Exploration of immune infiltration and feature genes in viral hepatitis-associated liver fibrosis using transcriptome data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36330414", "kind": "science-record", "revision": 4, "content_hash": "sha256:9357250c3bbe19f4a13ddb1df1b3741b9138c2072a8a56a75cdd6e728d754a19", "created_at": "2026-11-01T18:15:45Z", "updated_at": "2026-11-01T22:08:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of immune infiltration and feature genes in viral hepatitis-associated liver fibrosis using transcriptome data.", "doi": "10.21037/atm-22-2205", "pmid": "36330414", "authors": ["Jiali Pan", "Yu Tian", "Fengling Hu", "Jinghang Xu", "Ning Tan", "Yifan Han", "Qian Kang", "Hongyu Chen", "Yuqing Yang", "Xiaoyuan Xu"], "journal": "Annals of translational medicine", "year": 2022, "abstract": "Background: Immune cells play an essential role in virus-induced liver fibrosis. However, the underlying mechanisms remain unclear. In this study, we systematically explored immune cell infiltration and feature genes to provide new insights into viral hepatitis-associated liver fibrosis.\nMethods: The expression datasets GSE14323, GSE33650, GSE6764 (for testing), and GSE84044 (for validation) were downloaded from the Gene Expression Omnibus (GEO) database. Immune cell infiltration was assessed using the CIBERSORT algorithm, and characteristic subgroups were obtained using least absolute shrinkage and selection operator (LASSO) regression and Wilcoxon test. The association between feature genes and immune-infiltrating cells was explored using Spearman's correlation analysis. R software and IBM SPSS Statistics were utilized for data analysis and visualization.\nResults: We identified 10 differential immune cells between viral hepatitis-associated liver fibrosis and non-fibrosis, including naive B cells, plasma cells, resting CD4+ memory T cells, T follicular helper (Tfh) cells, regulatory T (Treg) cells, M0-M2 macrophages, and resting and activated mast cells. Six feature genes were identified: STAT1, CXCL10, PTPRC, IFIT3, OAS2, and MX1. They also differed significantly in the subgroups of non-fibrosis, mild to moderate fibrosis and severe fibrosis. Both the feature genes and immune cells were verified in the validation group. All the genes were positively associated with macrophages M1 and negatively associated with macrophages M2.\nConclusions: The six feature genes may be involved in viral hepatitis-associated liver fibrosis by promoting the polarization of macrophages from M0 to M1 and inhibiting their conversion to M2. Thus, these genes may serve as potential therapeutic targets.", "claims": [{"id": "claim-method", "statement": "Immune cell infiltration was assessed using the CIBERSORT algorithm, and characteristic subgroups were obtained using least absolute shrinkage and selection operator (LASSO) regression and Wilcoxon test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36330414", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Immune cell infiltration was assessed using the CIBERSORT algorithm, and characteristic subgroups were obtained using least absolute shrinkage and selection operator (LASSO) regression and Wilcoxon test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression datasets GSE14323, GSE33650, GSE6764 (for testing), and GSE84044 (for validation) were downloaded from the Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36330414", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The expression datasets GSE14323, GSE33650, GSE6764 (for testing), and GSE84044 (for validation) were downloaded from the Gene Expression Omnibus (GEO) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "All six feature genes were positively associated with M1 macrophages and negatively associated with M2 macrophages.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36330414", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "All the genes were positively associated with macrophages M1 and negatively associated with macrophages M2."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "All six feature genes were positively associated with M1 macrophages and negatively associated with M2 macrophages.", "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:36330414"], "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:GSE14323"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE14323"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36330414", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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