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. N⁶-methyladenosine (m⁶A) plays a crucial role in shaping cellular behavior by modulating transcript expression. However, the role of m⁶A 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 m⁶A regulators. To unravel the role of m⁶A 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 m⁶A modification in MSL TNBC is downregulated primarily due to the loss of methyltransferase-like 14 (METTL14). The diminished m⁶A 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.