Recognizing the role of Epstein-Barr virus in gastric cancer: transcriptomic insights into malignancy modulation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38355581", "kind": "science-record", "revision": 3, "content_hash": "sha256:27d94468e4da2582de82994795e8336deb5bf2803af93c9a6b0c7ae6f0d7e396", "created_at": "2026-11-01T19:20:18Z", "updated_at": "2026-11-01T22:11:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Recognizing the role of Epstein-Barr virus in gastric cancer: transcriptomic insights into malignancy modulation.", "doi": "10.1186/s12985-024-02307-z", "pmid": "38355581", "authors": ["Tabassom Sedaghat Anbouhi", "Hossein Sazegar", "Ebrahim Rahimi"], "journal": "Virology journal", "year": 2024, "abstract": "BACKGROUND: Studies show that Epstein-Barr virus (EBV) infection can play a role in malignancy and increase the risk of gastric cancer (GC). The objective of this research was to pinpoint genes whose expression may be influenced by EBV and play a role in the development of GC.\nMETHODS: Candidate genes potentially susceptible to expression modulation in the presence of EBV were identified through the analysis of GSE185627 and GSE51575 datasets. The association of candidate genes with GC and the survival rate of patients was investigated based on the cancer genome atlas (TCGA) data. Also, pathways related to candidate genes were examined through the MsigDB database. The PPI network was used to identify Hub genes. To corroborate the obtained results, we utilized the RT-qPCR method, employing GC samples from both EBV + and EBV-cases, as well as adjacent normal samples.\nRESULTS: Our results showed that genes upregulated by the EBV in the GC cell line, as well as in EBV + samples, are significantly linked to pathways involving the immune response, inflammation, and the P53 pathway. Conversely, genes downregulated by EBV are closely linked to pathways involving cell proliferation and mTORC1. Examining the candidate genes revealed that a considerable portion of genes susceptible to downregulation under the influence of EBV exhibit oncogenic roles based on TCGA data. Moreover, some of these genes are associated with an unfavorable prognosis. Protein-protein interaction network analysis of candidate genes highlighted IFI44L and OAS2 as potential hub genes in the EBV-GC axis. Our RT-qPCR results further validated these findings, demonstrating that the expression levels of IFI44L and OAS2 were higher in EBV + samples compared to both healthy and EBV-samples.\nCONCLUSION: Our study underscores the capacity of EBV to exert regulatory control over genes associated with GC malignancy. In addition to its inflammatory effects, EBV elicits transcriptomic changes that appear to attenuate the progression of GC.", "claims": [{"id": "claim-method", "statement": "Finally, using the Cox regression test, the relationship between the expression of candidate genes and the mortality rate of patients was evaluated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38355581", "locator": "sections[5] \"Survival analyses\" paragraph 2", "quote": "Finally, using the Cox regression test, the relationship between the expression of candidate genes and the mortality rate of patients was evaluated."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supporting and raw data are available upon a reasonable request to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38355581", "locator": "sections[22] \"Availability of supporting data\" paragraph 2", "quote": "Supporting and raw data are available upon a reasonable request to the corresponding author."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:38355581"], "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:GSE185627"], "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:GSE185627"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38355581", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12985-024-02307-z", "sha256": "sha256:b5fb0d8023421bec9729f011afffd02cd5e041858ca3997116895f36aa2cba7a", "bytes": 40390, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12985-024-02307-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10868016", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE185627", "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=GSE185627", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE185627", "version": null, "note": "Supporting and raw data are available upon a reasonable request to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Supporting and raw data are available upon a reasonable request to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5620878", "GSM5620879", "GSM5620880", "GSM5620881", "GSM5620882", "GSM5620883"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "EBV-induced CXCL8 upregulation promotes vasculogenic mimicry in gastric carcinoma via NF-κB signaling", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE51575", "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=GSE51575", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51575", "version": null, "note": "Supporting and raw data are available upon a reasonable request to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Supporting and raw data are available upon a reasonable request to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1248612", "GSM1248613", "GSM1248614", "GSM1248615", "GSM1248616", "GSM1248617", "GSM1248618", "GSM1248619", "GSM1248620", "GSM1248621", "GSM1248622", "GSM1248623", "GSM1248624", "GSM1248625", "GSM1248626", "GSM1248627", "GSM1248628", "GSM1248629", "GSM1248630", "GSM1248631", "GSM1248632", "GSM1248633", "GSM1248634", "GSM1248635", "GSM1248636", "GSM1248637", "GSM1248638", "GSM1248639", "GSM1248640", "GSM1248641", "GSM1248642", "GSM1248643", "GSM1248644", "GSM1248645", "GSM1248646", "GSM1248647", "GSM1248648", "GSM1248649", "GSM1248650", "GSM1248651", "GSM1248652", "GSM1248653", "GSM1248654", "GSM1248655", "GSM1248656", "GSM1248657", "GSM1248660", "GSM1248661", "GSM1248662", "GSM1248663", "GSM1248664", "GSM1248665"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "13607", "taxon": "Homo sapiens", "title": "mRNA Expression Profiling in EBV-postive Gastric Carcinoma and EBV-negative GC in comparison with their normal mucosa tissue", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE185627 not downloaded", "asset:data:geo:GSE185627 licence not read", "asset:data:geo:GSE51575 not downloaded", "asset:data:geo:GSE51575 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": "Finally, using the Cox regression test, the relationship between the expression of candidate genes and the mortality rate of patients was evaluated."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}], "targets": [], "gaps": []}, "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": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE185627", "GSE51575"], "resolved_accessions": ["GSE185627", "GSE51575"], "statements": ["Supporting and raw data are available upon a reasonable request to the corresponding author."], "basis": "The paper names GSE185627, GSE51575 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": ["cox_ph"], "assets": ["source:pmid:38355581", "data:geo:GSE185627"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE185627"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:08:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11754, "completion_tokens": 2220, "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:38355581", "type": "paper", "label": "pmid:38355581"}, {"id": "source:pmid:38355581", "type": "manuscript", "label": "PMID 38355581 full text"}, {"id": "data:geo:GSE185627", "type": "dataset", "label": "GEO GSE185627"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38355581", "type": "paper", "label": "pmid:38355581"}, {"id": "source:pmid:38355581", "type": "manuscript", "label": "PMID 38355581 full text"}, {"id": "data:geo:GSE185627", "type": "dataset", "label": "GEO GSE185627"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38355581", "type": "extraction", "used": ["source:pmid:38355581"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE185627", "type": "accession_resolution", "used": ["data:geo:GSE185627"], "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:38355581", "parent_hash": "sha256:e3df316071eac407a83b31cfd8de8e8aea976d2619f7ea4718dd0a5fc389eb9c", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE185627 licence not read", "asset:data:geo:GSE185627 not downloaded", "asset:data:geo:GSE51575 licence not read", "asset:data:geo:GSE51575 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["borate the obtained results, we utilized the RT-qPCR method, employing GC samples from both EBV +", "potential hub genes in the EBV-GC axis. Our RT-qPCR results further validated these findings, de", "ate the obtained results, we utilized the RT-qPCR method, employing GC samples from both EBV +", "tential hub genes in the EBV-GC axis. Our RT-qPCR results further validated these findings, de"], "order_basis": "paper_text_order:843", "id": "assay:1"}, {"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": ["Finally, using the Cox regression test, the relationship between the expression of candidate genes and the mortality rate of patients was evaluated."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}