m6A-modificated Linc00707 promotes the progression of TNBC via U2AF2-mediated alternative splicing of ATG4B.

BACKGROUND: Triple-negative breast cancer (TNBC) represents a clinically aggressive breast cancer subtype with limited therapeutic options. Emerging evidence suggests that long intergenic noncoding RNA 00707 (Linc00707) plays a role in TNBC; however, the upstream regulators governing Linc00707 expression and the mechanisms by which it contributes to tumor progression remain largely undefined.

METHOD: The FOXP3-mediated transcriptional regulation of Linc00707 was analyzed using chromatin immunoprecipitation and luciferase reporter assays. The post-transcriptional regulation of Linc00707 was examined by RNA immunoprecipitation (RIP), methylated RIP, and RNA pull-down assays to assess WTAP-dependent m6A modification, IGF2BP2-mediated stabilization, and U2AF2 interaction. RNA sequencing and biochemical analyses were used to identify downstream regulatory pathways. The binding of oligo-anti-Linc00707 to Linc00707 and its ability to disrupt U2AF2 association were confirmed by RIP and RNA fluorescence in situ hybridization (RNA-FISH). Cellular assays and nude mouse xenograft models were employed to evaluate functional and therapeutic effects.

RESULTS: FOXP3 was found to transcriptionally activate Linc00707 through direct promoter binding. The WTAP-mediated m6A modification enhanced the IGF2BP2-dependent stabilization of Linc00707. In the nucleus, Linc00707 interacted with the splicing factor U2AF2, with nucleotides 1-593 identified as a critical interaction region. Building on this observation, we further showed that the Linc00707-U2AF2 interaction functionally controls U2AF2 expression and stability via FOXP3. The Linc00707-U2AF2 complex was associated with altered alternative splicing of the autophagy-related gene ATG4B, contributing to enhanced TNBC cell proliferation, invasion, and autophagy suppression. Importantly, oligonucleotides complementary to the U2AF2-binding region of Linc00707 (oligo-anti-Linc00707) disrupted this interaction, attenuated Linc00707-driven oncogenic phenotypes, and restored autophagic activity. In vivo, oligo-anti-Linc00707 treatment significantly reduced tumor growth, supporting its therapeutic potential in TNBC.

CONCLUSIONS: FOXP3 activates Linc00707 transcription in TNBC. WTAP-mediated m6A modification enhances Linc00707 stability via IGF2BP2. Linc00707 recruits U2AF2 to drive oncogenic ATG4B splicing, promoting tumor progression. Oligo-anti-Linc00707 specifically blocks Linc00707-U2AF2 complex formation, reversing its tumor-promoting and autophagy-suppressing functions. Thus, targeting Linc00707 represents a promising therapeutic strategy for TNBC.