Potential prognosis index for m6A-related mRNA in cholangiocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35672673", "kind": "science-record", "revision": 4, "content_hash": "sha256:28c23f82ebacb533845f837f83a2a30c557cb0067b1e041e315068b054f5181e", "created_at": "2026-11-01T18:14:37Z", "updated_at": "2026-11-01T22:06:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Potential prognosis index for m6A-related mRNA in cholangiocarcinoma.", "doi": "10.1186/s12885-022-09665-3", "pmid": "35672673", "authors": ["Huaqiang Zhu", "Haini Zhao", "Jianlu Wang", "Shuchao Zhao", "Chaoqun Ma", "Dongliang Wang", "Hengjun Gao", "Faji Yang", "Qingqiang Ni", "Hongguang Li", "Xu Zhou", "Chunqing Zhang", "Jun Lu"], "journal": "BMC cancer", "year": 2022, "abstract": "BACKGROUND: Cholangiocarcinoma (CHOL) is a malignant tumor that originates in the extrahepatic bile duct and can extend from the hilar region to the lower end of the common bile duct. The prognosis of CHOL patients is particularly poor; therefore, in this study, we screened mRNAs correlated with N6-methyladenosine (m6A) to construct a risk model for prognosis in CHOL.\nMETHODS: The TCGA-CHOL dataset was applied to obtain and analyze the coexpression of 1281 m6A-related mRNAs, from which 14 were selected for further analysis through univariate proportional hazards (cox) regression analysis. Aryl hydrocarbon receptor interacting protein (AIP), CCAAT/enhancer binding protein beta (CEBPB), syndecan1 (SDC1), vacuolar protein sorting 25 homolog (VPS25) and syntaxin binding protein 2 (STXBP2) were then screened out through the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis to develop a precise m6A-related mRNA prognosis risk model (MRMRPM) with an area under curve (AUC) of 0.908 and 0.923 after 1 and 2 years, respectively. We divided the samples into high-risk and low-risk groups using the m6A-related mRNA prognosis risk model.\nRESULTS: Kaplan-Meier analysis indicated poor overall survival (OS) for the high-risk group. Two Gene Expression Omnibus (GEO) datasets (GSE89748 and GSE107943) were used to validate the risk model. The results of drug sensitivity and immune cell infiltration analysis showed that the risk model could serve as a prognosis index of potential immunotherapeutic characteristics and drug sensitivity. Furthermore, the proportion of resting dendritic cells and regulatory T cells was positively associated with an increased expression of four m6A-related mRNAs - AIP, CEBPB, SDC1, and VPS25 - in the high-risk CHOL group.\nCONCLUSIONS: Our findings suggest that this model can be a prognostic indicator for CHOL patients.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier analysis was performed using the “survival” package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35672673", "locator": "sections[9] \"Kaplan–Meier survival analysis\" paragraph 2", "quote": "Kaplan–Meier analysis was performed using the “survival” package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets GSE89748 and GSE107943 for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The datasets TCGA of CHOL for this study can be found in the TCGA project (https://portal.gdc.cancer.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35672673", "locator": "sections[32] \"notes\" paragraph 1", "quote": "The datasets GSE89748 and GSE107943 for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The datasets TCGA of CHOL for this study can be found in the TCGA project (https://portal.gdc.cancer.gov/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Aryl hydrocarbon receptor interacting protein (AIP), CCAAT/enhancer binding protein beta (CEBPB), syndecan1 (SDC1), vacuolar protein sorting 25 homolog (VPS25) and syntaxin binding protein 2 (STXBP2) were then screened out through the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis to develop a precise m6A-related mRNA prognosis risk model (MRMRPM) with an area under curve (AUC) of 0.908 and 0.923 after 1 and 2 years, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35672673", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Aryl hydrocarbon receptor interacting protein (AIP), CCAAT/enhancer binding protein beta (CEBPB), syndecan1 (SDC1), vacuolar protein sorting 25 homolog (VPS25) and syntaxin binding protein 2 (STXBP2) were then screened out through the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis to develop a precise m6A-related mRNA prognosis risk model (MRMRPM) with an area under curve (AUC) of 0.908 and 0.923 after 1 and 2 years, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Aryl hydrocarbon receptor interacting protein (AIP), CCAAT/enhancer binding protein beta (CEBPB), syndecan1 (SDC1), vacuolar protein sorting 25 homolog (VPS25) and syntaxin binding protein 2 (STXBP2) were then screened out through the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis to develop a precise m6A-related mRNA prognosis risk model (MRMRPM) with an area under curve (AUC) of 0.908 and 0.923 after 1 and 2 years, respectively.", "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:35672673"], "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:GSE107943"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE107943"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35672673", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-022-09665-3", "sha256": "sha256:4463a3547337dcc636fed473f94b7a371b7be416f52c40da25b97a11bd51a6fc", "bytes": 47247, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-022-09665-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9170563", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE107943", "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=GSE107943", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE107943", "version": null, "note": "The datasets GSE89748 and GSE107943 for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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