Intra-tumoral NK cells and their association with patient outcomes: a novel prognostic model incorporating NK cells and clinicopathologic features in gastric cancer.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41607772", "kind": "science-record", "revision": 2, "content_hash": "sha256:c213737a50cee1927534588e4db5fedecb18239b79952fe51f82ed44b20a20c9", "created_at": "2026-11-01T20:31:42Z", "updated_at": "2026-11-01T21:36:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Intra-tumoral NK cells and their association with patient outcomes: a novel prognostic model incorporating NK cells and clinicopathologic features in gastric cancer.", "doi": "10.3389/fimmu.2025.1760280", "pmid": "41607772", "authors": ["Masanori Oshi", "Yuko Tamura", "Rongrong Wu", "Colin J Rog", "Li Yan", "Kizuki Yuza", "Takashi Kosaka", "Hirotoshi Akiyama", "Takashi Ishikawa", "Kazuaki Takabe", "Itaru Endo"], "journal": "Frontiers in immunology", "year": 2025, "abstract": "Background: Natural killer (NK) cell infiltration has been implicated in the prognosis of gastric cancer patients. However, NK cell infiltration fraction has not yet been used routinely in clinical practice due to a lack of a measure for accurate quantification.\nMethods: NK cell infiltration fraction was quantified using a deconvolution tool and its clinical relevance was investigated in gastric cancer patients from our institution (Yokohama City University Hospital (YCU) and those present in publicly available cohorts with transcriptome data (TCGA, GSE84437 and GSE150290).\nResults: In the single cell sequencing cohort, the distribution of NK cells was similar to that of NK cell-related gene expression. High NK cell infiltration in gastric cancer correlated with enriched immune gene sets, such as IFN-α and IFN-γ responses, and also linked to increased cytolytic activity and low stromal cell infiltration along with higher mutation rates. Clinically, high NK cell infiltration was associated with better overall survival and improved response to neoadjuvant chemotherapy. Additionally, combining NK cell score with clinicopathological factors, including age at a diagnosis and AJCC T- and N-category, provided a powerful prognostic score for gastric cancer patients which was found to be consistent in multiple cohorts.\nConclusions: Gastric cancer with high NK cell infiltration is associated with increased immune activity and lower stromal cell infiltration, potentially impacting patient prognosis. Combining clinicopathological factors with NK cell score provides a powerful tool for prognostication of gastric cancer patients.", "claims": [{"id": "claim-method", "statement": "To this end, we utilized a LASSO Cox algorithm with several factors, including age at a diagnosis, AJCC-T and N category, and NK cell infiltration fraction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41607772", "locator": "sections[15] \"A novel score including NK cell infiltration fraction and clinicopathologic features was a strong prognostic biomarker in various independent cohorts\" paragraph 2", "quote": "To this end, we utilized a LASSO Cox algorithm with several factors, including age at a diagnosis, AJCC-T and N category, and NK cell infiltration fraction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: The Cancer Genome Atlas (TCGA) and GSE84437 are all publicly available without any restrictions via cBioportal or Gene Expression Omnibus (GEO). The dataset of YCU cohort is available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41607772", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: The Cancer Genome Atlas (TCGA) and GSE84437 are all publicly available without any restrictions via cBioportal or Gene Expression Omnibus (GEO). The dataset of YCU cohort is available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Interestingly, we found that high novel score was significantly associated with worse overall survival of gastric cancer patients not only in GSE84437 cohort but also in the TCGA and YCU cohorts (Figure 5A, p < 0.001, p < 0.001, and p = 0.046, respectively).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41607772", "locator": "sections[15] \"A novel score including NK cell infiltration fraction and clinicopathologic features was a strong prognostic biomarker in various independent cohorts\" paragraph 4", "quote": "Interestingly, we found that high novel score was significantly associated with worse overall survival of gastric cancer patients not only in GSE84437 cohort but also in the TCGA and YCU cohorts (Figure 5A, p < 0.001, p < 0.001, and p = 0.046, respectively)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Interestingly, we found that high novel score was significantly associated with worse overall survival of gastric cancer patients not only in GSE84437 cohort but also in the TCGA and YCU cohorts (Figure 5A, p < 0.001, p < 0.001, and p = 0.046, respectively).", "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:41607772"], "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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