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pmid:32580265
Survival Association and Cell Cycle Effects of B7H3 in Neuroblastoma.
Haibo Zhang · Jinsen Zhang · Chunjie Li · Hao Xu · Rui Dong · Clark C Chen · Wei Hua
Journal of Korean Neurosurgical Society · 2020 doi:10.3340/jkns.2019.0255
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Experiment
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Complete file
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Here we examine the expression pattern of B7H3 in clinical NB specimens and characterize the phenotype of B7H3 knock-down in NB cell line.\nMETHODS: Immunohistochemical (IHC) staining was carried out to assess the expression of B7H3 in clinical NB specimens. Survival association was analyzed using five Gene Expression Omnibus (GEO) datasets (GSE85047, GSE45480, GSE62564, GSE16476, GSE49710). Clonogenic survival and flow cytometry were performed after B7H3 knockdown to assess the cellular proliferation and cell survival in vitro. Impact of B7H3 silencing on NB growth was examined in vivo using the SH-SY5Y xenograft model.\nRESULTS: On IHC staining, B7H3 was widely expressed in clinical NB specimens. Analysis of the transcriptional profiles of five GEO datasets clinically annotated NB specimens revealed that decreased B7H3 expression was associated with improved overall survival. B7H3 knockdown suppressed the proliferation of the SH-SY5Y NB model in vitro and in vivo. Cell cycle analysis revealed that B7H3 silencing induced G1/S arrest. This arrest was associated with the suppression of E2F1 expression and induction of Rb expression.\nCONCLUSION: Our results demonstrate that B7H3 expression correlate with clinical survival in NB patients. 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"band": "verbatim", "quote": "Kaplan-Meier analysis revealed that high B7H3 expression was associated with poor OS in all five datasets (p<0.05, Fig. 1B-F)."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE85047", "GSE45480", "GSE62564", "GSE16476", "GSE49710"], "resolved_accessions": ["GSE85047", "GSE45480", "GSE62564", "GSE16476", "GSE49710"], "statements": ["The five microarray expression profiles (GSE85047, GSE45480, GSE62564, GSE16476, GSE49710) was extracted from the Gene Expression Omnibus (GEO) database from R2 : Genomics Analysis and Visualization Platform (http://r2.amc.nl)."], "basis": "The paper names GSE85047, GSE45480, GSE62564, GSE16476, GSE49710 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": ["survival_km"], "assets": ["source:pmid:32580265", "data:geo:GSE16476"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16476"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:44Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 18019, "completion_tokens": 1220, "cached_tokens": 792}}, "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:32580265", "type": "paper", "label": "pmid:32580265"}, {"id": "source:pmid:32580265", "type": "manuscript", "label": "PMID 32580265 full text"}, {"id": "data:geo:GSE16476", "type": "dataset", "label": "GEO GSE16476"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32580265", "type": "paper", "label": "pmid:32580265"}, {"id": "source:pmid:32580265", "type": "manuscript", "label": "PMID 32580265 full text"}, {"id": "data:geo:GSE16476", "type": "dataset", "label": "GEO GSE16476"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32580265", "type": "extraction", "used": ["source:pmid:32580265"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16476", "type": "accession_resolution", "used": ["data:geo:GSE16476"], "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:32580265", "parent_hash": "sha256:57ce3c3c2825670b5b056dcb16817827ac9056303837494b29b21923247d07c4", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE16476 licence not read", "asset:data:geo:GSE16476 not downloaded", "asset:data:geo:GSE45480 licence not read", "asset:data:geo:GSE45480 not downloaded", "asset:data:geo:GSE49710 licence not read", "asset:data:geo:GSE49710 not downloaded", "asset:data:geo:GSE62564 licence not read", "asset:data:geo:GSE62564 not downloaded", "asset:data:geo:GSE85047 licence not read", "asset:data:geo:GSE85047 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["imens and characterize the phenotype of B7H3 knock-down in NB cell line. METHODS: Immunohistochemica", "and flow cytometry were performed after B7H3 knockdown to assess the cellular proliferation and cel", "ociated with improved overall survival. B7H3 knockdown suppressed the proliferation of the SH-SY5Y"], "order_basis": "paper_text_order:260", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["of B7H3 knock-down in NB cell line. METHODS: Immunohistochemical (IHC) staining was carried out to assess the", "NB cell line. METHODS: Immunohistochemical (IHC) staining was carried out to assess the expr", "ing the SH-SY5Y xenograft model. RESULTS: On IHC staining, B7H3 was widely expressed in clini"], "order_basis": "paper_text_order:297", "id": "assay:2"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["GSE16476, GSE49710). Clonogenic survival and flow cytometry were performed after B7H3 knockdown to asses"], "order_basis": "paper_text_order:567", "id": "assay:3"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["of B7H3 silencing on NB growth was examined in vivo using the SH-SY5Y xenograft model. RESULTS:", "eration of the SH-SY5Y NB model in vitro and in vivo. Cell cycle analysis revealed that B7H3 sile"], "order_basis": "paper_text_order:735", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on NB growth was examined in vivo using the SH-SY5Y xenograft model. RESULTS: On IHC staining, B", "nockdown suppressed the proliferation of the SH-SY5Y NB model in vitro and in vivo. Cell cycle an", "classifier. Cell culture Human NB cell line (SH-SY5Y), which was a gift from Professor Liuguan Bi"], "order_basis": "paper_text_order:753", "id": "assay:5"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ETHODS Bioinformatic analysis of NB The five microarray expression profiles (GSE85047, GSE45480, GSE", "rray average method of the linear models for microarray data package in bioconductor was used to per"], "order_basis": "paper_text_order:1534", "id": "assay:6"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan-Meier analysis revealed that high B7H3 expression was associated with poor OS in all five datasets (p<0.05, Fig. 1B-F)."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}