Nomogram Personalizes and Visualizes the Overall Survival of Patients with Triple-Negative Breast Cancer Based on the Immune Genome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33299869", "kind": "science-record", "revision": 8, "content_hash": "sha256:871051422bc789503a953d2135611e393e615575034b60e50f712bb99ca2e377", "created_at": "2026-11-01T15:41:19Z", "updated_at": "2026-11-01T22:45:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Nomogram Personalizes and Visualizes the Overall Survival of Patients with Triple-Negative Breast Cancer Based on the Immune Genome.", "doi": "10.1155/2020/4029062", "pmid": "33299869", "authors": ["Peipei Wang", "Yang Fu", "Yueyun Chen", "Qing Li", "Ye Hong", "Ting Liu", "Zhenyu Ding"], "journal": "BioMed research international", "year": 2020, "abstract": "BACKGROUND: Triple-negative breast cancer (TNBC) is usually poorly differentiated, highly invasive, susceptible to distant metastasis, and less responsive to endocrine and targeted therapy. However, immunotherapy is a promising treatment for TNBC patients recently.\nMETHODS: The prognostic value of immune-related genes (IRGs) was explored by using RNA sequencing and microarray data of 123 and 107 TNBC patients from TCGA and GEO databases, respectively.\nRESULTS: In TCGA database, GO and KEGG pathway analysis of 119 differential IRGs indicated that they actively participate in the interaction of cytokines and receptors. A nomogram model constructed by the prognosis-related CCL25, IL29, TDGF3, GPR44, and GREM2 in the IRGs could personalize and visualize the 1-, 2-, 3-, 4-, and 5-year overall survival (OS) of TNBC patients. Moreover, TNBC patients could be defined as low-risk (risk score < 194) or high-risk (risk score ≥ 194) cohorts based on the risk score derived from the nomogram model. The results could be validated by the GSE58812 dataset. Furthermore, the risk score was an independent risk factor for TNBC patients (HR = 1.019, 95% CI 1.012-1.027, p < 0.001) and was positively related to stage (p = 0.017). Interestingly, the risk score could reflect the infiltration of B cells, CD4+ T cells, CD8+ T cells, dendritic cells, and neutrophils.\nCONCLUSION: These findings provided a reference for personalized OS prediction in TNBC patients and might be potential immune biomarkers for designing novel therapy.", "claims": [{"id": "claim-method", "statement": "The limma package in R (version 3.6.1) was used to select differential genes between 123 cases of primary TNBC and 13 normal tissues adjacent to tumor.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33299869", "locator": "sections[4] \"2.2. Differential Analysis of Genes\" paragraph 2", "quote": "The limma package in R (version 3.6.1) was used to select differential genes between 123 cases of primary TNBC and 13 normal tissues adjacent to tumor."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used and analyzed during the current study are available from UCSC Xena platform (https://xenabrowser.net/datapages/) and GEO database (https://www.ncbi.nlm.nih.gov/geo/). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33299869", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The data used and analyzed during the current study are available from UCSC Xena platform (https://xenabrowser.net/datapages/) and GEO database (https://www.ncbi.nlm.nih.gov/geo/). The data that support the findings of this study are available from the corresponding author upon reasonable request."}], "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:33299869"], "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:GSE58812"], "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:GSE58812"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33299869", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/4029062", "sha256": "sha256:b2dfa9d1c85fb9aefc6b153126c0923f573558e34b1f99045d945d586c385916", "bytes": 20641, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/4029062", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7709499", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE58812", "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=GSE58812", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58812", "version": null, "note": "The data used and analyzed during the current study are available from UCSC Xena platform (https://xenabrowser.net/datapages/) and GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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