Fifteen mRNA-lncRNA expression-based signature predicted the survival of late-staged head and neck squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32500914", "kind": "science-record", "revision": 7, "content_hash": "sha256:9535fa87ff1995d8a0219d23565c09e8e4641d2299de308462670d5c727706d8", "created_at": "2026-11-01T15:41:03Z", "updated_at": "2026-11-01T22:01:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Fifteen mRNA-lncRNA expression-based signature predicted the survival of late-staged head and neck squamous cell carcinoma.", "doi": "10.1042/BSR20200442", "pmid": "32500914", "authors": ["He Ren", "Huaping Li", "Ping Li", "Yuhui Xu", "Gang Liu", "Liping Sun"], "journal": "Bioscience reports", "year": 2020, "abstract": "BACKGROUND: Gene expression is necessary for regulation in almost all biological processes, at the same time, it is related to the prognosis for head and neck squamous cell carcinoma (HNSCC). The prognosis of late-staged HNSCC is important because of its guiding significance on the therapy strategies.\nMETHODS: In this work, we analyzed the relationship between gene expression and HNSCC in The Cancer Genome Atlas (TCGA) cohort, and optimized the panel with random forest survival analysis. Subsequently, a Cox multivariate regression-based model was developed to predict the clinical outcome of HNSCC. The performance of the model was assayed in the training cohort and validated in another three independent cohorts (GSE41614, E-TABM-302, E-MTAB-1328). The underlying pathways significantly associated with the model were identified. According to the results, patients of low-score group (median survival months: 27.4, 95% CI: 18.2-43) had a significant poor survival than those of high-score group (median survival months: 69.4, 95% CI: 58.7-72.1, P=2.7e-5), and the observation was repeatable in the other validation cohorts. Further analysis revealed that the model performed better than the other clinical indicators and is independent of these indicators.\nRESULTS: Comparison revealed that the model performed better than existing models for late HNSCC prognosis. Gene set enrichment analysis (GSEA) elucidated that the model was significantly associated with various cell processes and pathways.", "claims": [{"id": "claim-method", "statement": "To estimate the survival differences between the low- and high-risk groups, the Kaplan–Meier method with a log-rank test was chosen, and P<0.05 was considered as statistically significant in this step.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32500914", "locator": "sections[6] \"Statistical analysis\" paragraph 2", "quote": "To estimate the survival differences between the low- and high-risk groups, the Kaplan–Meier method with a log-rank test was chosen, and P<0.05 was considered as statistically significant in this step."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32500914"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32500914", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1042/BSR20200442", "sha256": "sha256:df44a66f1330269eddc63ab9f2ba13de39792fc413377cde5ccad014fe4f9eac", "bytes": 24977, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1042/BSR20200442", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7327439", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32500914:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bc02065fdb26f09c077138e014acfa2ac2d0750981c2db8a44e2f3e81f187a17", "bytes": 513, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T1", "version": null, "note": "Clinical information of cohorts used in this study", "structure": {"pmcid": "PMC7327439", "section_index": 8, "section_title": "Characteristics of datasets involved", "row_count": 8, "column_count": 6}, "table": {"label": "Table 1", "caption": "Clinical information of cohorts used in this study", "rows": [["Variables", "TCGA", "E-MTAB-302", "E-MTAB-1328", "GSE41618"], ["Median follow-up (months)", "56", "58", "57", "26"], ["Gender", "Male", "225", "69", "75", "38"], ["", "Female", "71", "5", "6", "18"], ["Age", "60−", "145", "40", "43", "31"], ["", "60+", "151", "34", "38", "25"], ["Grade", "4−", "92", "23", "24", "NA"], ["", "4", "204", "51", "57", "NA"]], "row_count": 8, "column_count": 6, "numeric_cells": 33, "header_rows": 1, "locator": "section[8]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32500914:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:db10e514e738f9b48eaa896f19fb44818f85262bd47a5a7e113d7f425b11148b", "bytes": 