Identification and Verification of Ubiquitin D as a Gene Associated with Hepatitis C Virus-Induced Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35728518", "kind": "science-record", "revision": 5, "content_hash": "sha256:a865bde32d9abf80ee0eb742d24bcaba746293195db14fd14cdccae1707156d4", "created_at": "2026-11-01T18:14:45Z", "updated_at": "2026-11-01T22:49:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Verification of Ubiquitin D as a Gene Associated with Hepatitis C Virus-Induced Hepatocellular Carcinoma.", "doi": "10.1159/000525543", "pmid": "35728518", "authors": ["Huanqin Li", "Shumin Liu", "Yun Lin", "Xiongfei Shi", "Na Du", "Jing Yao", "Ruiyang Liu", "Yan Du", "Kai Yang"], "journal": "Intervirology", "year": 2022, "abstract": "INTRODUCTION: Accumulated studies have suggested that hepatitis C virus (HCV) infection is one of the leading causes for hepatocellular carcinoma (HCC). However, the mechanisms underlying the effect of HCV on the occurrence of HCC are still poorly understood.\nMETHODS: HCV infection datasets (GSE82177 and GSE17856) and HCC datasets (The Cancer Genome Atlas Liver Hepatocellular Carcinoma and GSE89377) were downloaded from Gene Expression Omnibus or TCGA for analysis. The common differentially expressed genes in the above four datasets were identified by R software. The expression of ubiquitin D (UBD) in HCV-infected HepG2 cells was detected by RT-qPCR and Western blot, respectively. The interaction between NS3 and p53 was detected by co-immunoprecipitation. The influence of UBD on the proliferation and migration ability of HepG2 cells was evaluated by CCK-8 and wound healing assay, respectively.\nRESULTS: UBD was upregulated in both HCV-infected samples and HCC samples. HCV NS3 interacted with p53 and inhibited its expression. HCV NS3-induced UBD promoted the proliferation and migration of HepG2 cells.\nCONCLUSION: Our results suggest that HCV NS3-induced UBD is positively correlated with the development of HCV-related HCC during HCV infection. Targeting UBD could be a potential strategy for preventing and treating HCV-induced HCC.", "claims": [{"id": "claim-method", "statement": "Analysis of differentially expressed genes (DEGs) was performed with the DESeq2 and Limma package of R software [38]. We set adjusted p value (adj.p.val) < 0.05 and |log2 fold change (log2.fc.) >1 as the cutoff criteria. The common DEGs were identified by integrating each DEG in the four datasets with the Robust Rank Aggreg package of R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35728518", "locator": "sections[4] \"Identification of Common Differentially Expressed Genes in HCV Infection and HCC\" paragraph 2", "quote": "Analysis of differentially expressed genes (DEGs) was performed with the DESeq2 and Limma package of R software [38]. We set adjusted p value (adj.p.val) < 0.05 and |log2 fold change (log2.fc.) >1 as the cutoff criteria. The common DEGs were identified by integrating each DEG in the four datasets with the Robust Rank Aggreg package of R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets generated for this study are included in the manuscript/online supplementary Files. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35728518", "locator": "sections[25] \"Data Availability Statement\" paragraph 2", "quote": "All datasets generated for this study are included in the manuscript/online supplementary Files. Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "HCV NS3-induced UBD promoted the proliferation and migration of HepG2 cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35728518", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "HCV NS3-induced UBD promoted the proliferation and migration of HepG2 cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "HCV NS3-induced UBD promoted the proliferation and migration of HepG2 cells.", "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:35728518"], "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:GSE17856"], "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:GSE17856"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35728518", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1159/000525543", "sha256": "sha256:cd32562beb1b2ff95e4ed5375d9eeac781687dbb7b09d0b89f61d8e051be998a", "bytes": 41871, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1159/000525543", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9677847", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17856", "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=GSE17856", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17856", "version": null, "note": "All datasets generated for this study are included in the manuscript/online supplementary Files. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets generated for this study are included in the manuscript/online supplementary Files. 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CONCLUSION: Our results suggest that", "se Academy of Sciences, Shanghai, China) and cultured in DMEM medium (Gibco, Waltham, MA, USA) with 1"], "order_basis": "paper_text_order:702", "id": "assay:1"}, {"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": ["in HCV-infected HepG2 cells was detected by RT-qPCR and Western blot, respectively. The interact", "HCV-infected HepG2 cells was detected by RT-qPCR and Western blot, respectively. 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