← All .science files
pmid:37879404
Oncostatin M Induces IFITM1 Expression to Inhibit Hepatitis B Virus Replication Via JAK-STAT Signaling.
Yuchen Ye · Ya Fu · Caorui Lin · Ye Shen · Qingqing Yu · Xiaobao Yao · Qunfang Huang · Can Liu · Yongbin Zeng · Tianbin Chen · Songhang Wu · Zhen Xun · Qishui Ou
Cellular and molecular gastroenterology and hepatology · 2024 doi:10.1016/j.jcmgh.2023.10.003
Paper
complete
Experiment
partial
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 13 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 83 items
gaps array · 2 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 1 item
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 8 items
assays array · 6 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[3] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[4] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[5] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37879404", "kind": "science-record", "revision": 5, "content_hash": "sha256:59c95ba67d9eceaf9f17835c611a6c394a41b97e11b7c5d1896a8058a8e8ef7e", "created_at": "2026-11-01T19:02:44Z", "updated_at": "2026-11-01T22:52:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Oncostatin M Induces IFITM1 Expression to Inhibit Hepatitis B Virus Replication Via JAK-STAT Signaling.", "doi": "10.1016/j.jcmgh.2023.10.003", "pmid": "37879404", "authors": ["Yuchen Ye", "Ya Fu", "Caorui Lin", "Ye Shen", "Qingqing Yu", "Xiaobao Yao", "Qunfang Huang", "Can Liu", "Yongbin Zeng", "Tianbin Chen", "Songhang Wu", "Zhen Xun", "Qishui Ou"], "journal": "Cellular and molecular gastroenterology and hepatology", "year": 2024, "abstract": "BACKGROUND & AIMS: Functional cure is achieved by a limited number of patients with chronic hepatitis B (CHB) after nucleotide analogue(s) and interferon treatment. It is urgent to develop therapies that can help a larger proportion of patients achieve functional cure. The present study was designed to explore the anti-hepatitis B virus (HBV) potency of interleukin-6 family cytokines and to characterize the underlying mechanisms of the cytokine displaying the highest anti-HBV potency.\nMETHODS: HBV-infected cells were used to screened the anti-HBV potency of interleukin-6 family cytokines. The concentration of oncostatin M (OSM) in patients with chronic HBV infection was examined by enzyme-linked immunosorbent assay. The underlying mechanism of OSM anti-HBV was explored through RNA-seq. C57BL/6 mice injected with rAAV8-1.3HBV were used to explore the suppression effect of OSM on HBV in vivo.\nRESULTS: OSM is the most effective of the interleukin-6 family cytokines for suppression of HBV replication (percentage of average inhibition: hepatitis B surface antigen, 34.44%; hepatitis B e antigen, 32.52%; HBV DNA, 61.57%). Hepatitis B e antigen-positive CHB patients with high OSM levels had lower hepatitis B surface antigen and hepatitis B e antigen than those with low levels. OSM activated JAK-STAT signaling pathway promoting the formation of STAT1-IRF9 transcription factor complex. Following this, OSM increased the expression of various genes with known functions in innate and adaptive immunity, which was higher expression in patients with CHB in immune clearance phase than in immune tolerance phase (data from GEO: GSE65359). Interferon-induced transmembrane protein 1, one of the most differentially expressed genes, was identified as an HBV restriction factor involved in OSM-mediated anti-HBV effect. In vivo, we also found OSM significantly inhibited HBV replication and induced expression of antiviral effector interferon-induced transmembrane protein 1.\nCONCLUSIONS: Our study shows that OSM remodels the immune response against HBV and exerts potent anti-HBV activity, supporting its further development as a potential therapy for treating CHB.", "claims": [{"id": "claim-method", "statement": "Statistical significance was determined using Student unpaired 2-tailed t test, 1-way analysis of variance, Mann-Whitney test, or Kruskal-Wallis test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37879404", "locator": "sections[23] \"Statistical Analysis\" paragraph 2", "quote": "Statistical significance was determined using Student unpaired 2-tailed t test, 1-way analysis of variance, Mann-Whitney test, or Kruskal-Wallis test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "To evaluate the potential anti-HBV functional roles of these differentially expressed genes, we also analyzed a published dataset from human liver biopsy (GEO: GSE65359) and found that a lot of these genes were higher expression in patients with CHB in immune clearance phase than in immune tolerance phase (Figure 4A).