Identification and Validation of an m6A-Related LncRNA Signature to Predict Progression-Free Survival in Colorectal Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36032659", "kind": "science-record", "revision": 3, "content_hash": "sha256:c1de681f4de69712500cc3f816fa30596a70df8eac12312c8a5e0d558345687e", "created_at": "2026-11-01T18:15:11Z", "updated_at": "2026-11-01T21:28:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Validation of an m6A-Related LncRNA Signature to Predict Progression-Free Survival in Colorectal Cancer.", "doi": "10.3389/pore.2022.1610536", "pmid": "36032659", "authors": ["Yong Zhang", "Lu Li", "Feifei Chu", "Xingguo Xiao", "Li Zhang", "Kunkun Li", "Huili Wu"], "journal": "Pathology oncology research : POR", "year": 2022, "abstract": "The RNA methylation of N6 adenosine (m6A) plays a crucial role in various biological processes. Strong evidence reveals that the dysregulation of long non-coding RNAs (lncRNA) brings about the abnormality of downstream signaling in multiple ways, thus influencing tumor initiation and progression. Currently, it is essential to discover effective and succinct molecular biomarkers for predicting colorectal cancer (CRC) prognosis. However, the prognostic value of m6A-related lncRNAs for CRC remains unclear, especially for progression-free survival (PFS). Here, we screened 24 m6A-related lncRNAs in 622 CRC patients and identified five lncRNAs (SLCO4A1-AS1, MELTF-AS1, SH3PXD2A-AS1, H19 and PCAT6) associated with patient PFS. Compared to normal samples, their expression was up-regulated in CRC tumors from TCGA dataset, which was validated in 55 CRC patients from our in-house cohort. We established an m6A-Lnc signature for predicting patient PFS, which was an independent prognostic factor by classification analysis of clinicopathologic features. Moreover, the signature was validated in 1,077 patients from six independent datasets (GSE17538, GSE39582, GSE33113, GSE31595, GSE29621, and GSE17536), and it showed better performance than three known lncRNA signatures for predicting PFS. In summary, our study demonstrates that the m6A-Lnc signature is a promising biomarker for forecasting patient PFS in CRC.", "claims": [{"id": "claim-method", "statement": "To estimate whether m6A-LncScore could act as an independent factor in CRC to predict PFS, we performed univariate and multivariate Cox regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36032659", "locator": "sections[11] \"The Prognostic Value of m6A-LncScore Was Independent of Clinicopathological Factors for PFS\" paragraph 2", "quote": "To estimate whether m6A-LncScore could act as an independent factor in CRC to predict PFS, we performed univariate and multivariate Cox regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36032659", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In summary, our study demonstrates that the m6A-Lnc signature is a promising biomarker for forecasting patient PFS in CRC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36032659", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In summary, our study demonstrates that the m6A-Lnc signature is a promising biomarker for forecasting patient PFS in CRC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In summary, our study demonstrates that the m6A-Lnc signature is a promising biomarker for forecasting patient PFS in CRC.", "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:36032659"], "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:GSE17536"], "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:GSE17536"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36032659", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/pore.2022.1610536", "sha256": "sha256:36ed612ddee23df7a7a15b0cf20bd1080b66104d40ec66326a032d2f136be55c", "bytes": 45287, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/pore.2022.1610536", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9407446", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE17538", "GSE39582", "GSE33113", "GSE31595", "GSE29621", "GSE17536"], "resolved_accessions": ["GSE17538", "GSE39582", "GSE33113", "GSE31595", "GSE29621", "GSE17536"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE17538, GSE39582, GSE33113, GSE31595, GSE29621, GSE17536 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:36032659", "data:geo:GSE17536"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17536"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:01:58Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14284, "completion_tokens": 1745, "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:36032659", "type": "paper", "label": "pmid:36032659"}, {"id": "source:pmid:36032659", "type": "manuscript", "label": "PMID 36032659 full text"}, {"id": "data:geo:GSE17536", "type": "dataset", "label": "GEO GSE17536"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36032659", "type": "paper", "label": "pmid:36032659"}, {"id": "source:pmid:36032659", "type": "manuscript", "label": "PMID 36032659 full text"}, {"id": "data:geo:GSE17536", "type": "dataset", "label": "GEO GSE17536"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36032659", "type": "extraction", "used": ["source:pmid:36032659"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17536", "type": "accession_resolution", "used": ["data:geo:GSE17536"], "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:36032659", "parent_hash": "sha256:03d0c828d3bc5b4cd55766b3fc7f23f60f24bc444d1072388a49406ca1ead3e5", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17538 licence not read", "asset:data:geo:GSE17538 not downloaded", "asset:data:geo:GSE29621 licence not read", "asset:data:geo:GSE29621 not downloaded", "asset:data:geo:GSE31595 licence not read", "asset:data:geo:GSE31595 not downloaded", "asset:data:geo:GSE33113 licence not read", "asset:data:geo:GSE33113 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["To estimate whether m6A-LncScore could act as an independent factor in CRC to predict PFS, we performed univariate and multivariate Cox regression analysis."], "order_basis": "analysis_only", "id": "assay:1"}]}