M6A-mediated molecular patterns and tumor microenvironment infiltration characterization in nasopharyngeal carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38532632", "kind": "science-record", "revision": 3, "content_hash": "sha256:e8f5d9d738b61a446c2721d7e86cf67048bcdca0e6dd477e51ce642ee9c47548", "created_at": "2026-11-01T19:20:28Z", "updated_at": "2026-11-01T22:11:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "M6A-mediated molecular patterns and tumor microenvironment infiltration characterization in nasopharyngeal carcinoma.", "doi": "10.1080/15384047.2024.2333590", "pmid": "38532632", "authors": ["Yong Wang", "Lisha Peng", "Feng Wang"], "journal": "Cancer biology & therapy", "year": 2024, "abstract": "N6-methyladenosine (m6A) is the most predominant RNA epigenetic regulation in eukaryotic cells. Numerous evidence revealed that m6A modification exerts a crucial role in the regulation of tumor microenvironment (TME) cell infiltration in several tumors. Nevertheless, the potential role and mechanism of m6A modification in nasopharyngeal carcinoma (NPC) remains unknown. mRNA expression data and clinical information from GSE102349, and GSE53819 datasets obtained from Gene Expression Omnibus (GEO) was used for differential gene expression and subsequent analysis. Consensus clustering was used to identify m6A-related molecular patterns of 88 NPC samples based on prognostic m6A regulators using Univariate Cox analysis. The TME cell-infiltrating characteristics of each m6A-related subclass were explored using single-sample gene set enrichment (ssGSEA) algorithm and CIBERSORT algotithm. DEGs between two m6A-related subclasses were screened using edgeR package. The prognostic signature and predicated nomogram were constructed based on the m6A-related DEGs. The cell infiltration and expression of prognostic signature in NPC was determined using immunohistochemistry (IHC) analysis. Chi-square test was used to analysis the significance of difference of the categorical variables. And survival analysis was performed using Kaplan-Meier plots and log-rank tests. The NPC samples were divided into two m6A-related subclasses. The TME cell-infiltrating characteristics analyses indicated that cluster 1 is characterized by immune-related and metabolism pathways activation, better response to anit-PD1 and anti-CTLA4 treatment and chemotherapy. And cluster 2 is characterized by stromal activation, low expression of HLA family and immune checkpoints, and a worse response to anti-PD1 and anti-CTLA4 treatment and chemotherapy. Furthermore, we identified 1558 DEGs between two m6A-related subclasses and constructed prognostic signatures to predicate the progression-free survival (PFS) for NPC patients. Compared to non-tumor samples, REEP2, TMSB15A, DSEL, and ID4 were upregulated in NPC samples. High expression of REEP2 and TMSB15A showed poor survival in NPC patients. The interaction between REEP2, TMSB15A, DSEL, ID4, and m6A regulators was detected. Our finding indicated that m6A modification plays an important role in the regulation of TME heterogeneity and complexity.", "claims": [{"id": "claim-method", "statement": "Univariate Cox analysis was performed with survival R package to identify the m6A regulators with prognostic significance in NPC, the significant m6A regulators were identified using univariate Cox analysis of PFS with P-value <.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38532632", "locator": "sections[4] \"Construction of prognosis-related signature based on 21 m6A regulators\" paragraph 2", "quote": "Univariate Cox analysis was performed with survival R package to identify the m6A regulators with prognostic significance in NPC, the significant m6A regulators were identified using univariate Cox analysis of PFS with P-value <.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data in this study can be obtained from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). The analytical methods can be found in the methods section. R scripts written for performing analyses in this study are shared via GitHub (https://github.com/DrWangfeng/nasopharyngeal-carcinoma). And the supplementary files have been shared via GitHub (https://github.com/DrWangfeng/Supplementary-files.git).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38532632", "locator": "sections[34] \"Availability of data and materials\" paragraph 2", "quote": "All data in this study can be obtained from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). The analytical methods can be found in the methods section. R scripts written for performing analyses in this study are shared via GitHub (https://github.com/DrWangfeng/nasopharyngeal-carcinoma). And the supplementary files have been shared via GitHub (https://github.com/DrWangfeng/Supplementary-files.git)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Furthermore, we identified 1558 DEGs between two m6A-related subclasses and constructed prognostic signatures to predicate the progression-free survival (PFS) for NPC patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38532632", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Furthermore, we identified 1558 DEGs between two m6A-related subclasses and constructed prognostic signatures to predicate the progression-free survival (PFS) for NPC patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Furthermore, we identified 1558 DEGs between two m6A-related subclasses and constructed prognostic signatures to predicate the progression-free survival (PFS) for NPC patients.", "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:38532632"], "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. 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