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37879404", "locator": "sections[9] \"OSM Remodels the Immune Response Against HBV of Hepatocytes\" paragraph 2", "quote": "To evaluate the potential anti-HBV functional roles of these differentially expressed genes, we also analyzed a published dataset from human liver biopsy (GEO: GSE65359) and found that a lot of these genes were higher expression in patients with CHB in immune clearance phase than in immune tolerance phase (Figure 4A)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "OSM is the most effective of the interleukin-6 family cytokines for suppression of HBV replication, with average inhibition of 34.44% for HBsAg, 32.52% for HBeAg, and 61.57% for HBV DNA.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37879404", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "OSM is the most effective of the interleukin-6 family cytokines for suppression of HBV replication (percentage of average inhibition: hepatitis B surface antigen, 34.44%; hepatitis B e antigen, 32.52%; HBV DNA, 61.57%)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "OSM is the most effective of the interleukin-6 family cytokines for suppression of HBV replication, with average inhibition of 34.44% for HBsAg, 32.52% for HBeAg, and 61.57% for HBV DNA.", "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:37879404"], "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:GSE65359"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_mann_whitney", "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:GSE65359"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37879404", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.jcmgh.2023.10.003", "sha256": "sha256:58dd2b422b43372955f058b5a3b80f967c0ae0e6c44cc26ffa3d8b16afd755b8", "bytes": 44518, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.jcmgh.2023.10.003", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10760422", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65359", "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=GSE65359", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65359", "version": null, "note": "To evaluate the potential anti-HBV functional roles of these differentially expressed genes, we also analyzed a published dataset from human liver biopsy (GEO: GSE65359) and found that a lot of these genes were higher expression in patients with CHB in immune clearance phase than in immune tolerance phase (Figure 4A).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To evaluate the potential anti-HBV functional roles of these differentially expressed genes, we also analyzed a published dataset from human liver biopsy (GEO: GSE65359) and found that a lot of these genes were higher expression in patients with CHB in immune clearance phase than in immune tolerance phase (Figure 4A).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1593078", "GSM1593079", "GSM1593080", "GSM1593081", "GSM1593082", "GSM1593083", "GSM1593084", "GSM1593085", "GSM1593086", "GSM1593087", "GSM1593088", "GSM1593089", "GSM1593090", "GSM1593091", "GSM1593092", "GSM1593093", "GSM1593094", "GSM1593095", "GSM1593096", "GSM1593097", "GSM1593098", "GSM1593099", "GSM1593100", "GSM1593101", "GSM1593102", "GSM1593103", "GSM1593104", "GSM1593105", "GSM1593106", "GSM1593107", "GSM1593108", "GSM1593109", "GSM1593110", "GSM1593111", "GSM1593112", "GSM1593113", "GSM1593114", "GSM1593115", "GSM1593116", "GSM1593117", "GSM1593118", "GSM1593119", "GSM1593120", "GSM1593121", "GSM1593122", "GSM1593123", "GSM1593124", "GSM1593125", "GSM1593126", "GSM1593127", "GSM1593128", "GSM1593129", "GSM1593130", "GSM1593131", "GSM1593132", "GSM1593133", "GSM1593134", "GSM1593135", "GSM1593136", "GSM1593137", "GSM1593138", "GSM1593139", "GSM1593140", "GSM1593141", "GSM1593142", "GSM1593143", "GSM1593144", "GSM1593145", "GSM1593146", "GSM1593147", "GSM1593148", "GSM1593149", "GSM1593150", "GSM1593151", "GSM1593152", "GSM1593153", "GSM1593154", "GSM1593155", "GSM1593156", "GSM1593157", "GSM1593158", "GSM1593159", "GSM1593160"], "sample_count": 83, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Liver transcriptome profiles correlates with viral control during hepatitis B virus infection", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE65359 not downloaded", "asset:data:geo:GSE65359 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical significance was determined using Student unpaired 2-tailed t test, 1-way analysis of variance, Mann-Whitney test, or Kruskal-Wallis test."