Comprehensive Analysis of N7-Methylguanosine-Modified Long Non-Coding RNAs Identifies DPY19L1P1 as a Key Oncogenic Effector in Oral Squamous Cell Carcinoma

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Background: N7-methylguanosine (m7G) is an important RNA modification involved in the regulation of gene expression during transcription. While its roles in mRNAs and tRNAs are increasingly understood, the distribution and function of m7G in long non-coding RNAs (lncRNAs), particularly in oral squamous cell carcinoma (OSCC), remain poorly understood. This study aimed to systematically characterize the m7G methylation landscape of lncRNAs in OSCC and investigate the oncogenic function and regulatory mechanism of the m7G-modified lncRNA DPY19L1P1. Methods: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were performed on three pairs of OSCC and adjacent normal tissues to identify differentially m7G-modified and differentially expressed lncRNAs. Motif prediction, its potential functions are identified through analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. DPY19L1P1 was prioritized based on its high level of m7G modification and upregulation. Its clinical relevance was assessed using TCGA-HNSC datasets. In vitro and in vivo functional assays were performed to evaluate its oncogenic roles. The regulatory effects of methyltransferase-like 1 (METTL1) and WD repeat domain 4 (WDR4) on DPY19L1P1 were examined using expression correlation, MeRIP quantitative real-time PCR (qPCR), and splicing efficiency analyses. Results: A total of 5486 OSCC-specific m7G peaks and 5135 modified lncRNAs were identified. Compared to normal tissues, OSCC tissues exhibited broader distribution and higher levels of m7G modifications. Among 15,085 hyper-m7G-modified lncRNAs detected in OSCC, 80 were also upregulated. They are enriched in metabolic pathways associated with lncRNA cell adhesion and migration. DPY19L1P1 displayed the most prominent m7G methylation and expression levels, and was significantly associated with advanced clinical stage and poor differentiation, indicating its diagnostic potential. Mechanistically, METTL1 and WDR4 cooperatively enhanced both the m7G modification and expression of DPY19L1P1 by promoting its splicing efficiency. Furthermore, METTL1/WDR4 and DPY19L1P1 synergistically promoted OSCC progression, with DPY19L1P1 functioning as a key downstream effector. Functionally, DPY19L1P1 facilitated OSCC cell proliferation, migration, glycolysis-driven metabolic reprogramming, and epithelial–mesenchymal transition (EMT). Conclusion: This study provides a comprehensive profile of m7G-modified lncRNAs in OSCC and identifies DPY19L1P1 as a hyper-m7G-modified oncogenic lncRNA regulated by the METTL1/WDR4 complex. As a key downstream effector, DPY19L1P1 promotes OSCC progression through metabolic reprogramming and EMT, and may serve as a potential diagnostic biomarker and therapeutic target.

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