RNA methylation patterns, immune characteristics, and autophagy-related mechanisms mediated by N6-methyladenosine (m6A) regulatory factors in venous thromboembolism.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38658847", "kind": "science-record", "revision": 4, "content_hash": "sha256:1a5a1ad55c874081c99e1217ed23ee77e41fbc1cb1fd00f0abd5ac66984bf205", "created_at": "2026-11-01T19:20:38Z", "updated_at": "2026-11-01T22:54:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RNA methylation patterns, immune characteristics, and autophagy-related mechanisms mediated by N6-methyladenosine (m6A) regulatory factors in venous thromboembolism.", "doi": "10.1186/s12864-024-10294-2", "pmid": "38658847", "authors": ["Deshuai Zhang", "Wenxia Fu", "Shiwei Zhu", "Yitong Pan", "Ruogu Li"], "journal": "BMC genomics", "year": 2024, "abstract": "Recent studies have found a link between deep vein thrombosis and inflammatory reactions. N6-methyladenosine (m6A), a crucial element in immunological regulation, is believed to contribute to the pathophysiology of venous thromboembolism (VTE). However, how the m6A-modified immune microenvironment is involved in VTE remains unclear. In the present study, we identified a relationship between VTE and the expression of several m6A regulatory elements by analyzing peripheral blood samples from 177 patients with VTE and 88 healthy controls from public GEO databases GSE19151 and GSE48000. We used machine learning to identify essential genes and constructed a diagnostic model for VTE using multivariate logistic regression. Unsupervised cluster analysis revealed a marked difference between m6A modification patterns in terms of immune cell infiltration, inflammatory reactivity, and autophagy. We identified two m6A-related autophagy genes (i.e., CHMP2B and SIRT1) and the crucial m6A regulator YTHDF3 using bioinformatics. We also examined two potential mechanisms through which YTHDF3 may affect VTE. m6A modification, immunity, and autophagy are closely linked in VTE, offering novel mechanistic and therapeutic insights.", "claims": [{"id": "claim-method", "statement": "Using the limma package and cutoff criteria of adjusted p-value of 0.05 and |log2(fold change)| > 1 [25], we identified m6A regulators with expression differences between the VTE and control groups [25].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38658847", "locator": "sections[4] \"Identification of VTE-associated m6A regulators\" paragraph 2", "quote": "Using the limma package and cutoff criteria of adjusted p-value of 0.05 and |log2(fold change)| > 1 [25], we identified m6A regulators with expression differences between the VTE and control groups [25]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The analyses conducted in this study utilized R version 4.2.2 (https://cran.rstudio.com/), a widely used open-source programming language and software environment for statistical computing and graphics.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38658847", "locator": "sections[26] \"notes\" paragraph 1", "quote": "The analyses conducted in this study utilized R version 4.2.2 (https://cran.rstudio.com/), a widely used open-source programming language and software environment for statistical computing and graphics."}], "state": "complete"}, {"id": "claim-target-result", "statement": "m6A modification, immunity, and autophagy are closely linked in VTE, offering novel mechanistic and therapeutic insights.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38658847", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "m6A modification, immunity, and autophagy are closely linked in VTE, offering novel mechanistic and therapeutic insights."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "m6A modification, immunity, and autophagy are closely linked in VTE, offering novel mechanistic and therapeutic insights.", "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:38658847"], "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:GSE19151"], "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:GSE19151"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38658847", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12864-024-10294-2", "sha256": 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