Identifying potential biomarkers in hepatitis B virus infection and its response to the antiviral therapy by integrated bioinformatic analysis.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34041839", "kind": "science-record", "revision": 4, "content_hash": "sha256:c38d083e741bc60e9a4fb084edaf971afada033e50ab568f0df41d82b3e34ca5", "created_at": "2026-11-01T15:41:36Z", "updated_at": "2026-11-01T21:25:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying potential biomarkers in hepatitis B virus infection and its response to the antiviral therapy by integrated bioinformatic analysis.", "doi": "10.1111/jcmm.16655", "pmid": "34041839", "authors": ["Yi He", "Yingzhi Zhou", "Huimin Wang", "Jingyang Yin", "Yunan Chang", "Peng Hu", "Hong Ren", "Hongmei Xu"], "journal": "Journal of cellular and molecular medicine", "year": 2021, "abstract": "The antiviral treatment efficacy varies among chronic hepatitis B (CHB) patients and the underlying mechanism is unclear. An integrated bioinformatics analysis was performed to investigate the host factors that affect the therapeutic responsiveness in CHB patients. Four GEO data sets (GSE54747, GSE27555, GSE66698 and GSE66699) were downloaded from the Gene Expression Omnibus (GEO) database and analysed to identify differentially expressed genes(DEGs). Enrichment analyses of the DEGs were conducted using the DAVID database. Immune cell infiltration characteristics were analysed by CIBERSORT. Upstream miRNAs and lncRNAs of hub DEGs were identified by miRWalk 3.0 and miRNet in combination with the MNDR platform. As a result, seventy-seven overlapping DEGs and 15 hub genes were identified including CCL5, CXCL9, MYH2, CXCR4, CD74, CCL4, HLA-DRB1, ACTA1, CD69, CXCL10, HLA-DRB5, HLA-DQB1, CXCL13, STAT1 and CKM. The enrichment analyses revealed that the DEGs were mainly enriched in immune response and chemokine signalling pathways. Investigation of immune cell infiltration in liver samples suggested significantly different infiltration between responders and non-responders, mainly characterized by higher proportions of CD8+ T cells and activated NK cells in non-responders. The prediction of upstream miRNAs and lncRNAs led to the identification of a potential mRNA-miRNA-lncRNA regulatory network composed of 2 lncRNAs (H19 and GAS5) and 5 miRNAs (hsa-mir-106b-5p, hsa-mir-17-5p, hsa-mir-20a-5p, hsa-mir-6720-5p and hsa-mir-93-5p) targeting CCL5 mRNA. In conclusion, our study suggested that host genetic factors could affect therapeutic responsiveness in CHB patients. The antiviral process might be associated with the chemokine-mediated immune response and immune cell infiltration in the liver microenvironment.", "claims": [{"id": "claim-method", "statement": "The interactive web tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r), provided by the GEO database, was utilized to screen DEGs. |log2FC| > 1 was set as the cut‐off standards and P < .05 was considered to indicate statistical significance. The adjustment of P‐values and the Benjamini and Hochberg method were applied to optimize the statistical power and control false discovery rate.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34041839", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The interactive web tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r), provided by the GEO database, was utilized to screen DEGs. |log2FC| > 1 was set as the cut‐off standards and P < .05 was considered to indicate statistical significance. The adjustment of P‐values and the Benjamini and Hochberg method were applied to optimize the statistical power and control false discovery rate."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data sets used and analysed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34041839", "locator": "sections[26] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "Data sets used and analysed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34041839"], "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. 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