The necroptosis related gene LGALS3 can be used as a biomarker for the adverse progression from chronic HBV infection to HCC.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37180150", "kind": "science-record", "revision": 3, "content_hash": "sha256:8fec20c42e2bf9b906e0124f4cc5228baba4f89b07916eb5856c7f795b1b6530", "created_at": "2026-11-01T19:01:51Z", "updated_at": "2026-11-01T22:09:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The necroptosis related gene LGALS3 can be used as a biomarker for the adverse progression from chronic HBV infection to HCC.", "doi": "10.3389/fimmu.2023.1142319", "pmid": "37180150", "authors": ["Jianming Dong", "Rongzheng Zhang", "Yan Xia", "Xu Jiang", "Kun Zhou", "Jiaqi Li", "Mengrui Guo", "Xinyang Cao", "Shuyun Zhang"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "The number of patients with hepatocellular carcinoma (HCC) caused by hepatitis B virus (HBV) infection remains large, despite the remarkable effectiveness of antiviral drugs and vaccines for HBV in preventing and treating HBV infection. Necroptosis is closely related to the occurrence of inflammation, clearance of viral infection, and tumor progression. Presently, little is known about the changes in necroptosis-related genes in the progression from chronic HBV infection (CHI) to HBV-related hepatic fibrosis (HBV-HF) and HBV-related hepatocellular carcinoma (HBV-HCC). In this study, Cox regression analysis was performed using GSE14520 chip data and a necroptosis-related genes survival prognosis score (NRGPS) was established for HBV-HCC patients. NRGPS was constructed using three model genes (G6PD, PINK1 and LGALS3), and verified by data sequencing in the TCGA database. The HBV-HCC cell model was established by transfection of pAAV/HBV1.2C2, constructed by homologous recombination, into HUH7 and HEPG2 cells. The expression levels of G6PD, PINK1, and LGALS3 were detected using RT-qPCR. We further analyzed the expression of the model genes in GSE83148, GSE84044, and GSE14520 and found that LGALS3 was consistently highly expressed in CHI, high fibrosis score and high NRGPS. In addition, immune microenvironment analysis showed that LGALS3 was not only associated with the infiltration of regulatory T cells in the immune microenvironment but also with expression of CCL20 and CCR6. The expression levels of model genes, FOXP3 and CCR6, were analyzed using RT-qPCR in peripheral blood mononuclear cells of 31 hepatitis B surface antibody positive patients, 30 CHI, 21 HBV-HF, and 20 HBV-HCC. In further cell-model experiments, we analyzed the expression of CCL20 by RT-qPCR and the changes in cell proliferation and migration by CCK8 and transwell assays, respectively, in HBV-HCC cell models after LGALS3 knockdown. The findings of this study suggest that LGALS3 could be a biomarker for adverse progression following chronic HBV infection and may also be involved in the regulation of the immune microenvironment, making it a potential therapeutic target.", "claims": [{"id": "claim-method", "statement": "In this study, Cox regression analysis was performed using GSE14520 chip data and a necroptosis-related genes survival prognosis score (NRGPS) was established for HBV-HCC patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37180150", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this study, Cox regression analysis was performed using GSE14520 chip data and a necroptosis-related genes survival prognosis score (NRGPS) was established for HBV-HCC patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37180150", "locator": "sections[30] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Cox regression analysis using GSE14520 chip data established an NRGPS comprising G6PD, PINK1, and LGALS3 for HBV-HCC patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37180150", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this study, Cox regression analysis was performed using GSE14520 chip data and a necroptosis-related genes survival prognosis score (NRGPS) was established for HBV-HCC patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Cox regression analysis using GSE14520 chip data established an NRGPS comprising G6PD, PINK1, and LGALS3 for HBV-HCC patients.", "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:37180150"], "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:GSE14520"], "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:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37180150", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2023.1142319", "sha256": "sha256:eaaeda34a49d4650c3419a770f87ff7bec4c56733aa0073ca67c2d15d5bf0ec4", "bytes": 36522, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2023.1142319", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10169569", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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"group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Characterization of gene expression profile in HBV-related liver fibrosis patients", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE83148 not downloaded", "asset:data:geo:GSE83148 licence not read", "asset:data:geo:GSE84044 not downloaded", "asset:data:geo:GSE84044 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In this study, Cox 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The HBV-HCC cell model was established by transfection of pAAV/HBV1.2C2, constructed by homologous", "ctively, in HBV-HCC cell models after LGALS3 knockdown. The findings of this study suggest that LGA", "ALS3 in PBMCs ( Figures S4C–H ). Analysis of transfection efficiency The transfection efficiency of HE", "H ). Analysis of transfection efficiency The transfection efficiency of HEPG2 was 61.38 ± 2.44% and th"], "order_basis": "paper_text_order:1005", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d by homologous recombination, into HUH7 and HEPG2 cells. The expression levels of G6PD, PINK1,", "on efficiency The transfection efficiency of HEPG2 was 61.38 ± 2.44% and that of HUH7 was 81.85", "8% ( Figure S5A ). ELISA results showed that HEPG2 and HUH7 cells produced HBsAg after transfec", "GALS3 function After LGALS3 knockdown in the HEPG2# and HUH7# cell lines, LGALS3 gene expressio"], "order_basis": "paper_text_order:1091", "id": "assay:2"}, {"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": ["G6PD, PINK1, and LGALS3 were detected using RT-qPCR. We further analyzed the expression of the m", "l genes, FOXP3 and CCR6, were analyzed using RT-qPCR in peripheral blood mononuclear cells of 31", "ents, we analyzed the expression of CCL20 by RT-qPCR and the changes in cell proliferation and mi", "PD, PINK1, and LGALS3 were detected using RT-qPCR. We further analyzed the expression of the m"], "order_basis": "paper_text_order:1174", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["anges in cell proliferation and migration by CCK8 and transwell assays, respectively, in HBV-H", "gures 11A, B ). Moreover, the results of the CCK8 cell proliferation assay showed that the pro", "n before and after knockdown was detected by CCK8. (D, E) Transwell assay showed that cell mig"], "order_basis": "paper_text_order:1926", "id": "assay:4"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ssion profile chip datasets, we selected the Affymetrix HT Human Genome U133A Array dataset, which c"], "order_basis": "paper_text_order:2645", "id": "assay:5"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["at of HUH7 was 81.85 ± 2.68% ( Figure S5A ). ELISA results showed that HEPG2 and HUH7 cells pro"], "order_basis": "paper_text_order:10073", "id": "assay:6"}, {"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": ["In this study, Cox regression analysis was performed using GSE14520 chip data and a necroptosis-related genes survival prognosis score (NRGPS) was established for HBV-HCC patients."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}