A Novel Prognostic Signature of comprising Nine NK Cell signatures Based on Both Bulk RNA Sequencing and Single-Cell RNA Sequencing for Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37576389", "kind": "science-record", "revision": 2, "content_hash": "sha256:757ef42e0e418374986fdee0f4486737b0f6b6316570e3a2db699a0f42baa287", "created_at": "2026-11-01T19:02:21Z", "updated_at": "2026-11-01T21:31:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Novel Prognostic Signature of comprising Nine NK Cell signatures Based on Both Bulk RNA Sequencing and Single-Cell RNA Sequencing for Hepatocellular Carcinoma.", "doi": "10.7150/jca.85873", "pmid": "37576389", "authors": ["Qi Yu", "Xuefeng Shi", "Hongjian Wang", "Shun Zhang", "Songnian Hu", "Ting Cai"], "journal": "Journal of Cancer", "year": 2023, "abstract": "Background: Hepatocellular carcinoma (HCC) has limited prognostic prediction due to its heterogeneity. Understanding the role of natural killer (NK) cells in HCC is vital for prognosis and immunotherapy guidance. We aimed to identify NK cell marker genes through scRNA-seq and develop a prognostic signature for HCC. Methods: We analyzed scRNA-seq data (GSE149614) from 10 patients and bulk RNA-seq data from 786 patients with clinicopathological information. NK cell marker genes were identified using clustering and marker finding functions. A predictive risk signature was constructed using LASSO-COX algorithm. Functional annotations and immune cell infiltration analysis were performed, and the nomogram's performance was evaluated. Results: We identified 79 NK cell marker genes associated with NK cell-mediated cytotoxicity, apoptosis, and immune response. The multigene signature significantly correlated with overall survival (OS) in TCGA-LIHC cohort and was validated in other cohorts. Low-risk patients exhibited higher immune cell infiltration, including CD8+ T cells. The risk signature was an independent prognostic factor for OS (HR > 1, p < 0.001). The nomogram combining the risk signature and clinical predictors demonstrated robust prognostic ability. Conclusion: We developed a nine-gene signature prognostic model based on NK cell marker genes to accurately assess the prognostic risk of HCC. This model can be a valuable tool for personalized evaluation post-surgery. Our study underscores the potential of NK cells in HCC prognosis and highlights the importance of scRNA-seq analysis in identifying prognostic markers.", "claims": [{"id": "claim-method", "statement": "A predictive risk signature was constructed using LASSO-COX algorithm.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37576389", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "A predictive risk signature was constructed using LASSO-COX algorithm."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The scRNA-seq data from 10 primary tumor samples and 8 adjacent normal samples of GSE149614 dataset were obtained from the GEO database and were used to identify NK cell marker genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37576389", "locator": "sections[3] \"Data Collection and Preprocessing\" paragraph 2", "quote": "The scRNA-seq data from 10 primary tumor samples and 8 adjacent normal samples of GSE149614 dataset were obtained from the GEO database and were used to identify NK cell marker genes."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We developed a nine-gene signature prognostic model based on NK cell marker genes to accurately assess the prognostic risk of HCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37576389", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We developed a nine-gene signature prognostic model based on NK cell marker genes to accurately assess the prognostic risk of HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We developed a nine-gene signature prognostic model based on NK cell marker genes to accurately assess the prognostic risk of HCC.", "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:37576389"], "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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