Identification of key genes of anti-programmed death ligand 1 for meningioma immunotherapy by bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36538194", "kind": "science-record", "revision": 3, "content_hash": "sha256:2d2839a5f133553d92211f6b933ffa7f159f34750ebd170fd8b15d0a338a0379", "created_at": "2026-11-01T19:01:04Z", "updated_at": "2026-11-01T22:08:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes of anti-programmed death ligand 1 for meningioma immunotherapy by bioinformatic analysis.", "doi": "10.1007/s12032-022-01869-8", "pmid": "36538194", "authors": ["Lijian Zhang", "Luxuan Wang", "Yanli Tan", "Chunhui Li", "Chuan Fang"], "journal": "Medical oncology (Northwood, London, England)", "year": 2022, "abstract": "Meningioma is one of the most common primary tumors in the central nervous system (CNS). A deeper understanding of its molecular characterization could provide potential therapeutic targets to reduce recurrence. In this study, we attempted to identify specific gene mutations in meningioma for immunotherapy. One GSE43290 dataset was obtained from the Gene Expression Omnibus (GEO) database to find differentially expressed genes (DEGs) between meningioma tissues and normal meninges. In total, 420 DEGs were identified, including 15 up-regulated and 405 down-regulated genes. Functional enrichment analysis showed that these DEGs were mainly enriched in PI3K-Akt signaling pathway, Focal adhesion, and MAPK signaling pathway. We identified 20 hub genes by protein-protein interaction (PPI) analysis. Among the hub genes, the expression of FLT1, CXCL8, JUN, THBS1, FECAM1, CD34, and FGF13 were negatively correlated with Programmed Death Ligand-1 (PD-L1). Additionally, the expression of those genes was co-regulated by miR-155-5p. The findings suggest that miR-155-5p play an important role in the pathogenesis of meningioma and may represent potential therapeutic targets for its anti-PD-L1 immunotherapy.", "claims": [{"id": "claim-method", "statement": "The expression profiles of DEGs were obtained with GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) [18]. Genes with |log2FC|> 2 and P value < 0.05 were selected as DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36538194", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "The expression profiles of DEGs were obtained with GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) [18]. Genes with |log2FC|> 2 and P value < 0.05 were selected as DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets are available in the National Center of Biotechnology Information (NCBI) GEO (https://www.ncbi.nlm.nih.gov/geo/). one datasets GSE43290 was used in the present study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36538194", "locator": "sections[24] \"Data availability\" paragraph 2", "quote": "The datasets are available in the National Center of Biotechnology Information (NCBI) GEO (https://www.ncbi.nlm.nih.gov/geo/). one datasets GSE43290 was used in the present study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 420 differentially expressed genes between meningioma tissues and normal meninges, including 15 up-regulated and 405 down-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36538194", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total, 420 DEGs were identified, including 15 up-regulated and 405 down-regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 420 differentially expressed genes between meningioma tissues and normal meninges, including 15 up-regulated and 405 down-regulated genes.", "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:36538194"], "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:GSE43290"], "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:GSE43290"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36538194", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12032-022-01869-8", "sha256": "sha256:11d151e36722d7406d7874bf916abe00554398c5663aa3a0af555cb29767769f", "bytes": 32205, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12032-022-01869-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9768007", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE43290", "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=GSE43290", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43290", "version": null, "note": "The datasets are available in the National Center of Biotechnology Information (NCBI) GEO (https://www.ncbi.nlm.nih.gov/geo/). one datasets GSE43290 was used in the present study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets are available in the National Center of Biotechnology Information (NCBI) GEO (https://www.ncbi.nlm.nih.gov/geo/). one datasets GSE43290 was used in the present study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1060065", "GSM1060066", "GSM1060067", "GSM1060068", "GSM1060069", "GSM1060070", "GSM1060071", "GSM1060072", "GSM1060073", "GSM1060074", "GSM1060075", "GSM1060076", "GSM1060077", "GSM1060078", "GSM1060079", "GSM1060080", "GSM1060081", "GSM1060082", "GSM1060083", "GSM1060084", "GSM1060085", "GSM1060086", "GSM1060087", "GSM1060088", "GSM1060089", "GSM1060090", "GSM1060091", "GSM1060092", "GSM1060093", "GSM1060094", "GSM1060095", "GSM1060096", "GSM1060097", "GSM1060098", "GSM1060099", "GSM1060100", "GSM1060101", "GSM1060102", "GSM1060103", "GSM1060104", "GSM1060105", "GSM1060106", "GSM1060107", "GSM1060108", "GSM1060109", "GSM1060110", "GSM1060111", "GSM1060112", "GSM1060113", "GSM1060114", "GSM1060115"], "sample_count": 51, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from meningiomas and normal meninges", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE43290 not downloaded", "asset:data:geo:GSE43290 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R differential-expression analysis, with genes selected using |log2FC| > 2 and P value < 0.05.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The expression profiles of DEGs were obtained with GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) [18]. Genes with |log2FC|> 2 and P value < 0.05 were selected as DEGs."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE43290"], "resolved_accessions": ["GSE43290"], "statements": ["The datasets are available in the National Center of Biotechnology Information (NCBI) GEO (https://www.ncbi.nlm.nih.gov/geo/). one datasets GSE43290 was used in the present study."], "basis": "The paper names GSE43290 in National Center of Biotechnology Information (NCBI) GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:36538194", "data:geo:GSE43290"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE43290"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:20:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10617, "completion_tokens": 1035, "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:36538194", "type": "paper", "label": "pmid:36538194"}, {"id": "source:pmid:36538194", "type": "manuscript", "label": "PMID 36538194 full text"}, {"id": "data:geo:GSE43290", "type": "dataset", "label": "GEO GSE43290"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36538194", "type": "paper", "label": "pmid:36538194"}, {"id": "source:pmid:36538194", "type": "manuscript", "label": "PMID 36538194 full text"}, {"id": "data:geo:GSE43290", "type": "dataset", "label": "GEO GSE43290"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36538194", "type": "extraction", "used": ["source:pmid:36538194"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE43290", "type": "accession_resolution", "used": ["data:geo:GSE43290"], "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:36538194", "parent_hash": "sha256:40bd49f42167b7f930036adbf00ddeec575e2b28a8205d8bd0c9c8a98d8cbfdf", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE43290 licence not read", "asset:data:geo:GSE43290 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}