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Integrated multi-omics analysis reveals tumor-suppressive phenotypes and associated transcriptomic remodeling upon
Zhao Liu1, Yanwu Zhou2, Chun Li3
1Sixth Affiliated Hospital, Xinjiang Medical University, Urumqi, China.
Background:
Lung cancer (LC) remains a leading cause of cancer-related death globally. The methyltransferase METTL3, a core writer of RNA N6-methyladenosine (m6A) modification, is a key regulator in cancer. However, its systematic regulatory network, particularly in contexts where it exerts tumor-suppressive functions, remains to be fully elucidated. In this study, we aimed to systematically investigate the transcriptomic and epitranscriptomic remodeling induced by METTL3 overexpression in A549 lung cancer cells to uncover its potential tumor-suppressive mechanisms.
Methods:
Bioinformatics analysis of public databases was performed to evaluate METTL3 expression and prognostic significance in LC. Cell biology assays were conducted to assess phenotypic changes (proliferation, migration/invasion apoptosis) induced by METTL3 overexpression (METTL3-OE). RNA-sequencing (RNA-seq) was performed for METTL3-OE and negative control (NC) A549 cells. Publicly available methylated RNA immunoprecipitation sequencing (MeRIP-seq) datasets of LC cell line and tissues (GSE117299, GSE76367) were downloaded from the Gene Expression Omnibus (GEO) database. Bioinformatics analysis was performed to identify m6A-modified targets and infer their potential function. Key differentially expressed genes (DEGs) and alternative splicing events (ASEs) were validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR).
Results:
Analysis of public databases indicated that METTL3 was downregulated in LC tissues and its higher expression correlated with better patient prognosis. Functionally, METTL3 overexpression in A549 cells inhibited proliferation, migration, and invasion, while promoting apoptosis (P<0.05). RNA-seq identified 240 DEGs (227 up-/13 down-regulated). Upregulated DEGs were significantly enriched in antiviral response and antigen presentation pathways. METTL3-OE also altered 1,305 ASEs, with affected genes enriched in cell migration and apoptosis. Integrated analysis identified 22 genes (e.g., HLA-A/B/C, MYD88) that were upregulated by METTL3 overexpression and have been reported to harbor m6A modifications reported in LC tissues and A549 cells. Furthermore, analysis revealed an overlap of 222 genes between those undergoing METTL3-regulated splicing changes and genes documented as m6A-modified in the same LC datasets. RT-qPCR confirmed the upregulation of the immune-related genes (MYD88, HLA-A/B/C, IFIT1, IFIT3, OAS1, ISG20) and the altered splicing of NCOR2 and SIRT7 and AURKB (P<0.05).
Conclusions:
Our study demonstrates that METTL3 overexpression exerts tumor-suppressive effects in A549 cells and suggests that METTL3 may be involved in a multi-layered transcriptional and post-transcriptional response. This response includes the upregulation of immune-related genes-many of which are known m6A targets in LC-and the modulation of splicing in genes controlling cell fate, collectively contributing to the suppression of malignant phenotypes.