1453, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T2", "version": null, "note": "Genes in the risk score", "structure": {"pmcid": "PMC7327439", "section_index": 9, "section_title": "Identification of prognostic lncRNAs and model development", "row_count": 16, "column_count": 4}, "table": {"label": "Table 2", "caption": "Genes in the risk score", "rows": [["Gene symbol", "Ensembl IDs", "Description", "Coefficient"], ["KLHDC7B", "ENSG00000130487", "Kelch domain containing 7B", "1.37289399"], ["EMC4", "ENSG00000128463", "ER membrane protein complex subunit 4", "−0.327847579"], ["AHDC1", "ENSG00000126705", "AT-hook DNA binding motif containing 1", "0.01524505"], ["PNPLA4", "ENSG00000006757", "Patatin-like phospholipase domain containing 4", "−0.646201302"], ["PEX11A", "ENSG00000166821", "Peroxisomal biogenesis factor 11 α", "0.172110564"], ["BRD4", "ENSG00000141867", "Bromodomain containing 4", "0.068037273"], ["NR1H2", "ENSG00000131408", "Nuclear receptor subfamily 1 group H member 2", "0.731963077"], ["XCR1", "ENSG00000173578", "X–C motif chemokine receptor 1", "−0.226687207"], ["NFU1", "ENSG00000169599", "NFU1 iron–sulfur cluster scaffold", "−1.01799464"], ["ORC6", "ENSG00000091651", "Origin recognition complex subunit 6", "−0.247036767"], ["AP000229.1", "ENSG00000273492", "Novel transcript", "0.468081738"], ["FAM53B", "ENSG00000189319", "Family with sequence similarity 53 member B", "0.583104952"], ["MIR4435-2HG", "ENSG00000172965", "MIR4435-2 host gene", "0.266319204"], ["PLEKHG6", "ENSG00000008323", "Pleckstrin homology and RhoGEF domain containing G6", "0.233982315"], ["ITFG1", "ENSG00000129636", "Integrin α FG-GAP repeat containing 1", "−0.333125317"]], "row_count": 16, "column_count": 4, "numeric_cells": 46, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32500914:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c2c1832baba40e330ae513e6f0dccf8f5ec954877e6ce418078c072b18112057", "bytes": 418, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T3", "version": null, "note": "Cox multivariate regression of risk score and other clinical information", "structure": {"pmcid": "PMC7327439", "section_index": 12, "section_title": "Correlation between the model and clinicopathological features of HNSCC", "row_count": 5, "column_count": 4}, "table": {"label": "Table 3", "caption": "Cox multivariate regression of risk score and other clinical information", "rows": [["", "HR", "95% CI", "P"], ["Grade", "1.04", "0.681–1.59", "0.84508"], ["Gender", "0.93", "0.60–1.45", "0.7644"], ["Tumor size", "1.39", "1.13–1.71", "0.00137"], ["Risk score", "0.62", "0.49–0.79", "0.00017"]], "row_count": 5, "column_count": 4, "numeric_cells": 13, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T3"}}], "gaps": []}, "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": "To estimate the survival differences between the low- and high-risk groups, the Kaplan–Meier method with a log-rank test was chosen, and P<0.05 was considered as statistically significant in this step."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:32500914", "asset:table:pmid:32500914:1", "asset:table:pmid:32500914:2", "asset:table:pmid:32500914:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:03:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 21317, "completion_tokens": 1390, "cached_tokens": 528}}, "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:32500914", "type": "paper", "label": "pmid:32500914"}, {"id": "source:pmid:32500914", "type": "manuscript", "label": "PMID 32500914 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32500914", "type": "paper", "label": "pmid:32500914"}, {"id": "source:pmid:32500914", "type": "manuscript", "label": "PMID 32500914 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32500914", "type": "extraction", "used": ["source:pmid:32500914"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:32500914", "parent_hash": "sha256:8a5250461119d21b57677818d45b90683e6e2f474fe8029ccbb2f1a8d0a4bb45", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"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": ["To estimate the survival differences between the low- and high-risk groups, the Kaplan–Meier method with a log-rank test was chosen, and P<0.05 was considered as statistically significant in this step."], "order_basis": "analysis_only", "id": "assay:1"}]}