Construction of the Six-lncRNA Prognosis Signature as a Novel Biomarker in Esophageal Squamous Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35432441", "kind": "science-record", "revision": 5, "content_hash": "sha256:cb26432ba0ea4d899e2392c04baf7c38b36f6cfa95a2ed3908736789fa669286", "created_at": "2026-11-01T18:14:15Z", "updated_at": "2026-11-01T22:48:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of the Six-lncRNA Prognosis Signature as a Novel Biomarker in Esophageal Squamous Cell Carcinoma.", "doi": "10.3389/fgene.2022.839589", "pmid": "35432441", "authors": ["Ze-Jun Zheng", "Yan-Shang Li", "Jun-De Zhu", "Hai-Ying Zou", "Wang-Kai Fang", "Yi-Yao Cui", "Jian-Jun Xie"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Esophageal squamous cell carcinoma (ESCC) is a common malignant gastrointestinal tumor threatening global human health. For patients diagnosed with ESCC, determining the prognosis is a huge challenge. Due to their important role in tumor progression, long non-coding RNAs (lncRNAs) may be putative molecular candidates in the survival prediction of ESCC patients. Here, we obtained three datasets of ESCC lncRNA expression profiles (GSE53624, GSE53622, and GSE53625) from the Gene Expression Omnibus (GEO) database. The method of statistics and machine learning including survival analysis and LASSO regression analysis were applied. We identified a six-lncRNA signature composed of AL445524.1, AC109439.2, LINC01273, AC015922.3, LINC00547, and PSPC1-AS2. Kaplan-Meier and Cox analyses were conducted, and the prognostic ability and predictive independence of the lncRNA signature were found in three ESCC datasets. In the entire set, time-dependent ROC curve analysis showed that the prediction accuracy of the lncRNA signature was remarkably greater than that of TNM stage. ROC and stratified analysis indicated that the combination of six-lncRNA signature with the TNM stage has the highest accuracy in subgrouping ESCC patients. Furthermore, experiments subsequently confirmed that one of the lncRNAs LINC01273 may play an oncogenic role in ESCC. This study suggested the six-lncRNA signature could be a valuable survival predictor for patients with ESCC and have potential to be an auxiliary biomarker of TNM stage to subdivide ESCC patients more accurately, which has important clinical significance.", "claims": [{"id": "claim-method", "statement": "To single out those lncRNAs which were significantly associated with the prognosis of ESCC patients, both univariable Cox regression and KM survival analysis (the median lncRNA expression value as the cutoff value) were used in the training dataset. The LASSO regression method was then applied to obtain the strongest survival-related lncRNAs in the training set.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35432441", "locator": "sections[4] \"Construction of the Multi-lncRNA Predictive Models Related to Overall Survival\" paragraph 2", "quote": "To single out those lncRNAs which were significantly associated with the prognosis of ESCC patients, both univariable Cox regression and KM survival analysis (the median lncRNA expression value as the cutoff value) were used in the training dataset."}, {"asset": "source:pmid:35432441", "locator": "sections[4] \"Construction of the Multi-lncRNA Predictive Models Related to Overall Survival\" paragraph 2", "quote": "The LASSO regression method was then applied to obtain the strongest survival-related lncRNAs in the training set."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. These data can be found here: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53624/matrix/ ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53622/matrix/ ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53625/matrix/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35432441", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. These data can be found here: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53624/matrix/ ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53622/matrix/ ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53625/matrix/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study suggested the six-lncRNA signature could be a valuable survival predictor for patients with ESCC and have potential to be an auxiliary biomarker of TNM stage to subdivide ESCC patients more accurately, which has important clinical significance.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35432441", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study suggested the six-lncRNA signature could be a valuable survival predictor for patients with ESCC and have potential to be an auxiliary biomarker of TNM stage to subdivide ESCC patients more accurately, which has important clinical significance."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study suggested the six-lncRNA signature could be a valuable survival predictor for patients with ESCC and have potential to be an auxiliary biomarker of TNM stage to subdivide ESCC patients more accurately, which has important clinical significance.", "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:35432441"], "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:GSE53622"], "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:GSE53622"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35432441", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.839589", "sha256": "sha256:85deed932c546cfce853d73ed833f9bb7ac22b805fd6d218a46c664899f593dd", "bytes": 31887, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2022.839589", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9008717", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE53622", "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=GSE53622", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53622", "version": null, "note": "Publicly available datasets were analyzed in this study. 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downloaded", "asset:data:geo:GSE53625 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "reordered", "quote": "To single out those lncRNAs which were significantly associated with the prognosis of ESCC patients, both univariable Cox regression and KM survival analysis (the median lncRNA expression value as the cutoff value) were used in the training dataset. The LASSO regression method was then applied to obtain the strongest survival-related lncRNAs in the training set."}}, {"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": "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": "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": [], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE53624", "GSE53622", "GSE53625"], "resolved_accessions": ["GSE53624", "GSE53622", "GSE53625"], "statements": ["Publicly available datasets were analyzed in this study. These data can be found here: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53624/matrix/ ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53622/matrix/ ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53625/matrix/."], "basis": "The paper names GSE53624, GSE53622, GSE53625 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": ["survival_km"], "assets": ["source:pmid:35432441", "data:geo:GSE53622"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE53622"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:42:15Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10106, "completion_tokens": 2115, "cached_tokens": 264}}, "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:35432441", "type": "paper", "label": "pmid:35432441"}, {"id": "source:pmid:35432441", "type": "manuscript", "label": "PMID 35432441 full text"}, {"id": "data:geo:GSE53622", "type": "dataset", "label": "GEO GSE53622"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35432441", "type": "paper", "label": "pmid:35432441"}, {"id": "source:pmid:35432441", "type": "manuscript", "label": "PMID 35432441 full text"}, {"id": "data:geo:GSE53622", "type": "dataset", "label": "GEO GSE53622"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35432441", "type": "extraction", "used": ["source:pmid:35432441"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE53622", "type": "accession_resolution", "used": ["data:geo:GSE53622"], "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:35432441", "parent_hash": "sha256:e1465b95d02824c282fb6f9e9490b0837571d1901f2ffb54d8a148ca3c53705c", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE53622 licence not read", "asset:data:geo:GSE53622 not downloaded", "asset:data:geo:GSE53624 licence not read", "asset:data:geo:GSE53624 not downloaded", "asset:data:geo:GSE53625 licence not read", "asset:data:geo:GSE53625 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Materials and Methods Cell Culture and Cell Transfection Human ESCC cell lines KYSE410 and TE5 were c", "Following the instructions, siLINC01273 was transfected at a concentration of 40 nM using Lipofectam", "tration of 40 nM using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) with Opti-MEM (Gibco).", "nt (Invitrogen) with Opti-MEM (Gibco). After transfection for 48 h, the RNAs were harvested. Stratific"], "order_basis": "paper_text_order:1718", "id": "assay:1"}, {"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": ["n Human ESCC cell lines KYSE410 and TE5 were cultured in RPMI 1640 (Gibco) medium with 10% fetal bovi", "–penicillin solution (Gibco). All cells were cultured in a 5% CO2 constant temperature incubator. Sma"], "order_basis": "paper_text_order:1773", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["gilent-038314 CBC Homo sapiens lncRNA + mRNA microarray V2.0. 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