Unraveling the protective role of m6A methylation in SLC22A3 expression for breast Cancer intervention

Yu Xiao; Congcong Cao; Yaqi Zhang; Chao Zhao; Yuchen Liu

doi:10.1016/j.bbadis.2025.167962

Unraveling the protective role of m6A methylation in SLC22A3 expression for breast Cancer intervention

Biochim Biophys Acta Mol Basis Dis. 2025 Jun 24;1871(7):167962. doi: 10.1016/j.bbadis.2025.167962. Online ahead of print.

Authors

Yu Xiao¹, Congcong Cao², Yaqi Zhang³, Chao Zhao⁴, Yuchen Liu⁵

Affiliations

¹ Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Breast and Thyroid Department, Shenzhen 518035, China.
² Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.
³ Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.
⁴ Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China. Electronic address: chao.zhao@siat.ac.cn.
⁵ Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China. Electronic address: liuyuchen@szseyy.com.

PMID: 40570980
DOI: 10.1016/j.bbadis.2025.167962

Abstract

Background: The interplay between SLC22A3 expression and m6A RNA methylation is emerging as a significant factor in breast cancer pathology, yet the specific correlations and underlying mechanisms remain unclear.

Methods: The prognostic significance of SLC22A3 expression in breast cancer was assessed using the Cancer Genome Atlas data. In vitro experiments were conducted using a custom-engineered dCas13b-METTL3 plasmid, designed to selectively enhance m6A methylation of SLC22A3 mRNA. Functional alterations in breast cancer cells post-transfection were evaluated. Additionally, overexpression of the m6A reader protein IGF2BP2 was achieved, and subsequent changes in SLC22A3 expression and overall breast cancer cell transcriptome were analyzed. MeRIP-seq and mRNA-seq were employed to analyze the expression and m6A methylation of Slc22a3 in a transgenic mouse model of breast cancer.

Results: Bioinformatics analysis demonstrated a significant reduction in SLC22A3 expression in cancer tissues compared to adjacent non-cancerous tissues. Enhancement of SLC22A3 mRNA m6A methylation via the dCas13b-M3 plasmid in breast cancer cells led to increased SLC22A3 expression, accompanied by reduced cell proliferation and migration and induced apoptosis. Overexpression of IGF2BP2 similarly increased SLC22A3 expression. Further, RNA-seq identified 25 genes downstream of SLC22A3. Analysis of breast cancer tissues from mice revealed a decrease in both SLC22A3 expression and its m6A methylation as the breast cancer progressed.

Conclusion: SLC22A3 acts as protective factor in breast cancer. Enhanced m6A methylation of SLC22A3 mRNA and overexpression of the m6A reader IGF2BP2 upregulate its expression. The induction of SLC22A3 mRNA methylation through the m6A CRISPR approach effectively mitigates the malignancy of breast cancer cells.

Keywords: Breast cancer; CRISPR/dCas13b; RNA epigenetics; SLC22A3; m6A methylation.