Comprehensive profiling of cell subsets of gastric cancer and liver metastasis based on single cell RNA-sequencing analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38410212", "kind": "science-record", "revision": 4, "content_hash": "sha256:0ca0d591d5e5a3b4166d6c83692c4852b281dda7b521aadf33edd4ecc053a21d", "created_at": "2026-11-01T19:20:21Z", "updated_at": "2026-11-01T22:11:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive profiling of cell subsets of gastric cancer and liver metastasis based on single cell RNA-sequencing analysis.", "doi": "10.21037/tcr-23-1532", "pmid": "38410212", "authors": ["Meng Pan", "Peng Chen", "Qi Zhang", "Yuquan Yang", "Weichao Hu", "Guanglong Hu", "Rongsheng Wang", "Xiaopeng Chen"], "journal": "Translational cancer research", "year": 2024, "abstract": "Background: Liver metastasis (Li) is one of the most common distant metastatic sites for gastric cancer. A deeper understanding of its mechanism of action from a bioinformatics perspective may provide new insights. Therefore, the aim of this study was to use single cell RNA sequencing (scRNA-seq) to evaluate cell subtypes and understand the molecular mechanism of gastric cancer Li.\nMethods: The scRNA-seq data GSE163558 of gastric cancer and Li were downloaded from Gene Expression Omnibus (GEO). Single cell data were analyzed by various R packages such as Seurat, CellChat, gene set variation analysis (GSVA), monocle, gene set enrichment analysis (GSEA), and survival analysis and the results were plotted by ggplot2, R4.1.1. Protein expression was confirmed by immunohistochemistry in an additional patient cohort.\nResults: The genes APOD, CXCL5, and JUN are involved in epithelial cell metastasis. The infiltration of cytotoxic CD8 T cells was more frequent in gastric primary tumors (PTs) than in Lis. IL7R high natural killer (NK) cells that had high TXNIP and RIPOR2 expression were located at the site of Li and corresponded to a favorable prognosis. NK cells with high TNFAIP3 expression were located at the PT site and corresponded to a poor prognosis. Furthermore, the gene expression of myeloid cells was different depending on their localization in the PT site or Li. MHC-I signaling pathway was found to be activated in the PT compared to MHC-II at the site of Li, as revealed by cell-cell interaction, and HLA-E-CD94/NKG2A of NK cells was only activated in the PT and not in the Li.\nConclusions: The present study revealed the difference between Li and gastric PT by scRNA-seq, demonstrating the impact of partial gene expression on patient prognosis. Our study provides new insights into gastric cancer and Li.", "claims": [{"id": "claim-method", "statement": "The pseudotime analysis of epithelial cells by monocle2 was used combined with Seurat to evaluate gene changes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38410212", "locator": "sections[6] \"Pseudotime analysis of cell progression\" paragraph 2", "quote": "The pseudotime analysis of epithelial cells by monocle2 was used combined with Seurat to evaluate gene changes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1532/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38410212", "locator": "sections[28] \"fn-group\" paragraph 1", "quote": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1532/dss"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The prognostic results of APOD [P<0.001, hazard ratio (HR) >1], CXCL5 (P<0.001, HR >1), GC (P=0.0036, HR <1), and JUN (P=0.0087, HR >1) genes were statistically analyzed (Figure 2H-2K), revealing that results of these four genes in STAD and LIHC were consistent with those of the integrative analysis (Figure S2B-S2I).", "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:38410212"], "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. 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Methods: The scRNA-seq data GSE163558 of gastric cancer and Li were", "the difference between Li and gastric PT by scRNA-seq, demonstrating the impact of partial gene ex"], "order_basis": "paper_text_order:367", "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": ["R4.1.1. Protein expression was confirmed by immunohistochemistry in an additional patient cohort. Results: Th", "ab.github.io/monocle-release/). Patients and immunohistochemistry (IHC) The study was reviewed and approved by", "elease/). Patients and immunohistochemistry (IHC) The study was reviewed and approved by the", "tissues and Li tissues from these patients. 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