{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40628510", "kind": "science-record", "revision": 2, "content_hash": "sha256:2723a8b4c4952c54c45c20af4ed500e0a900abc7e0668e7a6dc11e865c0efc84", "created_at": "2026-11-01T20:30:43Z", "updated_at": "2026-11-01T21:35:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Application and mechanisms of targeting BRD4 in osteosarcoma.", "doi": "10.11817/j.issn.1672-7347.2025.240628", "pmid": "40628510", "authors": ["Ding Chen", "Jiaming Tian", "Yihe Dong", "Zi Li", "Jun Huang"], "journal": "Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences", "year": 2025, "abstract": "OBJECTIVES: Metastasis is the primary cause of death in osteosarcoma, and current clinical treatments remain limited. BRD4, a key epigenetic regulator, has shown therapeutic promise in various cancers through its inhibition. However, the mechanistic role of BRD4 in osteosarcoma remains poorly understood. This study aims to elucidate the molecular mechanisms by which BRD4 regulate osteosarcoma progression and to explore novel therapeutic strategies.\nMETHODS: Immunofluorescence was used to assess BRD4 expression levels in a tissue microarray containing 80 osteosarcoma samples from different patients. The Gene Expression Omnibus (GEO) dataset (GSE42352, containing survival data from 88 osteosarcoma patients) was downloaded to perform Kaplan-Meier survival analysis based on BRD4 gene expression levels. In vivo, an orthotopic intramedullary osteosarcoma model was established using HOS cells in C57 mice, followed by treatment with varying doses of the BRD4 inhibitor (+)-JQ1. Micro-CT, 3D reconstruction of bone tissue, and HE staining were employed to evaluate pathological changes in bone and intestinal lymph nodes. In vitro, cell viability was measured using the methyl thiazolyl tetrazolium (MTT) assay, while colony formation and Transwell assays assessed proliferative and invasive capacities. Chromatin-bound BRD4 was analyzed via co-immunoprecipitation combined with mass spectrometry (Co-IP/MS), and O-GlcNAc glycosylation sites and glycan chains of BRD4 were identified using Co-IP with Nano-LC MS/MS. Real-time PCR and Western blotting were used to analyze the relative mRNA and protein expression levels of target genes, respectively.\nRESULTS: BRD4 was positively expressed in 61.25% (49/80) of osteosarcoma tissues. Patients with high BRD4 expression exhibited significantly shorter survival times (P<0.05). In the orthotopic mouse model, intervention with (+)-JQ1, a potent and commonly used BETi, significantly inhibited tumor growth in vivo and reduced bone destruction (P<0.05). (+)-JQ1 treatment significantly suppressed the proliferation (P<0.001), invasion (P<0.001), and migration (P<0.05) of HOS cells. In osteosarcoma cells, BRD4 exhibited O-GlcNAc modifications at both N- and C- C-termini, particularly at Thr73, which is essential for protein stability. This modification also contributed to the activation of the EGFR tyrosine kinase inhibitor resistance pathway (KEGG Pathway: hsa01521). (+)-JQ1 treatment displaced BRD4 from enhancers and downregulated the transcription of pathway-related genes, such as EGFR and PDGFC, thereby suppressing the malignant behavior of osteosarcoma cells.\nCONCLUSIONS: BRD4 promotes osteosarcoma progression via O-GlcNAc modification at Thr73 and plays a crucial role in tumor growth and metastasis.", "claims": [{"id": "claim-method", "statement": "下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40628510", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40628510", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "BRD4在骨肉瘤组织中阳性表达率达61.25%(49/80)，且高表达患者的生存期显著缩短(P<0.05)。", "kind": "quantitative", "target": {"value": 61.25, "unit": "per cent", "tolerance": null, "source": "BRD4在骨肉瘤组织中阳性表达率达61.25%(49/80)，且高表达患者的生存期显著缩短(P<0.05)。"}, "evidence": [{"asset": "source:pmid:40628510", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "BRD4在骨肉瘤组织中阳性表达率达61.25%(49/80)，且高表达患者的生存期显著缩短(P<0.05)。