Establishment of a Macrophage Phenotypic Switch Related Prognostic Signature in Patients With Pancreatic Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33747931", "kind": "science-record", "revision": 7, "content_hash": "sha256:43b0d3313c9f4e3f32c147d8d191f6104ef2e63c79e48e9febc364bfab863262", "created_at": "2026-11-01T15:41:29Z", "updated_at": "2026-11-01T22:03:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment of a Macrophage Phenotypic Switch Related Prognostic Signature in Patients With Pancreatic Cancer.", "doi": "10.3389/fonc.2021.619517", "pmid": "33747931", "authors": ["Mu-Xing Li", "Hang-Yan Wang", "Chun-Hui Yuan", "Zhao-Lai Ma", "Bin Jiang", "Lei Li", "Li Zhang", "Dian-Rong Xiu"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "INTRODUCTION: Macrophage phenotype switch plays a vital role in the progression of malignancies. We aimed to build a prognostic signature by exploring the expression pattern of macrophage phenotypic switch related genes (MRGs) in the Cancer Genome Atlas (TCGA)-pancreatic adenocarcinoma (PAAD), Genotype-Tissue Expression (GTEx)-Pancreas, and Gene Expression Omnibus (GEO) databases.\nMETHODS: We identified the differentially expressed genes between the PAAD and normal tissues. We used single factor Cox proportional risk regression analysis, Least Absolute Shrinkage and Selection Operator (LASSO) analysis, and multivariate Cox proportional hazard regression analysis to establish the prognosis risk score by the MRGs. The relationships between the risk score and immune landscape, \"key driver\" mutations and clinicopathological factors were also analyzed. Gene-set enrichment analysis (GSEA) analysis was also performed.\nRESULTS: We detected 198 differentially expressed MRGs. The risk score was constructed based on 9 genes (KIF23, BIN1, LAPTM4A, ERAP2, ATP8B2, FAM118A, RGS16, ELMO1, RAPGEFL1). The median overall survival time of patients in the low-risk group was significantly longer than that of patients in the high-risk group (P < 0.001). The prognostic value of the risk score was validated in GSE62452 dataset. The prognostic performance of nomogram based on risk score was superior to that of TNM stage. And GSEA analysis also showed that the risk score was closely related with P53 signaling pathway, pancreatic cancer and T cell receptor signaling pathway. qRT-PCR assay showed that the expressions of the 9 MRGs in PDAC cell lines were higher than those in human pancreatic ductal epithelium cell line.\nCONCLUSIONS: The nine gene risk score could be used as an independent prognostic index for PAAD patients. Further studies validating the prognostic value of the risk score are warranted.", "claims": [{"id": "claim-method", "statement": "The differentially expressed MRGs between tumor and normal samples were identified using the Wilcoxon signed-rank test in R (version 4.0.2, https://www.r-project.org/) with a threshold of |log(foldchange)| > 1 and a false discovery rate (FDR) < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33747931", "locator": "sections[5] \"Screening of Differentially Expressed MRGs\" paragraph 2", "quote": "The differentially expressed MRGs between tumor and normal samples were identified using the Wilcoxon signed-rank test in R (version 4.0.2, https://www.r-project.org/) with a threshold of |log(foldchange)| > 1 and a false discovery rate (FDR) < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE62452"], "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:group_comparison_wilcoxon", "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:GSE62452"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33747931", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2021.619517", "sha256": "sha256:9ac52040c90f93a8ab047f4e2b21d333648f739d0c0ee9809904774e86b9bb4b", "bytes": 30204, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2021.619517", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7966706", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62452", "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=GSE62452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62452", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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