PVR-A Prognostic Biomarker Correlated with Immune Cell Infiltration in Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36552960", "kind": "science-record", "revision": 3, "content_hash": "sha256:9036f71ee29970878cc443bf8836cc975c739b63770e73780dbc4f433e0d84ff", "created_at": "2026-11-01T19:01:05Z", "updated_at": "2026-11-01T22:08:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PVR-A Prognostic Biomarker Correlated with Immune Cell Infiltration in Hepatocellular Carcinoma.", "doi": "10.3390/diagnostics12122953", "pmid": "36552960", "authors": ["Wen-Feng Liu", "Bing Quan", "Miao Li", "Feng Zhang", "Ke-Shu Hu", "Xin Yin"], "journal": "Diagnostics (Basel, Switzerland)", "year": 2022, "abstract": "The poliovirus receptor (PVR) is a member of the immunoglobulin superfamily (Ig SF) and is essential for the promotion of cancer cell proliferation and invasion. However, the correlation between PVR expression and prognosis as well as immune infiltration in hepatocellular carcinoma (HCC) remains unclear. The expression level of PVR was quantified using the Tumor and Tumor Immunity Evaluation Resource (TIMER) and Sangerbox. The Gene Expression Omnibus (GEO) database was used to validate the PVR expression. The receiver operating characteristic (ROC) curve was used to evaluate the feasibility of using PVR as a differentiating factor according to the area under curve (AUC) score. A PVR binding protein network was built using the STRING tool. An enrichment analysis using the R package clusterProfiler was used to explore the potential function of PVR. Immune infiltration analysis was calculated with ESTIMATE algorithms. We also assessed the correlation between PVR expression and immune infiltration by the single-sample Gene Set Enrichment Analysis (ssGSEA) method from the R package GSVA and TIMER database. The results showed that PVR was commonly overexpressed in multiple types of tumors including HCC. The data of GSE64041 confirmed the same result. The ROC curve suggested that PVR could be a potential diagnostic biomarker. Additionally, high mRNA expression of PVR in HCC was significantly correlated with poor overall survival (OS) and relapse free survival (RFS). Results also indicated correlations between PVR mRNA expression with the level of infiltration immune cells including B cells, CD8+ T cells, cytotoxic cells, DCs, CD56dim NK cells, pDCs, and Th2 cells. Furthermore, the PVR level was significantly correlated with immune markers for immunosuppressive cells in HCC. In conclusion, PVR might be an important regulator of tumor immune cell infiltration and a valuable prognostic biomarker in HCC. However, additional work is needed to fully elucidate the underlying mechanisms.", "claims": [{"id": "claim-method", "statement": "The Kaplan–Meier plot (http://kmplot.com/analysis/ (Last accessed on 15 November 2022)) was applied to evaluate the prognostic significance of PVR in HCC patients. Using the auto select best cutoff algorithm on the website, HCC patients were divided into two cohorts (high vs. low expression). Then, the hazard ratio (HR) and log-rank p-value were calculated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36552960", "locator": "sections[5] \"2.3. Prognostic Analysis of PVR in HCC Patients\" paragraph 2", "quote": "The Kaplan–Meier plot (http://kmplot.com/analysis/ (Last accessed on 15 November 2022)) was applied to evaluate the prognostic significance of PVR in HCC patients. Using the auto select best cutoff algorithm on the website, HCC patients were divided into two cohorts (high vs. low expression). Then, the hazard ratio (HR) and log-rank p-value were calculated."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data are available on request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36552960", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "All data are available on request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Elevated PVR mRNA expression in HCC was significantly associated with poor overall survival and relapse-free survival.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "The log-rank analysis revealed a significant correlation between the elevated PVR mRNA levels and poor OS and RFS in the HCC patients (p < 0.05) (Figure 3A,B)."}, "evidence": [{"asset": "source:pmid:36552960", "locator": "sections[10] \"3.2. Prognostic Significance of PVR Expression in HCC\" paragraph 2", "quote": "The log-rank analysis revealed a significant correlation between the elevated PVR mRNA levels and poor OS and RFS in the HCC patients (p < 0.05) (Figure 3A,B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Elevated PVR mRNA expression in HCC was significantly associated with poor overall survival and relapse-free survival.", "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:36552960"], "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:GSE64041"], "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:GSE64041"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36552960", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/diagnostics12122953", "sha256": "sha256:05a13f3652e3ed9058a08f9766b5d60a86a7b8420fa2f2ec406eb8b45e3e66e4", "bytes": 