Clinical significance for diagnosis and prognosis of POP1 and its potential role in breast cancer: a comprehensive analysis based on multiple databases.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36084948", "kind": "science-record", "revision": 4, "content_hash": "sha256:791c9928e521e3f7dda0cc9d5771cf5d5373876117cf320fdc7ce62ac63c33cf", "created_at": "2026-11-01T18:15:18Z", "updated_at": "2026-11-01T22:07:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Clinical significance for diagnosis and prognosis of POP1 and its potential role in breast cancer: a comprehensive analysis based on multiple databases.", "doi": "10.18632/aging.204255", "pmid": "36084948", "authors": ["Xiao He", "Ji Wang", "Honghao Yu", "Wenchang Lv", "Yichen Wang", "Qi Zhang", "Zeming Liu", "Yiping Wu"], "journal": "Aging", "year": 2022, "abstract": "BACKGROUND: Breast cancer (BC) is one of the most common cancers in women. The discovery of available biomarkers is crucial for early diagnosis and improving prognosis. The effect of POP1 in BC remains unrevealed. Our study aims to explore the expression of POP1 in BC and demonstrate its clinical significance and potential molecular mechanisms.\nMETHODS: The Cancer Genome Atlas (TCGA) BC cohort transcriptome data and corresponding clinical information were downloaded. GSE42568 cohort, GSE162228 cohort, GSE7904 cohort, and GSE161533 cohort in the Gene Expression Omnibus (GEO) database were used as verification groups. R software and several web tools were used for statistical analysis. Moreover, the proliferation, transwell, wound healing experiments, and flow cytometry were used for in vitro investigation.\nRESULTS: Compared with normal breast tissue, POP1 expression was up-regulated in BC tissue with a higher mutation rate. POP1 had good diagnostic value for BC and could be utilized as a new marker. POP1 was significantly correlated with multiple pathways in BC and played an important role in the immune infiltration of BC. High-POP1 expression patients were more prone to be responded to immunotherapy and had a significantly higher percentage of immunotherapy response rate. Moreover, POP1 promoted proliferation and migration and inhibited apoptosis in BC cells.\nCONCLUSIONS: POP1 expression was up-regulated in BC and was associated with a poor prognosis. Patients with high-POP1 expression were more likely to be responded to immunotherapy. Our study can provide a potential marker POP1 for BC, which is beneficial in the diagnosis and treatment of BC.", "claims": [{"id": "claim-method", "statement": "The results suggested that the heterogeneity was less than 50%, so the fixed effect model was applied for analysis (Figure 4A, SMD = 0.95, 95% CI: 0.78, 1.12).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36084948", "locator": "sections[19] \"Meta-analysis of multiple cohorts to demonstrate the POP1 role in BC\" paragraph 2", "quote": "The results suggested that the heterogeneity was less than 50%, so the fixed effect model was applied for analysis (Figure 4A, SMD = 0.95, 95% CI: 0.78, 1.12)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets provided for this study can be found in online repositories. The name and accession number(s) of the repository/repositories can be found in the article Supplementary Materials.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36084948", "locator": "sections[14] \"Availability of data and materials\" paragraph 2", "quote": "The datasets provided for this study can be found in online repositories. The name and accession number(s) of the repository/repositories can be found in the article Supplementary Materials."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Meta-analysis of five TCGA and GEO cohorts confirmed higher POP1 expression in breast cancer, with a pooled standardized mean difference of 0.95.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36084948", "locator": "sections[19] \"Meta-analysis of multiple cohorts to demonstrate the POP1 role in BC\" paragraph 2", "quote": "The results suggested that the heterogeneity was less than 50%, so the fixed effect model was applied for analysis (Figure 4A, SMD = 0.95, 95% CI: 0.78, 1.12)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Meta-analysis of five TCGA and GEO cohorts confirmed higher POP1 expression in breast cancer, with a pooled standardized mean difference of 0.95.", "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:36084948"], "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:GSE161533"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:fixed_effects_pool", "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:GSE161533"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:fixed_effects_pool"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36084948", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.204255", "sha256": "sha256:3281e28ae123dd6ce07d6bdbdcfe46612fc1a7bd4acd444e482cac5d886e0423", "bytes": 51317, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.204255", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9512506", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE161533", "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=GSE161533", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE161533", "version": null, "note": "The datasets provided for this study can be found in online repositories. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36084948", "data:geo:GSE161533"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "fixed_effects_pool", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE161533"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:04:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15057, "completion_tokens": 1858, "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:36084948", "type": "paper", "label": "pmid:36084948"}, {"id": "source:pmid:36084948", "type": "manuscript", "label": "PMID 36084948 full text"}, {"id": "data:geo:GSE161533", "type": "dataset", "label": "GEO GSE161533"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36084948", "type": "paper", "label": "pmid:36084948"}, {"id": "source:pmid:36084948", "type": "manuscript", "label": "PMID 36084948 full text"}, {"id": "data:geo:GSE161533", "type": "dataset", "label": "GEO GSE161533"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36084948", "type": "extraction", "used": ["source:pmid:36084948"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE161533", "type": "accession_resolution", "used": ["data:geo:GSE161533"], "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:36084948", "parent_hash": "sha256:5717e6471c44f92ca2df886a46eccff33ba4cd7ba99d51ce23465403e653fb71", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE161533 licence not read", "asset:data:geo:GSE161533 not downloaded", "asset:data:geo:GSE162228 licence not read", "asset:data:geo:GSE162228 not downloaded", "asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE7904 licence not read", "asset:data:geo:GSE7904 not downloaded", "execution.not_run", "method.fixed_effects_pool", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:fixed_effects_pool"], "assays": [{"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": ["n, transwell, wound healing experiments, and flow cytometry were used for in vitro investigation. RESULT"], "order_basis": "paper_text_order:872", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ed proliferation and migration and inhibited apoptosis in BC cells. CONCLUSIONS: POP1 expression wa"], "order_basis": "paper_text_order:1467", "id": "assay:2"}, {"role": "analysis", "definition_id": "meta_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The results suggested that the heterogeneity was less than 50%, so the fixed effect model was applied for analysis (Figure 4A, SMD = 0.95, 95% CI: 0.78, 1.12)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}