "label": "PMID 40225293 full text"}, {"id": "data:geo:GSE113510", "type": "dataset", "label": "GEO GSE113510"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40225293", "type": "extraction", "used": ["source:pmid:40225293"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE113510", "type": "accession_resolution", "used": ["data:geo:GSE113510"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40225293", "parent_hash": "sha256:3eff6fe652b5748405b0a8e55c6b7b917818039d9636f2d7773339558f9bdee8", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE113510 licence not read", "asset:data:geo:GSE113510 not downloaded", "asset:data:geo:GSE199689 licence not read", "asset:data:geo:GSE199689 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["time quantitative polymerase chain reaction (RT-qPCR) and Western blotting (WB). Results: Integra", "e quantitative polymerase chain reaction (RT-qPCR) and Western blotting (WB). Results: Integra", "everal biological pathways and processes. RT‒qPCR and WB confirmed the differential expression"], "order_basis": "paper_text_order:1689", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tive polymerase chain reaction (RT-qPCR) and Western blotting (WB). Results: Integrated analysis of the GE"], "order_basis": "paper_text_order:1702", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["After normalization and comparison of gene expression levels between the TMZ-sensitive and TMZ-resistant groups, DEGs were screened using the R package “limma” with the cutoff criteria |log2-fold change| >1 and adjusted p value < 0.05."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}