Type I and type II interferon responses in two human liver cell lines (Huh-7 and HuH6).

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26981398", "kind": "science-record", "revision": 6, "content_hash": "sha256:a3e370769c768399e3201c408e8dfbc97b72b450d2769e22e592684fbdd34857", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T21:20:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Type I and type II interferon responses in two human liver cell lines (Huh-7 and HuH6).", "doi": "10.1016/j.gdata.2015.12.017", "pmid": "26981398", "authors": ["Oliver Grünvogel", "Katharina Esser-Nobis", "Marc P Windisch", "Michael Frese", "Martin Trippler", "Ralf Bartenschlager", "Volker Lohmann", "Marco Binder"], "journal": "Genomics data", "year": 2016, "abstract": "Most studies investigating the biology of Hepatitis C virus (HCV) have used the human hepatoma cell line Huh-7 or subclones thereof, as these are the most permissive cell lines for HCV infection and replication. Other cell lines also support replication of HCV, most notably the human hepatoblastoma cell line HuH6. HCV replication in cell culture is generally highly sensitive to interferons (IFNs) and differences in the IFN-mediated inhibition of virus replication may reflect alterations in the IFN-induced antiviral response inherent to different host cells. For example, HCV replication is highly sensitive to IFN-γ treatment in Huh-7, but not in HuH6 cells. In this study, we used microarray-based gene expression profiling to compare the response of Huh-7 and HuH6 cells to stimulation with IFN-α and IFN-γ. Furthermore, we determined whether the resistance of HCV replication in HuH6 cells can be linked to differences in the expression profile of IFN-regulated genes. Although both cells lines responded to IFNs with rapid changes in gene expression, thereby demonstrating functional type I and type II signaling pathways, differences were observed for a number of genes. Raw and normalized expression data have been deposited in GEO under accession number GSE68927.", "claims": [{"id": "claim-method", "statement": "As a quantitative measure to score differentially induced ISGs, we calculated a weighted rank difference (WRD) for each gene.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981398", "locator": "sections[8] \"ISGs differentially induced in Huh-7 versus HuH6\" paragraph 4", "quote": "As a quantitative measure to score differentially induced ISGs, we calculated a weighted rank difference (WRD) for each gene."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw and normalized expression data have been deposited in GEO under accession number GSE68927.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981398", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw and normalized expression data have been deposited in GEO under accession number GSE68927."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used RMA normalization of Affymetrix microarray data and weighted rank difference (WRD) analysis to compare IFN-stimulated gene responses, while the source data are available through GEO accession GSE68927 and its direct accession link.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981398", "locator": "sections[6] \"Signal processing and normalization\" paragraph 2", "quote": "Signals were normalized within one cell line (three treatment groups per cell line: mock, IFN-α and IFN-γ) using the RMA method and expressed on a log2-transformed scale."}, {"asset": "source:pmid:26981398", "locator": "sections[8] \"ISGs differentially induced in Huh-7 versus HuH6\" paragraph 4", "quote": "As a quantitative measure to score differentially induced ISGs, we calculated a weighted rank difference (WRD) for each gene."}, {"asset": "source:pmid:26981398", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw and normalized expression data have been deposited in GEO under accession number GSE68927."}, {"asset": "source:pmid:26981398", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68927"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used RMA normalization of Affymetrix microarray data and weighted rank difference (WRD) analysis to compare IFN-stimulated gene responses, while the source data are available through GEO accession GSE68927 and its direct accession link.", "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:26981398"], "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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ISGs were sorted for the magnitude of their induction (fold-change, FC) within each sample. The 20 genes most strongly induced by IFN-α (left) or IFN-γ (right) are listed for Huh-7 and HuH6, respectively. Fold-changes are given on a log2 scale (i.e. FC 7.35 translates to a 163-fold upregulation).", "structure": {"pmcid": "PMC4778650", "section_index": 7, "section_title": "Analysis of IFN-induced genes", "row_count": 22, "column_count": 8}, "table": {"label": "Table 1", "caption": "Top 20 induced ISGs upon IFN treatment in Huh-7 and HuH6 cells. ISGs were sorted for the magnitude of their induction (fold-change, FC) within each sample. The 20 genes most strongly induced by IFN-α (left) or IFN-γ (right) are listed for Huh-7 and HuH6, respectively. 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ISGs were defined as “present” and upregulated at least 1.5-fold (0.58 on a log2 scale) in either Huh-7 or HuH6 and sorted for their weighted rank difference (WRD). Highest WRD corresponds to the strongest difference in induction between Huh-7 and HuH6 (see text). FC: fold-change (log2 scale).", "structure": {"pmcid": "PMC4778650", "section_index": 8, "section_title": "ISGs differentially induced in Huh-7 versus HuH6", "row_count": 42, "column_count": 12}, "table": {"label": "Table 2", "caption": "ISGs differentially induced in Huh-7 versus HuH6. ISGs were defined as “present” and upregulated at least 1.5-fold (0.58 on a log2 scale) in either Huh-7 or HuH6 and sorted for their weighted rank difference (WRD). Highest WRD corresponds to the strongest difference in induction between Huh-7 and HuH6 (see text). FC: fold-change (log2 scale).", "rows": [["IFN-α", "IFN-γ"], ["Gene symbol", "FC Huh-7", "FC HuH6", "rank Huh-7", "rank HuH6", "WRD", "Gene symbol", "FC Huh-7", "FC HuH6", "rank Huh-7", "rank HuH6", "WRD"], ["MX1", "7.35", "1.49", "1", "56", "1.93", "ERAP2", "1.08", "4.75", "126", "8", "1.76"], ["IFI44", "0.47", "4.92", "277", "11", "1.85", "CXCL9", "3.74", "0.31", "16", "234", "1.74"], ["TDO2", "3.07", "− 0.19", "27", "287", "1.66", "BTN3A3", "3.28", "0.04", "23", "265", "1.68"], ["IFI16", "0.06", "2.56", "290", "35", "1.57", "MX1", "3.16", "− 0.1", "26", "285", "1.67"], ["GBP1", "3.11", "0.19", "25", "178", "1.51", "CXCL10", "4.62", "1.06", "10", "103", "1.65"], ["SLFN5", "0.08", "1.66", "287", "49", "1.42", "CARD16", "3.27", "0.24", "24", "243", "1.64"], ["RASGRP3", "0.68", "2.13", "204", "39", "1.36", "IFI27", "1.21", "4.5", "111", "12", "1.61"], ["IL8", "1.7", "− 0.36", "59", "301", "1.34", "APOL3", "0.37", "2.84", "228", "30", "1.53"], ["IFI27", "4.11", "6.91", "15", "3", "1.33", 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