CD69 serves as a potential diagnostic and prognostic biomarker for hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37156819", "kind": "science-record", "revision": 4, "content_hash": "sha256:c2405730e26a873e61e5b8a87c7e9e1da703329345aace7ffa2e989c05b0f4a2", "created_at": "2026-11-01T19:01:49Z", "updated_at": "2026-11-01T22:51:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CD69 serves as a potential diagnostic and prognostic biomarker for hepatocellular carcinoma.", "doi": "10.1038/s41598-023-34261-1", "pmid": "37156819", "authors": ["Kaihua Tang", "Xiaoting Li", "Jianwen Mo", "Yixuan Chen", "Chengyu Huang", "Ting Li", "Tianjian Luo", "Zhijian Zhong", "Yongqiang Jiang", "Dengfeng Yang", "Weiliang Mo"], "journal": "Scientific reports", "year": 2023, "abstract": "The prevalence and mortality of hepatocellular carcinoma (HCC) are still increasing. This study aimed to identify potential therapeutic targets related to patient prognosis. Data were downloaded from TCGA, GSE25097, GSE36376, and GSE76427 datasets. Differential analysis and enrichment analysis were performed in HCC. Cell deaths were evaluated, and least absolute shrinkage and selection operator regression (LASSO) regression was analyzed to screen candidate genes. Additionally, immune cell infiltration in HCC was assessed. We identified 4088 common DEGs with the same direction of differential expression in all four datasets, they were mainly enriched in immunoinflammation and cell cycle pathways. Apoptosis was significantly suppressed in HCC in GSEA and GSVA. After LASSO regression analysis, we screened CD69, CDC25B, MGMT, TOP2A, and TXNIP as candidate genes. Among them, CD69 significantly influenced the overall survival of HCC patients in both TCGA and GSE76427. CD69 may be a protective factor for outcome of HCC patients. In addition, CD69 was positive correlation with T cells and CD3E. CD69, CDC25B, MGMT, TOP2A, and TXNIP were potential diagnostic and prognostic target for HCC, especially CD69.", "claims": [{"id": "claim-method", "statement": "Differential analysis for HCC and controls were performed to identify differentially expressed genes (DEGs) using limma package (v3.54.2) in R20 for datasets in GEO and using DESeq2 (v1.38.3) package in R21 for TCGA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37156819", "locator": "sections[4] \"Identification of differentially expressed genes and biological functions\" paragraph 2", "quote": "Differential analysis for HCC and controls were performed to identify differentially expressed genes (DEGs) using limma package (v3.54.2) in R20 for datasets in GEO and using DESeq2 (v1.38.3) package in R21 for TCGA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are downloaded from TCGA, GSE25097, GSE36376, and GSE76427 datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37156819", "locator": "sections[17] \"Data availability\" paragraph 2", "quote": "All data generated or analyzed during this study are downloaded from TCGA, GSE25097, GSE36376, and GSE76427 datasets."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After LASSO regression analysis, we screened CD69, CDC25B, MGMT, TOP2A, and TXNIP as candidate genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37156819", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "After LASSO regression analysis, we screened CD69, CDC25B, MGMT, TOP2A, and TXNIP as candidate genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After LASSO regression analysis, we screened CD69, CDC25B, MGMT, TOP2A, and TXNIP as candidate genes.", "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:37156819"], "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:GSE25097"], "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:GSE25097"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37156819", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-023-34261-1", "sha256": "sha256:74f0be0ac979f9091ac4278e2502464f208bbeb859a700ea6241230814fe77bf", "bytes": 33925, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-023-34261-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10167346", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25097", "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=GSE25097", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25097", "version": null, "note": "All data generated or analyzed during this study are downloaded from TCGA, GSE25097, GSE36376, and GSE76427 datasets.", "structure": 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