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "BRD4在骨肉瘤组织中阳性表达率达61.25%(49/80)，且高表达患者的生存期显著缩短(P<0.05)。", "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:40628510"], "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:GSE42352"], "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:GSE42352"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40628510", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.11817/j.issn.1672-7347.2025.240628", "sha256": "sha256:ca179b428dcb4bb6f3d5aa4a3b3eff9928f4de16e1a8169b0a0f683aa65b016e", "bytes": 22360, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.11817/j.issn.1672-7347.2025.240628", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC13345772", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE42352", "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=GSE42352", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42352", "version": null, "note": "下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1038236", "GSM1038237", "GSM1038238", "GSM1038239", "GSM1038240", "GSM1038241", "GSM1038242", "GSM1038243", "GSM1038244", "GSM1038245", "GSM1038246", "GSM1038247", "GSM1038248", "GSM1038249", "GSM1038250", "GSM1038251", "GSM1038252", "GSM1038253", "GSM1038254", "GSM717846", "GSM717847", "GSM717848", "GSM717849", "GSM717850", "GSM717851", "GSM717852", "GSM717853", "GSM717854", "GSM717855", "GSM717856", "GSM717857", "GSM825623", "GSM825624", "GSM825625", "GSM825626", "GSM825627", "GSM825628", "GSM825629", "GSM825630", "GSM825631", "GSM825632", "GSM825633", "GSM825634", "GSM825635", "GSM825636", "GSM825637", "GSM825638", "GSM825639", "GSM825640", "GSM825641", "GSM825642", "GSM825643", "GSM825644", "GSM825645", "GSM825646", "GSM825647", "GSM825648", "GSM825649", "GSM825650", "GSM825651", "GSM825652", "GSM825653", "GSM825654", "GSM825655", "GSM825656", "GSM825657", "GSM825658", "GSM825659", "GSM825660", "GSM825661", "GSM825662", "GSM825663", "GSM825664", "GSM825665", "GSM825666", "GSM825667", "GSM825668", "GSM825669", "GSM825670", "GSM825671", "GSM825672", "GSM825673", "GSM825674", "GSM825675", "GSM825676", "GSM825677", "GSM825678", "GSM825679", "GSM825680", "GSM825681", "GSM825682", "GSM825683", "GSM825684", "GSM825685", "GSM825686", "GSM825687", "GSM825688", "GSM825689", "GSM825690", "GSM825691", "GSM825692", "GSM825693", "GSM825694", "GSM825695", "GSM825696", "GSM825697", "GSM825698", "GSM825699", "GSM825700", "GSM825701", "GSM825702", "GSM825703", "GSM825704", "GSM825705", "GSM825706", "GSM825707", "GSM825708", "GSM825709"], "sample_count": 118, "group_sizes": null, "group_sizes_basis": null, "platform": "10295", "taxon": "Homo sapiens", "title": "Genome-wide gene expression profiling of mesenchymal stem cells, osteosarcoma cells, and osteosarcoma cell lines.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE42352 not downloaded", "asset:data:geo:GSE42352 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "survival_km", "expected_value": 61.25, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "survival_km", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. 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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": ["GSE42352"], "resolved_accessions": ["GSE42352"], "statements": ["下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。"], "basis": "The paper names GSE42352 in 基因表达综合(Gene Expression Omnibus，GEO) and the accession resolves in the repository. 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METHODS: Immunofluorescence was used to assess BRD4 expression levels in"], "order_basis": "paper_text_order:479", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["to assess BRD4 expression levels in a tissue microarray containing 80 osteosarcoma samples from diff"], "order_basis": "paper_text_order:552", "id": "assay:2"}, {"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": ["r survival times (P<0.05). In the orthotopic mouse model, intervention with (+)-JQ1, a potent and com", "alysis based on BRD4 gene expression levels. In vivo, an orthotopic intramedullary osteosarcoma m", "d BETi, significantly inhibited tumor growth in vivo and reduced bone destruction (P<0.05). (+)-J", "r survival times (P<0.05). 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Real-time PCR and Western blotting were used to analyze th"], "order_basis": "paper_text_order:1538", "id": "assay:6"}, {"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": ["Co-IP with Nano-LC MS/MS. Real-time PCR and Western blotting were used to analyze the relative mRNA and p"], "order_basis": "paper_text_order:1557", "id": "assay:7"}, {"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": ["下载基因表达综合(Gene Expression Omnibus，GEO)基因芯片数据集(GSE42352，含88例骨肉瘤患者生存信息)，采用Kaplan-Meier(K-M)曲线分析BRD4的表达水平对骨肉瘤患者生存期的影响。"], "order_basis": "consumes_earlier_output", "id": "assay:8"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. 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Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}