Tumor microenvironment characterization in cervical cancer identifies prognostic relevant gene signatures.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33901225", "kind": "science-record", "revision": 8, "content_hash": "sha256:94cbf646b8326b6979594f9cb092bd01d8b3ba61b073eefa631501d78f3c20cd", "created_at": "2026-11-01T15:41:33Z", "updated_at": "2026-11-01T22:03:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Tumor microenvironment characterization in cervical cancer identifies prognostic relevant gene signatures.", "doi": "10.1371/journal.pone.0249374", "pmid": "33901225", "authors": ["Linyu Peng", "Gati Hayatullah", "Haiyan Zhou", "Shuzhen Chang", "Liya Liu", "Haifeng Qiu", "Xiaoran Duan", "Liping Han"], "journal": "PloS one", "year": 2021, "abstract": "OBJECTIVE: The aim of this study is to systematically analyze the transcriptional sequencing data of cervical cancer (CC) to find an Tumor microenvironment (TME) prognostic marker to predict the survival of CC patients.\nMETHODS: The expression profiles and clinical follow-up information of CC were downloaded from the TCGA and GEO. The RNA-seq data of TCGA-CESC samples were used for CIBERSORT analysis to evaluate the penetration pattern of TME in 285 patients, and construct TMEscore. Other data sets were used to validate and evaluate TMEscore model. Further, survival analysis of TMEscore related DEGs was done to select prognosis genes. Functional enrichment and PPI networks analysis were performed on prognosis genes.\nRESULTS: The TMEscore model has relatively good results in TCGA-CESC (HR = 2.47,95% CI = 1.49-4.11), TCGA-CESC HPV infection samples (HR = 2.13,95% CI = 1-4.51), GSE52903 (HR = 2.65, 95% CI = 1.06-6.6), GSE44001 (HR = 2.1, 95% CI = 0.99-4.43). Patients with high/low TMEscore have significant difference in prognosis (log-rank test, P = 0.00025), and the main difference between high TMEscore subtypes and low TMEscore subtypes is immune function-related pathways. Moreover, Kaplan-Meier survival curves found out a list of identified prognosis genes (n = 86) which interestingly show significant enrichment in immune-related functions. Finally, PPI network analysis shows that highly related nodes such as CD3D, CD3E, CD8A, CD27 in the module may become new targets of CC immunotherapy.\nCONCLUSIONS: TMEscore may become a new prognostic indicator predicting the survival of CC patients. The prognostic genes (n = 86) may help provide new strategies for tumor immunotherapy.", "claims": [{"id": "claim-method", "statement": "The survival curve is generated by Kaplan-Meier method (R package survminer) and the difference is analyzed by log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33901225", "locator": "sections[15] \"7. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE44001"], "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:GSE44001"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33901225", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0249374", "sha256": 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