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pmid:33030278
Tumor purity as a prognosis and immunotherapy relevant feature in gastric cancer.
Zhe Gong · Jieyun Zhang · Weijian Guo
Cancer medicine · 2020 doi:10.1002/cam4.3505
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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However, the current staging and prognostic prediction system in gastric cancer (GC) paid little attention to TME. Therefore, we carried out the study to explore the role of tumor purity in GC. We retrospectively collected the clinical and transcriptomic data from four public data sets (n = 1340), GSE15459, GSE26253, GSE62254, and The Cancer Genome Atlas (TCGA). About 34 GC patients from Fudan University Shanghai Cancer Center (FUSCC) were assigned as an independent validation group. Tumor purity was measured by a computational method. Low tumor purity was associated with unfavorable prognosis, upregulated EMT and stemness pathways, more infiltrating of Tregs, M1 and M2 macrophages and a higher expression level of various immune checkpoints and chemokines recruiting immune suppressive cells. Our study indicates low tumor purity in GC was associated with unfavorable prognosis and immune-evasion phenotype. 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"read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#cam43505-tbl-0003", "version": null, "note": "The expression levels of immune checkpoints and chemokines between different tumor purity groups in TCGA and FUSCC cohorts", "structure": {"pmcid": "PMC7724479", "section_index": 11, "section_title": "Low‐purity group had a higher expression level of immune checkpoints and chemokines", "row_count": 14, "column_count": 8}, "table": {"label": "Table 3", "caption": "The expression levels of immune checkpoints and chemokines between different tumor purity groups in TCGA and FUSCC cohorts", "rows": [["", "Variable", "TCGA‐STAD", "FUSCC"], ["low purity", "high‐purity", "low purity", "high purity"], ["avg.", "avg.", "p value", "avg.", "avg.", "p value"], ["Immune checkpoints", "PD‐L1", "155.72", "45.36", "0.009", "2.29", "2.06", "0.769"], ["PD‐1", "119.82", "42.55", "<0.001", "2.47", "0.65", "0.011"], ["LAG3", "312.98", "110.78", "<0.001", "3.59", "1.53", 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[{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-2", "family": null, "specific": null, "label": "ESTIMATE algorithm", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used ESTIMATE R package to infer tumor purity in gastric tumor tissue."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE15459", "GSE26253", "GSE62254"], "resolved_accessions": ["GSE15459", "GSE26253", "GSE62254"], "statements": ["The data sets generated and analyzed during the current study are available in the TCGA, GEO, and CCLE repository, TCGA: https://portal.gdc.cancer.gov GEO: https://www.ncbi.nlm.nih.gov/geo CCLE: https://portals.broadinstitute.org/ccle. FUSCC cohort data used and analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE15459, GSE26253, GSE62254 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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