CYB561 a potential prognostic biomarker for liver hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39708189", "kind": "science-record", "revision": 3, "content_hash": "sha256:af09379275dd6d6b4db631f0cf4aa1e50c39db75c26387a1a927240fbca2cebf", "created_at": "2026-11-01T20:30:01Z", "updated_at": "2026-11-01T22:13:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CYB561 a potential prognostic biomarker for liver hepatocellular carcinoma.", "doi": "10.1007/s10238-024-01522-w", "pmid": "39708189", "authors": ["Yanchun Zhao", "Jingfang Du", "Jian Zhuo", "Quanai Zhang", "Luxian Dai", "Yubao Tang", "Yao Wang", "Ankang Sheng", "Hanyu Yao", "Weiguang Liu"], "journal": "Clinical and experimental medicine", "year": 2024, "abstract": "Liver hepatocellular carcinoma (LIHC) is a malignancy characterized by a high rate of recurrence, metastasis, and poor prognosis. Cytochrome b561 (CYB561) has been previously reported to be associated with tumor progression, but it has not been revealed in LIHC. The aim of this study was to investigate the prognostic value and potential function of CYB561 in LICH. The expression level, clinical correlation, prognosis, and biological function of CYB561 in LIHC were analyzed using The Cancer Genome Atlas（TCGA), Gene Expression Omnibus (GEO), TIMER2, Kaplan-Meier Plotter, and GEPIA2 databases. The expression of CYB561 in LIHC tissue samples was analyzed by immunohistochemical staining. The effect of CYB561 on the proliferation and migration of LIHC cells was investigated by using CYB561 knockdown in vitro. GSE149614 dataset was used to analyze the expression distribution of CYB561 in LIHC on a single-cell dimension. This study showed that CYB561 mRNA and protein were highly expressed in LIHC. High expression of CYB561 suggests poor prognosis in LICH patients and is an independent risk factor for LIHC. Wound-healing experiment, transwell experiment, and clonal formation experiment confirmed that CYB561 knockdown could inhibit the proliferation and migration of LIHC cells. Functional enrichment analysis showed that CYB561 was related to biological processes such as cell adhesion and immune response. KEGG enrichment analysis showed that CYB561 interacts with tumor-related signaling pathways. Single-cell analysis showed that CYB561 was mainly expressed in hepatocytes. Cells with high CYB561 expression had a higher degree of malignancy. Our study found that abnormal expression of CYB561 in LIHC suggested poor prognosis of LIHC and was related to tumor migration and proliferation. CYB561 is a potential prognostic predictor or therapeutic biomarker.", "claims": [{"id": "claim-method", "statement": "Clinical data from TCGA-LIHC patients were used for clinical correlation analysis and univariate and multivariate COX regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39708189", "locator": "sections[7] \"Transcriptomic analysis of CYB561\" paragraph 2", "quote": "Clinical data from TCGA-LIHC patients were used for clinical correlation analysis and univariate and multivariate COX regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are openly available on the TCGA database and the GEO database. No datasets were generated or analyzed during the current study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39708189", "locator": "sections[27] \"Data Availability\" paragraph 2", "quote": "The data that support the findings of this study are openly available on the TCGA database and the GEO database. No datasets were generated or analyzed during the current study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High CYB561 expression is associated with poor prognosis in LIHC and CYB561 is an independent risk factor for overall survival.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "patients in the group with high CYB561 mRNA expression had worse OS (p < 0.05, HR = 1.9, Fig. 3A)."}, "evidence": [{"asset": "source:pmid:39708189", "locator": "sections[19] \"CYB561 expression suggests poor prognosis in LIHC\" paragraph 4", "quote": "patients in the group with high CYB561 mRNA expression had worse OS (p < 0.05, HR = 1.9, Fig. 3A)."}, {"asset": "source:pmid:39708189", "locator": "sections[19] \"CYB561 expression suggests poor prognosis in LIHC\" paragraph 4", "quote": "multi-factor COX regression analysis showed that CYB561 was an independent risk factor for OS in LIHC patients (p < 0.05, HR = 1.146, Fig. 3D)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High CYB561 expression is associated with poor prognosis in LIHC and CYB561 is an independent risk factor for overall survival.", "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:39708189"], "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:GSE112790"], "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:GSE112790"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39708189", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s10238-024-01522-w", "sha256": "sha256:db588f734d7a11348536d361c62213e74acd79e6e46936feea16e4011fc4a7e7", "bytes": 34734, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s10238-024-01522-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11663187", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE112790", "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=GSE112790", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE112790", "version": null, "note": "The data that support the findings of this study are openly available on the TCGA database and the GEO database. 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