An Integrated Transcriptional and Post-Transcriptional Regulatory Circuit Orchestrated by NUDT21 Maintains the Proliferation and Survival of Neuroblastoma

Abstract Background Neuroblastoma (NB) is the most prevalent pediatric solid tumor, associated with a poor prognosis. While alternative polyadenylation (APA) is a key post-transcriptional regulatory mechanism in many cancers, its role in NB remains largely unexplored. Methods We used public expression profiles from NB and normal samples, along with single-cell transcriptomic data from our MYCN-transgenic mouse models, to screen NB-upregulated APA related genes. Knockdown method was used to examine the function of NUDT21 in NB cells and in nude mice. RNA-seq and PAS-seq were performed to identify differentially expressed genes with APA events. CUT&Tag was used to analyze transcriptional activation of downstream genes. Results NUDT21 was found substantially upregulated in NB, driven by NB master transcription factors (TFs) like MYCN. NUDT21 knockdown inhibited NB cell proliferation, induced cycle arrest and apoptosis in vitro, and suppressed xenograft growth in nude mice. Mechanistically, NUDT21 silencing triggered global APA remodeling, with approximately 85% of APA genes shifting to proximal poly(A) sites. Integrative PAS-seq and RNA-seq analyses revealed that NUDT21 regulated E2F target genes (e.g., MKI67) via APA, promoting longer 3′ UTR isoforms to enhance mRNA stability and translation. CUT&Tag analysis further indicated direct transcriptional regulation on E2F target genes by NUDT21 through promoter binding. This convergence of APA-mediated post-transcriptional regulation and transcriptional activation on the E2F network established a sophisticated oncogenic paradigm. Conclusions Our study identified NUDT21 as a critical driver of NB progression through both transcriptional and post-transcriptional mechanisms, laying the foundation for NUDT21-targeted NB therapies.