Identification of PPAR-related differentially expressed genes liver hepatocellular carcinoma and construction of a prognostic model based on data analysis and molecular docking.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38652093", "kind": "science-record", "revision": 3, "content_hash": "sha256:1f6bf4ef313f9c71ace8688ead5806e7114f86a86a8ddc160c6ecfb73e013d1a", "created_at": "2026-11-01T19:20:37Z", "updated_at": "2026-11-01T22:11:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of PPAR-related differentially expressed genes liver hepatocellular carcinoma and construction of a prognostic model based on data analysis and molecular docking.", "doi": "10.1111/jcmm.18304", "pmid": "38652093", "authors": ["Yumeng Wang", "Shuqiang Li", "Zihang Liu", "Xuanzheng Li", "Yifan Yu", "Hao Liu"], "journal": "Journal of cellular and molecular medicine", "year": 2024, "abstract": "Liver hepatocellular carcinoma (LIHC) is a significant global health issue with limited treatment options. In this study, single-cell RNA sequencing (scRNA-seq) data were used to explore the molecular mechanisms of LIHC development and identify potential targets for therapy. The expression of peroxisome proliferator-activated receptors (PPAR)-related genes was analysed in LIHC samples, and primary cell populations, including natural killer cells, T cells, B cells, myeloid cells, endothelial cells, fibroblasts and hepatocytes, were identified. Analysis of the differentially expressed genes (DEGs) between normal and tumour tissues revealed significant changes in gene expression in various cell populations. PPAR activity was evaluated using the 'AUCell' R software, which indicated higher scores in the normal versus the malignant hepatocytes. Furthermore, the DEGs showed significant enrichment of pathways related to lipid and glucose metabolism, cell development, differentiation and inflammation. A prognostic model was then constructed using 8 PPARs-related genes, including FABP5, LPL, ACAA1, PPARD, FABP4, PLIN1, HMGCS2 and CYP7A1, identified using least absolute shrinkage and selection operator-Cox regression analysis, and validated in the TCGA-LIHC, ICGI-LIRI and GSE14520 datasets. Patients with low-risk scores had better prognosis in all cohorts. Based on the expression of the eight model genes, two clusters of patients were identified by ConsensusCluster analysis. We also predicted small-molecule drugs targeting the model genes, and identified perfluorohexanesulfonic acid, triflumizole and perfluorononanoic acid as potential candidates. Finally, wound healing assay confirmed that PPARD can promote the migration of liver cancer cells. Overall, our study offers novel perspectives on the molecular mechanisms of LIHC and potential areas for therapeutic intervention, which may facilitate the development of more effective treatment regimens.", "claims": [{"id": "claim-method", "statement": "The prognostic PPARs‐related genes were screened by Least Absolute Shrinkage and Selection Operator (LASSO)‐Cox regression analysis using the ‘glmnet’ R package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38652093", "locator": "sections[6] \"Construction of the PPARs‐related gene signature and unsupervised clustering\" paragraph 2", "quote": "The prognostic PPARs‐related genes were screened by Least Absolute Shrinkage and Selection Operator (LASSO)‐Cox regression analysis using the ‘glmnet’ R package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets can be downloaded from the TCGA (https://portal.gdc.com), GEO (http://www.ncbi.nlm.nih.gov/geo/), and ICGC (https://icgc.org/) websites.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38652093", "locator": "sections[31] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The datasets can be downloaded from the TCGA (https://portal.gdc.com), GEO (http://www.ncbi.nlm.nih.gov/geo/), and ICGC (https://icgc.org/) websites."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study constructed and externally validated an eight-gene PPAR-related prognostic model for LIHC using LASSO-Cox regression analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38652093", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A prognostic model was then constructed using 8 PPARs‐related genes, including FABP5, LPL, ACAA1, PPARD, FABP4, PLIN1, HMGCS2 and CYP7A1, identified using least absolute shrinkage and selection operator‐Cox regression analysis, and validated in the TCGA‐LIHC, ICGI‐LIRI and GSE14520 datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study constructed and externally validated an eight-gene PPAR-related prognostic model for LIHC using LASSO-Cox regression analysis.", "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:38652093"], "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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In this study, single-cell RNA sequencing (scRNA-seq) data were used to explore the mo", ". In this study, single-cell RNA sequencing (scRNA-seq) data were used to explore the molecular mec"], "order_basis": "paper_text_order:255", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["reatment options. In this study, single-cell RNA sequencing (scRNA-seq) data were used to explore the mo"], "order_basis": "paper_text_order:267", "id": "assay:2"}, {"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": ["hinese Academy of Sciences. HepG2 cells were cultured in minimum essential medium (MEM; Invitrogen; T", "al bovine serum (FBS), while HUH7 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; In", "human non‐small cell lung cancer cell lines HepG2 and HUH7 were purchased from the Cell Bank o", "ell Bank of the Chinese Academy of Sciences. HepG2 cells were cultured in minimum essential med"], "order_basis": "paper_text_order:3175", "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": ["The prognostic PPARs‐related genes were screened by Least Absolute Shrinkage and Selection Operator (LASSO)‐Cox regression analysis using the ‘glmnet’ R package."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}