Association of GATA3 expression in triple-positive breast cancer with overall survival and immune cell infiltration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39090342", "kind": "science-record", "revision": 3, "content_hash": "sha256:fe1fd22c23c813edbcff7e339ae19c62e71aaf3afc402f3e0f11bf53cab20d15", "created_at": "2026-11-01T20:29:10Z", "updated_at": "2026-11-01T22:12:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Association of GATA3 expression in triple-positive breast cancer with overall survival and immune cell infiltration.", "doi": "10.1038/s41598-024-68788-8", "pmid": "39090342", "authors": ["Xiuwen Chen", "Weilin Zhao", "Yugang Huang", "Senyuan Luo", "Xianbin Tang", "Qiong Yi"], "journal": "Scientific reports", "year": 2024, "abstract": "Breast cancer remains a leading cause of cancer-related mortality among women, with triple-positive breast cancer (TPBC) being a particularly aggressive subtype. GATA binding protein 3 (GATA3) plays a crucial role in the luminal differentiation of breast epithelium and T-cell differentiation. However, the relationship between GATA3 and immune infiltration in TPBC remains unclear. This study collected and analyzed TPBC data from The Cancer Genome Atlas (TCGA), METABRIC, and GSE123845 databases. Univariate and multivariate Cox regression analyses, along with Kaplan-Meier survival analyses, were employed to assess the prognostic value of GATA3 and other clinical features. Subsequently, Gene Set Enrichment Analysis (GSEA) was conducted to explore the potential biological functions and regulatory mechanisms of GATA3 in TPBC. Additionally, ssGSEA analysis revealed the connection between GATA3 and immune infiltration. And the effects of neoadjuvant chemotherapy and immunotherapy on GATA3 expression were also explored. Finally, clinical samples were used to detect the relationship between GATA3 expression and tumor infiltrating lymphocyte (TIL) levels. Our results demonstrated that GATA3 was significantly overexpressed in TPBC tissues compared to normal tissues (P < 0.05). A positive correlation between GATA3 mRNA and protein levels was observed (R = 0.55, P < 0.05). Notably, high GATA3 expression was associated with poor overall survival (HR = 1.24, 95% confidence interval (CI) 1.25-11.76, P < 0.05). GSEA indicated significant enrichment of immune-related gene sets in low GATA3 expression groups. Furthermore, pathologic complete response (pCR) patients exhibited significantly lower GATA3 expression compared to residual disease (RD) patients. Mutation analysis revealed higher PIK3CA and TP53 mutation rates in high GATA3 expression groups. Finally, clinical validation data showed that the degree of TILs was significantly higher in the low GATA3 expression group. In conclusion, this study suggests that high GATA3 expression may be associated with poor prognosis and may reduce immune infiltration in TPBC.", "claims": [{"id": "claim-method", "statement": "The single-sample Gene Set Enrichment Analysis (ssGSEA) method, implemented in the GSVA R package20, was used to estimate the ratio of immune cell infiltration between the GATA3 high- and low-expression subgroups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39090342", "locator": "sections[6] \"Association between GATA3 expression and immune infiltration\" paragraph 2", "quote": "The single-sample Gene Set Enrichment Analysis (ssGSEA) method, implemented in the GSVA R package20, was used to estimate the ratio of immune cell infiltration between the GATA3 high- and low-expression subgroups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The TCGA dataset was obtained from https://portal.gdc.cancer.gov/. The METABRIC dataset was obtained from the https://www.cbioportal.org/study/summary?id=brca_metabric. The GSE123845 dataset was obtained from the https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE123845. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39090342", "locator": "sections[24] \"Data availability\" paragraph 2", "quote": "The TCGA dataset was obtained from https://portal.gdc.cancer.gov/. The METABRIC dataset was obtained from the https://www.cbioportal.org/study/summary?id=brca_metabric. The GSE123845 dataset was obtained from the https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE123845. Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High GATA3 expression may be associated with poor prognosis and may reduce immune infiltration in TPBC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39090342", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In conclusion, this study suggests that high GATA3 expression may be associated with poor prognosis and may reduce immune infiltration in TPBC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High GATA3 expression may be associated with poor prognosis and may reduce immune infiltration in TPBC.", "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:39090342"], "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:GSE123845"], "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:GSE123845"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39090342", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-68788-8", "sha256": "sha256:9d05643b56f1a1542fbdf1b2d1c7425b668bc5a693651ef1bed101fc29bd6634", "bytes": 45879, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-68788-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11294334", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE123845", "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=GSE123845", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE123845", "version": null, "note": "The TCGA dataset was obtained from https://portal.gdc.cancer.gov/. 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Some example images of the GATA3 IHC results were shown in Figure S4. Based on st", "al sample. High GATA3 protein expression (A, IHC × 100) but low TILs (B, HE × 100) in the hig", "p. There is low GATA3 protein expression (C, IHC × 100) but high TILs (D, HE × 100) in the lo"], "order_basis": "paper_text_order:5073", "id": "assay:1"}, {"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": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}