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}], "targets": [], "gaps": ["method.group_comparison_mann_whitney"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE65359"], "resolved_accessions": ["GSE65359"], "statements": ["To evaluate the potential anti-HBV functional roles of these differentially expressed genes, we also analyzed a published dataset from human liver biopsy (GEO: GSE65359) and found that a lot of these genes were higher expression in patients with CHB in immune clearance phase than in immune tolerance phase (Figure 4A)."], "basis": "The paper names GSE65359 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:37879404", "data:geo:GSE65359"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_mann_whitney", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65359"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:56:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 13379, "completion_tokens": 981, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37879404", "type": "paper", "label": "pmid:37879404"}, {"id": "source:pmid:37879404", "type": "manuscript", "label": "PMID 37879404 full text"}, {"id": "data:geo:GSE65359", "type": "dataset", "label": "GEO GSE65359"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37879404", "type": "paper", "label": "pmid:37879404"}, {"id": "source:pmid:37879404", "type": "manuscript", "label": "PMID 37879404 full text"}, {"id": "data:geo:GSE65359", "type": "dataset", "label": "GEO GSE65359"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37879404", "type": "extraction", "used": ["source:pmid:37879404"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65359", "type": "accession_resolution", "used": ["data:geo:GSE65359"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37879404", "parent_hash": "sha256:fb24aa3b7e881cf366b103704c4bfb37152089297a299f7a2d03fc3328ff9852", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE65359 licence not read", "asset:data:geo:GSE65359 not downloaded", "execution.not_run", "method.group_comparison_mann_whitney", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_mann_whitney"], "assays": [{"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s with chronic HBV infection was examined by enzyme-linked immunosorbent assay. The underlying mechanism of OSM anti-HBV wa", "concentration of serum OSM was quantified by enzyme-linked immunosorbent assay (R&D Systems, Minneapolis, MN) according to"], "order_basis": "paper_text_order:750", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["chanism of OSM anti-HBV was explored through RNA-seq. C57BL/6 mice injected with rAAV8-1.3HBV wer"], "order_basis": "paper_text_order:847", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["explore the suppression effect of OSM on HBV in vivo. RESULTS: OSM is the most effective of the i", "or involved in OSM-mediated anti-HBV effect. In vivo, we also found OSM significantly inhibited H"], "order_basis": "paper_text_order:954", "id": "assay:3"}, {"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": ["G2.2.15, HepAD38, Huh7, and HepG2 cells were cultured in Dulbecco’s modified Eagle medium (Meilunbio,", "he manufacturer’s instructions. Cell Culture HepG2.2.15, HepAD38, Huh7, and HepG2 cells were cu", "Cell Culture HepG2.2.15, HepAD38, Huh7, and HepG2 cells were cultured in Dulbecco’s modified E", "ced at 37°C in 5% CO2 humidified incubators. HepG2.2.15 and HepAD38 stably expresses HBV genome"], "order_basis": "paper_text_order:3114", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["stably expresses HBV genome. Huh7 cells were transfected with HBV 1.3-mer wild-type replicon (QCHENG", "replicon (QCHENG BIO, Shanghai, China) using transfection reagent FuGENE HD (Promega, Fitchburg, WI) t", "HD (Promega, Fitchburg, WI) to generate HBV transfection–based cell culture Huh7-1.3. HBV particles h", "e was targeted and mutated using a transient transfection of RNP containing the gRNA sequence: CTCGCTG"], "order_basis": "paper_text_order:3480", "id": "assay:5"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical significance was determined using Student unpaired 2-tailed t test, 1-way analysis of variance, Mann-Whitney test, or Kruskal-Wallis test."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}