Uncovering biomarkers and molecular pathways linking NAFLD and AIS: Insights from bioinformatic analysis and experiment.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41021615", "kind": "science-record", "revision": 4, "content_hash": "sha256:f2fd69aebf317c2c4241a8817c385248e8fafe918c0a3c1c591b76194b065508", "created_at": "2026-11-01T20:31:05Z", "updated_at": "2026-11-01T22:57:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Uncovering biomarkers and molecular pathways linking NAFLD and AIS: Insights from bioinformatic analysis and experiment.", "doi": "10.1371/journal.pone.0333719", "pmid": "41021615", "authors": ["Junjie Su", "Fenglei Sun"], "journal": "PloS one", "year": 2025, "abstract": "BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) and acute ischemic stroke (AIS) are both closely related to chronic inflammation and metabolic disorders, but the molecular mechanisms between them are not yet clear. This study aims to explore the common molecular characteristics between NAFLD and AIS using bioinformatics methods.\nMETHODS: We integrated transcriptomic data from GEO (GSE89632 for NAFLD and GSE16561 for AIS) to identify shared molecular signatures. Differentially expressed genes (DEGs) were screened using the limma package, and co-expression modules were identified via WGCNA. Functional enrichment and immune infiltration analyses were conducted using standard bioinformatics tools. Key genes were selected through LASSO and random forest algorithms, and candidate drugs were predicted using the CMap database. Experimental validation included qPCR, immunohistochemistry, and drug intervention in HepG2 and HMC3 cell models, as well as a high-fat diet-induced NAFLD mouse model.\nRESULTS: Through differential expression analysis, 65 common DEGs were identified in both NAFLD and AIS. Functional enrichment analysis showed that these genes mainly involve signal pathways related to immune regulation and inflammatory responses. Immune infiltration analysis showed a significant increase in monocytes, B cells, and plasma cells in NAFLD patients. Ultimately, four potential biomarkers were screened out using LASSO regression and random forest algorithms: CEBPD, SOCS2, THBS1, and IFIT2. Using cMAP, 10 candidate therapeutic drugs, including lamotrigine, were identified. Expression of CEBPD and SOCS2 was consistently upregulated in NAFLD clinical datasets, FFA-treated HepG2 cells, and liver tissues of HFD-induced NAFLD mice, but not in AIS datasets or OGD-treated microglial cells. Furthermore, lamotrigine, cinnarizine, and lenvatinib significantly suppressed FFA-induced CEBPD and SOCS2 expression in HepG2 cells (p < 0.05), supporting their potential regulatory effects.\nCONCLUSIONS: This study identified common DEGs between NAFLD and AIS and experimentally validated CEBPD as a potential marker, revealing possible common molecular mechanisms between the two diseases, providing new directions for future diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "Using the limma package in RStudio, differential analysis was performed with the lmFit and eBayes functions.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41021615", "locator": "sections[4] \"2.2 Differential expression gene analysis\" paragraph 2", "quote": "Using the limma package in RStudio, differential analysis was performed with the lmFit and eBayes functions."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets files are available from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database (accession numbers GSE89632, GSE16561,GSE58979,GSE63067,GSE22255).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41021615", "locator": "sections[30] \"Data Availability\" paragraph 2", "quote": "All datasets files are available from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database (accession numbers GSE89632, GSE16561,GSE58979,GSE63067,GSE22255)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 65 common differentially expressed genes between NAFLD and AIS.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41021615", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Through differential expression analysis, 65 common DEGs were identified in both NAFLD and AIS."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 65 common differentially expressed genes between NAFLD and AIS.", "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:41021615"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:41021615", "data:geo:GSE115469"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE115469"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:02:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13911, "completion_tokens": 1764, "cached_tokens": 256}}, "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:41021615", "type": "paper", "label": "pmid:41021615"}, {"id": "source:pmid:41021615", "type": "manuscript", "label": "PMID 41021615 full text"}, {"id": "data:geo:GSE115469", "type": "dataset", "label": "GEO GSE115469"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41021615", "type": "paper", "label": "pmid:41021615"}, {"id": "source:pmid:41021615", "type": "manuscript", "label": "PMID 41021615 full text"}, {"id": "data:geo:GSE115469", "type": "dataset", "label": "GEO GSE115469"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41021615", "type": "extraction", "used": ["source:pmid:41021615"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE115469", "type": "accession_resolution", "used": ["data:geo:GSE115469"], "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:41021615", "parent_hash": "sha256:a5cf4623bc41095da4ad5def31025e3ed4af07373a11ee33980e28da1349d7b5", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE115469 licence not read", "asset:data:geo:GSE115469 not downloaded", "asset:data:geo:GSE16561 licence not read", "asset:data:geo:GSE16561 not downloaded", "asset:data:geo:GSE22255 licence not read", "asset:data:geo:GSE22255 not downloaded", "asset:data:geo:GSE58979 licence not read", "asset:data:geo:GSE58979 not downloaded", "asset:data:geo:GSE63067 licence not read", "asset:data:geo:GSE63067 not downloaded", "asset:data:geo:GSE89632 licence not read", "asset:data:geo:GSE89632 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["p database. Experimental validation included qPCR, immunohistochemistry, and drug intervention", "nd IFIT2) across different liver cell types. qPCR Validation and Western blot analysis showed", "del. (D) Drug validation. (E) The results of qPCR. (F,G) Western blot analysis of CEBPD and SO"], "order_basis": "paper_text_order:946", "id": "assay:1"}, {"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": ["base. Experimental validation included qPCR, immunohistochemistry, and drug intervention in HepG2 and HMC3 cel", ". (B) OGD-induced HMC3 microglial cells. (C) IHC analysis in NAFLD mouse model. (D) Drug vali", "er confirmed in our NAFLD mouse model, where IHC analysis revealed significantly elevated pro"], "order_basis": "paper_text_order:952", "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": ["munohistochemistry, and drug intervention in HepG2 and HMC3 cell models, as well as a high-fat", "ated in NAFLD clinical datasets, FFA-treated HepG2 cells, and liver tissues of HFD-induced NAFL", "ed FFA-induced CEBPD and SOCS2 expression in HepG2 cells (p < 0.05), supporting their potential", "lture and drug intervention HepG2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supp"], "order_basis": "paper_text_order:999", "id": "assay:3"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ls, as well as a high-fat diet-induced NAFLD mouse model. RESULTS: Through differential expression an", "ls, as well as a high-fat diet-induced NAFLD mouse model. RESULTS: Through differential express", "microglial cells. (C) IHC analysis in NAFLD mouse model. (D) Drug validation. (E) The results of qPC", "findings was further confirmed in our NAFLD mouse model, where IHC analysis revealed significantly e"], "order_basis": "paper_text_order:1068", "id": "assay:4"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ferent liver cell types. qPCR Validation and Western blot analysis showed that the expression levels o", "g validation. (E) The results of qPCR. (F,G) Western blot analysis of CEBPD and SOCS2 expression in co"], "order_basis": "paper_text_order:6806", "id": "assay:5"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Using the limma package in RStudio, differential analysis was performed with the lmFit and eBayes functions."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}