36480, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/diagnostics12122953", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9777148", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE64041", "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=GSE64041", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64041", "version": null, "note": "All data are available on request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data are available on request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2052455", "GSM2052456", "GSM2052457", "GSM2052458", "GSM2052459", "GSM2052460", "GSM2052461", "GSM2052462", "GSM2052463", "GSM2052464", "GSM2052465", "GSM2052466", "GSM2052467", "GSM2052468", "GSM2052469", "GSM2052470", "GSM2052471", "GSM2052472", "GSM2052473", "GSM2052474", "GSM2052475", "GSM2052476", "GSM2052477", "GSM2052478", "GSM2052479", "GSM2052480", "GSM2052481", "GSM2052482", "GSM2052483", "GSM2052484", "GSM2052485", "GSM2052486", "GSM2052487", "GSM2052488", "GSM2052489", "GSM2052490", "GSM2052491", "GSM2052492", "GSM2052493", "GSM2052494", "GSM2052495", "GSM2052496", "GSM2052497", "GSM2052498", "GSM2052499", "GSM2052500", "GSM2052501", "GSM2052502", "GSM2052503", "GSM2052504", "GSM2052505", "GSM2052506", "GSM2052507", "GSM2052508", "GSM2052509", "GSM2052510", "GSM2052511", "GSM2052512", "GSM2052513", "GSM2052514", "GSM2052515", "GSM2052516", "GSM2052517", "GSM2052518", "GSM2052519", "GSM2052520", "GSM2052521", "GSM2052522", "GSM2052523", "GSM2052524", "GSM2052525", "GSM2052526", "GSM2052527", "GSM2052528", "GSM2052529", "GSM2052530", "GSM2052531", "GSM2052532", "GSM2052533", "GSM2052534", "GSM2052535", "GSM2052536", "GSM2052537", "GSM2052538", "GSM2052539", "GSM2052540", "GSM2052541", "GSM2052542", "GSM2052543", "GSM2052544", "GSM2052545", "GSM2052546", "GSM2052547", "GSM2052548", "GSM2052549", "GSM2052550", "GSM2052551", "GSM2052552", "GSM2052553", "GSM2052554", "GSM2052555", "GSM2052556", "GSM2052557", "GSM2052558", "GSM2052559", "GSM2052560", "GSM2052561", "GSM2052562", "GSM2052563", "GSM2052564", "GSM2052565", "GSM2052566", "GSM2052567", "GSM2052568", "GSM2052569", "GSM2052570", "GSM2052571", "GSM2052572", "GSM2052573", "GSM2052574", "GSM2052575", "GSM2052576", "GSM2052577", "GSM2052578", "GSM2052579"], "sample_count": 125, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profiling in paired human hepatocellular carcinoma and liver parenchyma biopsies and normal liver biopsies.", "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:GSE64041 not downloaded", "asset:data:geo:GSE64041 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The Kaplan–Meier plot (http://kmplot.com/analysis/ (Last accessed on 15 November 2022)) was applied to evaluate the prognostic significance of PVR in HCC patients. Using the auto select best cutoff algorithm on the website, HCC patients were divided into two cohorts (high vs. low expression). Then, the hazard ratio (HR) and log-rank p-value were calculated."}}, {"id": "method-2", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE64041"], "resolved_accessions": ["GSE64041"], "statements": ["All data are available on request."], "basis": "The paper names GSE64041 in Gene Expression Omnibus (GEO) datasets and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:36552960", "data:geo:GSE64041"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE64041"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:20:58Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11562, "completion_tokens": 2099, "cached_tokens": 128}}, "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:36552960", "type": "paper", "label": "pmid:36552960"}, {"id": "source:pmid:36552960", "type": "manuscript", "label": "PMID 36552960 full text"}, {"id": "data:geo:GSE64041", "type": "dataset", "label": "GEO GSE64041"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36552960", "type": "paper", "label": "pmid:36552960"}, {"id": "source:pmid:36552960", "type": "manuscript", "label": "PMID 36552960 full text"}, {"id": "data:geo:GSE64041", "type": "dataset", "label": "GEO GSE64041"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36552960", "type": "extraction", "used": ["source:pmid:36552960"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE64041", "type": "accession_resolution", "used": ["data:geo:GSE64041"], "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:36552960", "parent_hash": "sha256:575f93a86213d5f9a0fe8a3d0d753936e2f5e393786bb9c7012887c5d3a55b96", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE64041 licence not read", "asset:data:geo:GSE64041 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": 0.93, "evidence": ["ina). Reverse transcription and quantitative real-time PCR were conducted referring to the kit or the S"], "order_basis": "paper_text_order:2384", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["d reverse primer: GTTTGGACTCCGAATAGCTGG. For immunohistochemistry, formalin-fixed paraffin-embedded sections ("], "order_basis": "paper_text_order:2779", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Kaplan–Meier plot (http://kmplot.com/analysis/ (Last accessed on 15 November 2022)) was applied to evaluate the prognostic significance of PVR in HCC patients. Using the auto select best cutoff algorithm on the website, HCC patients were divided into two cohorts (high vs. low expression). Then, the hazard ratio (HR) and log-rank p-value were calculated."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}