Prognostic assessment of early-stage liver cirrhosis induced by HCV using an integrated model of CX3CR1-associated immune infiltration genes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39800763", "kind": "science-record", "revision": 2, "content_hash": "sha256:9683f595acabc7d5e6868ed8c160f54d902a4334a67aa7ba26b8ca0f5f7677a6", "created_at": "2026-11-01T20:30:06Z", "updated_at": "2026-11-01T21:34:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic assessment of early-stage liver cirrhosis induced by HCV using an integrated model of CX3CR1-associated immune infiltration genes.", "doi": "10.1038/s41598-024-80422-1", "pmid": "39800763", "authors": ["Haozheng Cai", "Jing Zhang", "Chuwen Chen", "Junyi Shen", "Xiaoyun Zhang", "Wei Peng", "Chuan Li", "Haopeng Lv", "Tianfu Wen"], "journal": "Scientific reports", "year": 2025, "abstract": "Chemokine (C-X3-C motif) Receptor 1 (CX3CR1) primarily mediates the chemotaxis and adhesion of immune cells. However, its role in hepatitis C virus (HCV)-induced early-stage liver cirrhosis remains unexplored. GSE15654 was downloaded from the GEO database. The Cox regression model, CIBERSORT, and LASSO technique were utilized to identify CX3CR1-associated immune infiltration genes (IIGs). Surgical resection samples were collected for verification, including 3 healthy controls (HC), 4 individuals with HCV-induced hepatic cirrhosis, and 3 with HCV-induced liver failure. High CX3CR1 expression correlated with worse prognosis in early-stage cirrhosis. CX3CR1-associated IIGs, namely ACTIN4, CD1E, TMCO1, and WSF1, were identified, showing specific expression in the livers of individuals with post-hepatic cirrhosis and liver failure compared to HC. LOC400499 and MTHFD2 were elevated in individuals with liver failure in comparison to those with hepatocirrhosis. Notably, high infiltration of plasma cells and low infiltration of monocytes were predictive of poor prognosis in early-stage cirrhosis. The combined risk model predicted that high expression of CX3CR1-associated IIGs and increased infiltration of plasma cells were associated with unfavorable prognosis in individuals with HCV-induced early-stage liver cirrhosis. The developed combined risk model effectively predicted the prognosis of these individuals.", "claims": [{"id": "claim-method", "statement": "The Cox regression model, CIBERSORT, and LASSO technique were utilized to identify CX3CR1-associated immune infiltration genes (IIGs).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39800763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The Cox regression model, CIBERSORT, and LASSO technique were utilized to identify CX3CR1-associated immune infiltration genes (IIGs)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analysed during the current study are available are publicly available. The data can be found here: Gene Expression Omnibus GEO, available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15654.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39800763", "locator": "sections[24] \"Data availability\" paragraph 2", "quote": "The datasets generated and/or analysed during the current study are available are publicly available. The data can be found here: Gene Expression Omnibus GEO, available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15654."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High CX3CR1 expression correlated with worse prognosis in early-stage cirrhosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39800763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "High CX3CR1 expression correlated with worse prognosis in early-stage cirrhosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High CX3CR1 expression correlated with worse prognosis in early-stage cirrhosis.", "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:39800763"], "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:GSE15654"], "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:GSE15654"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39800763", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-80422-1", "sha256": "sha256:c82f08f04a8986476431f975709dfe93efc1675b79fdb632711ad454b0d0296a", "bytes": 53196, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-80422-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11725579", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15654", "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=GSE15654", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15654", "version": null, "note": "The datasets generated and/or analysed during the current study are available are publicly available. 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RNA-seq analysis of clinical samples Seven liver fib", "r fibrosis clinical samples were analysed by RNA-seq. Total RNA was isolated from liver specimens", "NA Isolation Kit (Foregene, Chengdu, China). RNA-sequencing (RNA-seq) libraries were constructed and seq", "(Foregene, Chengdu, China). RNA-sequencing (RNA-seq) libraries were constructed and sequenced us"], "order_basis": "paper_text_order:3987", "id": "assay:1"}, {"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 Cox regression model, CIBERSORT, and LASSO technique were utilized to identify CX3CR1-associated immune infiltration genes (IIGs)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}