Transcriptome-wide m6A methylome analysis uncovered the changes of m6A modification in oral pre-malignant cells compared with normal oral epithelial cells

Xun Chen; Liutao Chen; Yuquan Tang; Yi He; Kuangwu Pan; Linyu Yuan; Weihong Xie; Shangwu Chen; Wei Zhao; Dongsheng Yu

doi:10.3389/fonc.2022.939449

Transcriptome-wide m⁶A methylome analysis uncovered the changes of m⁶A modification in oral pre-malignant cells compared with normal oral epithelial cells

Front Oncol. 2022 Sep 28:12:939449. doi: 10.3389/fonc.2022.939449. eCollection 2022.

Authors

Xun Chen¹, Liutao Chen^{2

3}, Yuquan Tang¹, Yi He¹, Kuangwu Pan¹, Linyu Yuan¹, Weihong Xie¹, Shangwu Chen^{2

3}, Wei Zhao¹, Dongsheng Yu¹

Affiliations

¹ Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.
² Guangdong Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
³ State Key Laboratory for Biocontrol, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.

Abstract

As the most common post-transcriptional RNA modification, m⁶A methylation extensively regulates the structure and function of RNA. The dynamic and reversible modification of m⁶A is coordinated by m⁶A writers and erasers. m⁶A reader proteins recognize m⁶A modification on RNA, mediating different downstream biological functions. mRNA m⁶A modification and its corresponding regulators play an important role in cancers, but its characteristics in the precancerous stage are still unclear. In this study, we used oral precancerous DOK cells as a model to explore the characteristics of transcriptome-wide m⁶A modification and major m⁶A regulator expression in the precancerous stage compared with normal oral epithelial cell HOEC and oral cancer cell SCC-9 through MeRIP-seq and RT-PCR. Compared with HOEC cells, we found 1180 hyper-methylated and 1606 hypo-methylated m⁶A peaks and 354 differentially expressed mRNAs with differential m⁶A peaks in DOK cells. Although the change of m⁶A modification in DOK cells was less than that in SCC-9 cells, mRNAs with differential m⁶A in both cell lines were enriched into many identical GO terms and KEGG pathways. Among the 20 known m⁶A regulatory genes, FTO, ALKBH5, METTL3 and VIRMA were upregulated or downregulated in DOK cells, and the expression levels of 10 genes such as METTL14/16, FTO and IGF2BP2/3 were significantly changed in SCC-9 cells. Our data suggest that precancerous cells showed, to some extent, changes of m⁶A modification. Identifying some key m⁶A targets and corresponding regulators in precancerous stage may provide potential intervention targets for the prevention of cancer development through epigenetic modification in the future.

Keywords: MeRIP sequencing; dysplastic oral keratinocyte (DOK); human oral epithelial cell (HOEC); m6A modification; m6A regulatory genes; oral squamous cell carcinoma cell; precancerous cells.