Splicing factor TRA2A contributes to esophageal cancer progression via a noncanonical role in lncRNA m⁶A methylation

Abstract

Transformer 2 alpha homolog (TRA2A), a member of the serine/arginine-rich splicing factor family, has been shown to control mRNA splicing in development and cancers. However, it remains unclear whether TRA2A is involved in lncRNA regulation. In the present study, we found that TRA2A was upregulated and correlated with poor prognosis in esophageal cancer. Downregulation of TRA2A suppressed the tumor growth in xenograft nude mice. Epitranscriptomic microarray showed that depletion of TRA2A affected global lncRNA methylation similarly to the key m 6 A methyltransferase, METTL3, by silencing. MeRIP-qPCR, RNA pull-down, CLIP analyses, and stability assays indicated that ablation of TRA2A reduced m 6 A-modification of the oncogenic lncRNA MALAT1, thus inducing structural alterations and reduced stability. Furthermore, Co-IP experiments showed TRA2A directly interacted with METTL3 and RBMX, which also affected the writer KIAA1429 expression. Knockdown of TRA2A inhibited cell proliferation in a manner restored by RBMX/KIAA1429 overexpression. Clinically, MALAT1, RBMX, and KIAA1429 were prognostic factors of worse survival in ESCA patients. Structural similarity-based virtual screening in FDA-approved drugs repurposed nebivolol, a β 1 -adrenergic receptor antagonist, as a potent compound to suppress the proliferation of esophageal cancer cells. Cellular thermal shift and RIP assay indicated that nebivolol may compete with MALAT1 to bind TRA2A. In conclusion, our study revealed the noncanonical function of TRA2A, which coordinates with multiple methylation proteins to promote oncogenic MALAT1 during ESCA carcinogenesis.

SR proteins in cancer: function, regulation, and small inhibitor

“…have reported that m 6 A sites are enriched in exonic regions flanking 5′- and 3′-splice sites, that overlap with the ESE binding regions, suggesting that m 6 A signals may be related to the activity of SR proteins [ 101 ]. Further supporting this point, we and others recently found that several SR proteins, including TRA2A, SRSF3, and SRSF7, can interact with METTL3 and other proteins in RNA methylation, and the m 6 A signal in pre-mRNA is essential for SR proteins to participate in RNA processing [ 94 , 96 , 98 , 102 ].…”

“…Recently, we have demonstrated that TRA2A induces esophageal cancer progression via MALAT1 [ 97 ]. Mechanistically, TRA2A directly interacts with core methyltransferase METTL3 and the m 6 A reader RBMX to regulate the methylation and stability of MALAT1 [ 98 ].…”

“…Inspired by this preliminary study, we utilized indacaterol as a structural template to select nebivolol, a β1-adrenergic receptor antagonist, as an RRM domain antagonist of TRA2A. Follow-up experiments confirmed that nebivolol can compete with RNA targets of TRA2A to interfere with its downstream signaling in esophageal cancer cells [ 98 ]. Similarly, potent compounds have also been repurposed for SRSF3 inhibition [ 109 ].…”