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pmid:33216732
Oncostatin M expression and TP53 mutation status regulate tumor-infiltration of immune cells and survival outcomes in cholangiocarcinoma.
Qi Liu · Tian Lan · Yuxuan Song · Jianpeng Cai · Xi Yu · Wei Chen
Aging · 2020 doi:10.18632/aging.103936
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Complete file
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We identified 96 differentially expressed genes (DEGs), including 13 upregulated and 83 downregulated genes, in CCA tissues as regulatory T cells were significantly higher and the proportions of activated natural killer cells and monocytes were significantly lower in CCA tissues than the precancerous tissues. The survival outcomes of CCA patients were associated with the TP53 gene mutation status, levels of Oncostatin M (OSM) expression, and the proportions of tumor-infiltrating immune cell types, including dendritic cells, monocytes, and T follicular helper cells. Functional enrichment analysis of the DEGs in the high OSM-expressing CCA tissues showed that pathways related to tumor progression and immune response were significantly upregulated. Our study demonstrates that OSM expression and TP53 mutation status regulate the tumor infiltration by immune cells and survival outcomes in CCA. 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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": ["GSE32225"], "resolved_accessions": ["GSE32225"], "statements": ["We obtained transcriptome data from the TCGA database that included 9 precancerous and 36 CCA tissue samples"], "basis": "The paper names GSE32225 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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RNA-seq data processing We used the R software packa", "wn in the Supplementary Table 2. We obtained transcriptome data from the TCGA database that included 9", "ttps://www.r-project.org) to analyze the RNA transcriptome and somatic nucleotide variation data. We id"], "order_basis": "paper_text_order:148", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ndent predictor of prognosis in CCA patients Western blot assays in 12 paired CCA tumor and adjacent n", "or (T) and adjacent non-tumor tissues (P) by western blotting. (B) Representative immunostaining images of", "or RNA high-throughput sequencing and 12 for western blotting. This study was approved by the Ethics Commi"], "order_basis": "paper_text_order:4655", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["clinicopathological characteristics and OSM immunohistochemistry. We also recruited 5 out of 208 patients bet", "(P) by western blotting. (B) Representative immunostaining images of OSM in CCA. (C) Boxplots depicted", "Sen university cohort of 203 CCA patients by IHC and divided the patients into high- and low-", "=101 and n=102, respectively) using a median IHC expression score of 4 (Figure 6B). Kaplan-Me"], "order_basis": "paper_text_order:5061", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan-Meier survival curve analysis and log-rank test showed that overall survival was significantly shorter for CCA patients with low OSM expression (OSMlow group) compared to those in the OSMhighgroup (Figure 5D)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}