Characterization of m6A methylation modifications in gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38206646", "kind": "science-record", "revision": 4, "content_hash": "sha256:379eeb74283cd5838d03e8f05a56d665e4facac1325094c7069299023406cafe", "created_at": "2026-11-01T19:20:07Z", "updated_at": "2026-11-01T22:53:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterization of m6A methylation modifications in gastric cancer.", "doi": "10.18632/aging.205341", "pmid": "38206646", "authors": ["Wei Yin", "Zhanwei Huo", "Jiawei Zuo", "Haixiao Wang", "Bi Chen", "Liqing Zhou"], "journal": "Aging", "year": 2024, "abstract": "Widely recognized as an essential epitranscriptomic modification, RNA N6-methyladenosine (m6A) is involved in both physiological and pathological processes. Here, we want to investigate m6A modification's potential roles in gastric cancer. Gastric cancer samples were selected from TCGA-STAD and GEO (GSE84426, GSE84433) datasets. Based on 18 regulators of m6A, m6A modification patterns were thoroughly evaluated in gastric cancer samples. Principal component analysis algorithms were used to construct the m6Ascore, using which, m6A modification features in tumor somatic mutations and immune checkpoint blockade therapy were analyzed. 34 gastric cancer samples were collected to verify the effectiveness of the m6Ascore. Here, we determined three different m6A modification patterns. m6Acluster-C modification pattern presented immune activation-associated enrichment pathways and have significant survival advantages. Then, in gastric cancer, m6Ascore could act as an independent prognostic biomarker. A significant survival benefit was exhibited in patients with high m6Ascore. Moreover, the modification signature of m6A uncovered in this study would help to predict immune checkpoint blockade therapy's responses. In conclusion, our discoveries all pointed to the fact that modification patterns of m6A were linked to the TME. Moreover, evaluation of individual tumor's m6A modification pattern will help to guide immunotherapy strategies that shows more therapeutic effects.", "claims": [{"id": "claim-method", "statement": "Since m6A modification features individual heterogeneity and high complexity, a set of scoring system, termed m6Ascore, was built using R 4.3.1. to perform principal component analysis (PCA) based on these phenotype gene, in order to quantify the m6A modification pattern of individual gastric cancer patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38206646", "locator": "sections[17] \"Generation of m6Ascore\" paragraph 2", "quote": "Since m6A modification features individual heterogeneity and high complexity, a set of scoring system, termed m6Ascore, was built using R 4.3.1. to perform principal component analysis (PCA) based on these phenotype gene, in order to quantify the m6A modification pattern of individual gastric cancer patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this study are openly available in the TCGA database and GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38206646", "locator": "sections[11] \"Data availability\" paragraph 2", "quote": "The data presented in this study are openly available in the TCGA database and GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The m6Ascore was established as an independent prognostic biomarker for gastric cancer, with a significant survival benefit in patients with a high m6Ascore.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38206646", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Then, in gastric cancer, m6Ascore could act as an independent prognostic biomarker."}, {"asset": "source:pmid:38206646", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A significant survival benefit was exhibited in patients with high m6Ascore."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The m6Ascore was established as an independent prognostic biomarker for gastric cancer, with a significant survival benefit in patients with a high m6Ascore.", "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:38206646"], "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:GSE84426"], "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:GSE84426"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38206646", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.205341", "sha256": "sha256:d422d88c929d52483e5236966c1b13e4b0ce92727b23e349a2ed86d3e9fcfdb0", "bytes": 39495, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.205341", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10817395", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84426", "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=GSE84426", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84426", "version": null, "note": "The data presented in this study are openly available in the TCGA database and GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are openly available in the TCGA database and GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2235556", "GSM2235557", "GSM2235558", "GSM2235559", "GSM2235560", "GSM2235561", "GSM2235562", "GSM2235563", "GSM2235564", "GSM2235565", "GSM2235566", "GSM2235567", "GSM2235568", "GSM2235569", "GSM2235570", "GSM2235571", "GSM2235572", "GSM2235573", "GSM2235574", "GSM2235575", "GSM2235576", "GSM2235577", "GSM2235578", "GSM2235579", "GSM2235580", "GSM2235582", "GSM2235584", "GSM2235585", "GSM2235586", "GSM2235587", "GSM2235588", "GSM2235589", "GSM2235593", "GSM2235595", "GSM2235596", "GSM2235597", "GSM2235598", "GSM2235599", "GSM2235600", "GSM2235601", "GSM2235602", "GSM2235603", "GSM2235604", "GSM2235605", "GSM2235606", "GSM2235607", "GSM2235608", "GSM2235609", "GSM2235610", "GSM2235611", "GSM2235612", "GSM2235613", "GSM2235614", "GSM2235615", "GSM2235616", "GSM2235617", "GSM2235618", "GSM2235619", "GSM2235620", "GSM2235621", "GSM2235622", "GSM2235623", "GSM2235624", "GSM2235625", "GSM2235626", "GSM2235627", "GSM2235628", "GSM2235629", "GSM2235630", "GSM2235631", "GSM2235632", "GSM2235633", "GSM2235634", "GSM2235635", "GSM2235636", "GSM2235637"], "sample_count": 76, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer. 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