m6A methylation profiling as a prognostic marker in nasopharyngeal carcinoma - Insights from MeRIP-Seq and RNA-Seq

Sep 21, 2026

Nasopharyngeal carcinoma (NPC) shows unclear mechanisms and often presents at middle to late stages, making reliable prognostic markers essential. This study investigated N6-methyladenosine (m6A) dysregulation, linking altered RNA structure and RNA-protein interactions to tumorigenesis and progression. Using MeRIP-Seq in patient tissues and integrating large-scale transcriptome data, differentially expressed m6A-related genes were analyzed with Cox regression and LASSO modeling.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages12

Reading Time30 min

AccessFree to download

Background

Methods

Results

Conclusions

TYPE Original Research PUBLISHED 12 December 2024 DOI 10.3389/fimmu.2024.1492648 OPEN ACCESS EDITED BY Zhihao Wang, Wuhan University, China REVIEWED BY Zhuangzhuang Geng, Children ’s Hospital of Philadelphia, United States Xinyu Cao, University of Illinois Chicago, United States *CORRESPONDENCE Yingming Sun [yingmingsun@fjmu.edu.cn](yingmingsun@fjmu.edu.cn)[ ](yingmingsun@fjmu.edu.cn)Qinying Liu [liuqinyingbio@163.com](liuqinyingbio@163.com)[ ](liuqinyingbio@163.com)Sufang Qiu [sufangqiu@fjmu.edu.cn](sufangqiu@fjmu.edu.cn) †These authors have contributed equally to this work RECEIVED 07 September 2024 ACCEPTED 21 November 2024 PUBLISHED 12 December 2024 CITATION Chen X, Xu W, Pan J, Yang H, Li Y, Chen X, Sun Y, Liu Q and Qiu S (2024) m6Amethylation proﬁling as a prognostic marker in nasopharyngeal carcinoma: insights from MeRIP-Seq and RNA-Seq. Front. Immunol. 15:1492648 . doi: 10.3389/fimmu.2024.1492648 COPYRIGHT © 2024 Chen, Xu, Pan, Yang, Li, Chen, Sun, Liu and Qiu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. m6A methylation proﬁlingas a prognostic marker innasopharyngeal carcinoma: insights from MeRIP-Seq and RNA-Seq Xiaochuan Chen 1†, Wenqian Xu 1†, Junping Pan 1†, Hanxuan Yang1, Yi Li 1, Xin Chen 1, Yingming Sun 2*, Qinying Liu 3* and Sufang Qiu 1* 1 Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China, 2 Department of Radiation and Medical Oncology, Afﬁliated Sanming First Hospital of Fujian Medical University, Sanming, China, 3 Fujian Provincial Key Laboratory of Tumor Biotherapy, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China Background: Nasopharyngeal carcinoma (NPC) is a type of malignant tumors commonly found in Southeast Asia and China, with insidious onset and clinical symptoms. N6-methyladenosine (m6A) modiﬁcation signiﬁcantly contributes to tumorigenesis and progression by altering RNA secondary structure and inﬂuencing RNA-protein binding at the transcriptome level. However, the mechanism and role of abnormal m6A modiﬁcation in nasopharyngeal carcinoma remain unclear. Methods: Nasopharyngeal Carcinoma tissues from 3 patients and noncancerous nasopharyngeal tissues from 3 individuals, all from Fujian Cancer Hospital, were sequenced for m6A methylation. These were combined with transcriptome sequencing data from 192 nasopharyngeal cancer tissues. Genes linked to prognosis were discovered using differential analysis and univariate Cox regression. Subsequently, a prognostic model associated with m6A was developed through the application of LASSO regression analysis. The model’s accuracy was veriﬁed using both internal transcriptome databases and external databases. An extensive evaluation of the tumor’s immune microenvironment and signaling pathways was performed, analyzing both transcriptomic and single-cell data. Results: The m6A methylation sequencing analysis revealed 194 genes with varying expression levels, many of which are predominantly associated with immune pathways. By integrating transcriptome sequencing data, 19 m6Amodiﬁed genes were found to be upregulated in tumor tissues, leading to the development of a three-gene (EME1, WNT4, SHISA2) risk prognosis model. The group with lower risk exhibited notable enrichment in pathways related to immunity, displaying traits like enhanced survival rates, stronger immune proﬁles, and increased responsiveness to immunotherapy when compared to the higher-risk group. Single-cell analy

FAQs

What is the main purpose of this study on NPC?

To determine whether m6A methylation–related genes can serve as prognostic markers in nasopharyngeal carcinoma and clarify their biological and immune-related implications.

What datasets and sequencing approaches were used?

m6A methylation was profiled using MeRIP-Seq on NPC and noncancerous tissues, and the analysis integrated transcriptome sequencing data from a large NPC cohort, with additional single-cell and transcriptomic evaluations.

How was the prognostic model constructed?

Prognosis-associated genes were identified using differential analysis and univariate Cox regression, then a three-gene risk model was built using LASSO regression and validated using internal and external transcriptome databases.

What were the key findings regarding risk groups and immune features?

Lower-risk patients showed enrichment in immunity-related pathways, better survival-related characteristics, more favorable immune profiles, and increased responsiveness to immunotherapy compared with the higher-risk group.

Sep 21, 2026

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