Genomic landscape of the immune microenvironments of brain metastases in breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32867782", "kind": "science-record", "revision": 7, "content_hash": "sha256:f83ac2db416ae0c56b5fb3c5de51186cfa4fc1cc7a41aa779293f9a71027d4c0", "created_at": "2026-11-01T15:41:09Z", "updated_at": "2026-11-01T22:02:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genomic landscape of the immune microenvironments of brain metastases in breast cancer.", "doi": "10.1186/s12967-020-02503-9", "pmid": "32867782", "authors": ["Wei-Cheng Lu", "Hui Xie", "Ce Yuan", "Jin-Jiang Li", "Zhao-Yang Li", "An-Hua Wu"], "journal": "Journal of translational medicine", "year": 2020, "abstract": "BACKGROUND: This study was intended to investigate the genomic landscape of the immune microenvironments of brain metastases in breast cancer.\nMETHODS: Three gene expression profile datasets (GSE76714, GSE125989 and GSE43837) of breast cancer with brain metastases were downloaded from Gene Expression Omnibus (GEO) database. After differential expression analysis, the tumor immune microenvironment and immune cell infiltration were analyzed. Then immune-related genes were identified, followed by function analysis, transcription factor (TF)-miRNA-mRNA co-regulatory network analysis, and survival analysis of metastatic recurrence.\nRESULTS: The present results showed that the tumor immune microenvironment in brain metastases was immunosuppressed compared with primary caner. Compared with primary cancer samples, the infiltration ratio of plasma cells in brain metastases samples was significantly higher, while the infiltration ratio of macrophages M2 cells in brain metastases samples was significantly lower. Total 42 immune-related genes were identified, such as THY1 and NEU2. CD1B, THY1 and DOCK2 were found to be implicated in the metastatic recurrence of breast cancer.\nCONCLUSIONS: Targeting macrophages or plasma cells may be new strategies for immunotherapy of breast cancer with brain metastases. THY1 and NEU2 may be potential therapeutic targets for breast cancer with brain metastases, and THY1, CD1B and DOCK2 may serve as potential prognostic markers for improvement of brain metastases survival.", "claims": [{"id": "claim-method", "statement": "Using the R corrplot package [20], spearman correlation test was conducted on the DEGs and infiltration abundance of differential immune cell subsets, and the DEGs with p value < 0.05 and correlation coefficient |r| > 0.30 were screened, which were considered as the DEGs related to immune cell subgroup.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32867782", "locator": "sections[8] \"Identification of immune-related DEGs\" paragraph 2", "quote": "Using the R corrplot package [20], spearman correlation test was conducted on the DEGs and infiltration abundance of differential immune cell subsets, and the DEGs with p value < 0.05 and correlation coefficient |r| > 0.30 were screened, which were considered as the DEGs related to immune cell subgroup."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available from University of California Santa Cruz Genome Browser and GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32867782", "locator": "sections[32] \"Availability of data and materials\" paragraph 2", "quote": "The data that support the findings of this study are available from University of California Santa Cruz Genome Browser and GEO database."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32867782"], "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:GSE125989"], "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:GSE125989"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32867782", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12967-020-02503-9", "sha256": 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