METTL14 suppresses the expression of YAP1 and the stemness of triple-negative breast cancer.

Background: Triple-negative breast cancer (TNBC) has pronounced stemness that is associated with relapse. N-methyladenosine (mA) plays a crucial role in shaping cellular behavior by modulating transcript expression. However, the role of mA in TNBC stemness, as well as the mechanisms governing its abundance, has yet to be elucidated.

Methods: We analyzed proteomic and transcriptomic data derived from breast cancer cohorts, with an emphasis on mA regulators. To unravel the role of mA in TNBC, we employed RNA sequencing, methylated RNA immunoprecipitation sequencing, RNA immunoprecipitation, chromatin immunoprecipitation, and luciferase reporter assays with mesenchymal stem-like (MSL) TNBC models. The clinical relevance was validated using human tissue microarrays and publicly accessible databases.

Results: Our findings indicate that the global level of mA modification in MSL TNBC is downregulated primarily due to the loss of methyltransferase-like 14 (METTL14). The diminished mA modification is crucial for the maintenance of TNBC stemness, as it increases the expression of yes-associated protein 1 (YAP1) by blocking YTH domain-containing family protein 2 (YTHDF2)-mediated transcript decay, thereby promoting the activation of Hippo-independent YAP1 signaling. YAP1 is essential for sustaining the stemness regulated by METTL14. Furthermore, we demonstrated that the loss of METTL14 expression results from lysine-specific demethylase 1 (LSD1)-mediated removal of histone H3 lysine 4 methylation at the promoter region, which is critical for LSD1-driven stemness in TNBC.

Conclusion: These findings present an epi-transcriptional mechanism that maintains Hippo-independent YAP1 signaling and plays a role in preserving the undifferentiated state of TNBC, which indicates the potential for targeting the LSD1-METTL14 axis to address TNBC stemness.