Tumor purity-associated genes influence hepatocellular carcinoma prognosis and tumor microenvironment.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37434985", "kind": "science-record", "revision": 3, "content_hash": "sha256:b18aafffda65d5660596ab158a95be7ad234cb19bfbde70fb8cea86c4c21a80b", "created_at": "2026-11-01T19:02:12Z", "updated_at": "2026-11-01T22:09:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Tumor purity-associated genes influence hepatocellular carcinoma prognosis and tumor microenvironment.", "doi": "10.3389/fonc.2023.1197898", "pmid": "37434985", "authors": ["Yan Zhao", "Xu Xu", "Yue Wang", "Lin D Wu", "Rui L Luo", "Ren P Xia"], "journal": "Frontiers in oncology", "year": 2023, "abstract": "Introduction: Tumor purity takes on critical significance to the progression of solid tumors. The aim of this study was at exploring potential prognostic genes correlated with tumor purity in hepatocellular carcinoma (HCC) by bioinformatics analysis.\nMethods: The ESTIMATE algorithm was applied for determining the tumor purity of HCC samples from The Cancer Genome Atlas (TCGA). The tumor purity-associated genes with differential expression (DEGs) were identified based on overlap analysis, weighted gene co-expression network analysis (WGCNA), and differential expression analysis. The prognostic genes were identified in terms of the prognostic model construction based on the Kaplan-Meier (K-M) survival analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses. The expression of the above-described genes was further validated by the GSE105130 dataset from the Gene Expression Omnibus (GEO) database. We also characterized the clinical and immunophenotypes of prognostic genes. Gene set enrichment analysis (GSEA) was carried out for exploring the biological signaling pathway.\nResults: A total of 26 tumor purity-associated DEGs were identified, which were involved in biological processes such as immune/inflammatory responses and fatty acid elongation. Ultimately, we identified ADCK3, HK3, and PPT1 as the prognostic genes for HCC. Moreover, HCC patients exhibiting higher ADCK3 expression and lower HK3 and PPT1 expressions had a better prognosis. Furthermore, high HK3 and PPT1 expressions and low ADCK3 expression resulted in high tumor purity, high immune score, high stromal score, and high ESTIMATE score. GSEA showed that the abovementioned prognostic genes showed a significant correlation with immune-inflammatory response, tumor growth, and fatty acid production/degradation.\nDiscussion: In conclusion, this study identified novel predictive biomarkers (ADCK3, HK3, and PPT1) and studied the underlying molecular mechanisms of HCC pathology initially.", "claims": [{"id": "claim-method", "statement": "The prognostic genes were identified in terms of the prognostic model construction based on the Kaplan–Meier (K–M) survival analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37434985", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The prognostic genes were identified in terms of the prognostic model construction based on the Kaplan–Meier (K–M) survival analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses."}], "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 in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37434985", "locator": "sections[26] \"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 in the article/ Supplementary Material ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Ultimately, we identified ADCK3, HK3, and PPT1 as the prognostic genes for HCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37434985", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Ultimately, we identified ADCK3, HK3, and PPT1 as the prognostic genes for HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Ultimately, we identified ADCK3, HK3, and PPT1 as the prognostic genes for 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:37434985"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE105130"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE105130"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37434985", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2023.1197898", "sha256": "sha256:0301603dd88fa2967221e23d93513a56039b1ddaa06e2c0d2ee52cbb2bf910f3", "bytes": 49683, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2023.1197898", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10330704", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE105130", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105130", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE105130", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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"The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE105130", "GSE36376"], "resolved_accessions": ["GSE105130", "GSE36376"], "statements": ["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 in the article/ Supplementary Material ."], "basis": "The paper names GSE105130, GSE36376 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:37434985", "data:geo:GSE105130"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE105130"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:46:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13888, "completion_tokens": 1396, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37434985", "type": "paper", "label": "pmid:37434985"}, {"id": "source:pmid:37434985", "type": "manuscript", "label": "PMID 37434985 full text"}, {"id": "data:geo:GSE105130", "type": "dataset", "label": "GEO GSE105130"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37434985", "type": "paper", "label": "pmid:37434985"}, {"id": "source:pmid:37434985", "type": "manuscript", "label": "PMID 37434985 full text"}, {"id": "data:geo:GSE105130", "type": "dataset", "label": "GEO GSE105130"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37434985", "type": "extraction", "used": ["source:pmid:37434985"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE105130", "type": "accession_resolution", "used": ["data:geo:GSE105130"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37434985", "parent_hash": "sha256:30f44fa973306f309cbee3ef0b31f0c078ff1c4f0c1de783c34849e2ea7a1292", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE105130 licence not read", "asset:data:geo:GSE105130 not downloaded", "asset:data:geo:GSE36376 licence not read", "asset:data:geo:GSE36376 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["hepatocellular carcinoma cell lines (Huh-1, HepG2, and SK-HeP-1) in comparison with normal hep"], "order_basis": "paper_text_order:7066", "id": "assay:1"}, {"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": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}