The MALAT1-EZH2 axis regulates PRC2 activity and promotes the mesenchymal phenotype in pediatric atypical teratoid/rhabdoid tumors

Atypical teratoid/rhabdoid tumors (AT/RT) are aggressive pediatric CNS malignancies characterized by SMARCB1 loss, which leads to the dysregulated expression of Enhancer of Zeste Homolog 2 (EZH2), a key catalytic component of the Polycomb Repressive Complex 2 (PRC2). This dysregulation results in aberrant trimethylation of histone H3 at lysine 27 (H3K27me3), driving tumor progression. While EZH2 inhibitors like tazemetostat are in clinical use, their efficacy remains limited, necessitating a deeper understanding of PRC2 regulation. We investigated the role of long non-coding RNAs (lncRNAs) in modulating the EZH2-PRC2 axis in AT/RT. Expression levels of lncRNAs (MALAT1, ANRIL, KCNQ1OT1) were analyzed via RT-PCR in 10 archival AT/RT patient tissues. RNA immunoprecipitation (RIP) was performed to identify direct interactions with EZH2. The functional impact of MALAT1 inhibition on H3K27me3 levels, mesenchymal markers (CDH2, TWIST, ZEB1), and tumorigenic behaviors (migration, invasion, sphere formation) was evaluated in vitro. MALAT1, ANRIL, and KCNQ1OT1 were significantly overexpressed in AT/RT tissues (p < 0.05). RIP assays revealed that only MALAT1 directly interacts with EZH2 in DAOY and primary AT/RT cells. MALAT1 knockdown significantly reduced H3K27me3 levels (p < 0.05) and markedly impaired cell migration, invasion, and sphere-forming capacity. These phenotypic changes were associated with the downregulation of key mesenchymal markers (CDH2, TWIST, ZEB1). Our findings identify MALAT1 as a critical epigenetic regulator in AT/RT that interacts with EZH2 to maintain the PRC2-mediated repressive landscape. Targeting the MALAT1-EZH2 axis provides a novel translational perspective to enhance the efficacy of epigenetic therapies in AT/RT. MALAT1 is significantly upregulated in AT/RT and correlates with aggressive clinicopathological features. MALAT1 physically interacts with EZH2, sustaining the H3K27me3 repressive landscape in patient-derived cells. Inhibition of the MALAT1-EZH2 axis reverses the mesenchymal phenotype and impairs tumor sphere growth. EZH2 inhibition triggers a compensatory increase in MALAT1, suggesting a novel feedback loop and resistance mechanism. Dual targeting of MALAT1 and EZH2 represents a promising therapeutic strategy for pediatric rhabdoid tumors.