Combined analysis of bulk and single-cell RNA sequencing reveals novel natural killer cell-related prognostic biomarkers for predicting immunotherapeutic response in hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37056756", "kind": "science-record", "revision": 2, "content_hash": "sha256:79fc745f98ad86aa82d8cf1da6278a168eb4ffa1ad779916ffa9ce92239f9bbf", "created_at": "2026-11-01T19:01:42Z", "updated_at": "2026-11-01T21:30:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Combined analysis of bulk and single-cell RNA sequencing reveals novel natural killer cell-related prognostic biomarkers for predicting immunotherapeutic response in hepatocellular carcinoma.", "doi": "10.3389/fimmu.2023.1142126", "pmid": "37056756", "authors": ["Kai Zhang", "Enwu Yuan"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "Introduction: Natural killer (NK) cells play an irreplaceable and important role as a subtype of innate immune cells in the contemporary setting of antitumor immunity.\nMethods: We chose a total of 1,196 samples for this analysis from the public dataset's six separate cohorts. To identify 42 NK cell marker genes, we first carried out a thorough study of single-cell RNA sequencing data from the GSE149614 cohort of hepatocellular carcinoma (HCC).\nResults: Using the NK cell marker genes in the TCGA cohort, we next created a seven-gene prognostic signature, separating the patients into two categories with distinct survival patterns. This signature's prognostic prediction ability was well verified across several validation cohorts. Patients with high scores had higher TIDE scores but lower immune cell infiltration percentages. Importantly, low-scoring patients had superior immunotherapy response and prognosis than high-scoring patients in an independent immunotherapy cohort (IMvigor210). Finally, we used CD56 and TUBA1B antibodies for immunohistochemical labeling of HCC tissue sections, and we discovered a lower number of CD56+ cells in the HCC tissue sections with high TUBA1B expression.\nDiscussion: In summary, our research created a unique prognostic profile based on NK cell marker genes that may accurately predict how well immunotherapy would work for HCC patients.", "claims": [{"id": "claim-method", "statement": "A univariate Cox regression analysis with P less than 0.05 was then used to further identify the genes among these NK marker genes that are associated with prognosis. We used the LASO-Cox regression to compress the number of genes and created a risk profile based on the outcomes of the multivariate Cox model using the equation: Risk score =∑iCoefficient (Genei)*Expression (Genei).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37056756", "locator": "sections[4] \"Identification of NK cells and their hub genes\" paragraph 2", "quote": "A univariate Cox regression analysis with P less than 0.05 was then used to further identify the genes among these NK marker genes that are associated with prognosis. We used the LASO-Cox regression to compress the number of genes and created a risk profile based on the outcomes of the multivariate Cox model using the equation: Risk score =∑iCoefficient (Genei)*Expression (Genei)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found within the article/ Supplementary Materials .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37056756", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found within the article/ Supplementary Materials ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the NK cell marker genes in the TCGA cohort, we next created a seven-gene prognostic signature, separating the patients into two categories with distinct survival patterns.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37056756", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Using the NK cell marker genes in the TCGA cohort, we next created a seven-gene prognostic signature, separating the patients into two categories with distinct survival patterns."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the NK cell marker genes in the TCGA cohort, we next created a seven-gene prognostic signature, separating the patients into two categories with distinct survival patterns.", "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:37056756"], "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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(A) The TSNE plots showed the distr"], "order_basis": "paper_text_order:0", "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": ["ally, we used CD56 and TUBA1B antibodies for immunohistochemical labeling of HCC tissue sections, and we disc", "629) and CD56 (Abcam, ab75813) antibodies in IHC experiments on formalin-fixed de-paraffinize"], "order_basis": "paper_text_order:1192", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["A univariate Cox regression analysis with P less than 0.05 was then used to further identify the genes among these NK marker genes that are associated with prognosis. 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