In-depth Inference of Transcriptional Regulatory Networks Identifies NPM1 as a Druggable Master Regulator in Medulloblastoma

Abstract Medulloblastoma (MB) is a highly malignant embryonic brain tumor with distinct cytogenetic heterogeneity in children. Despite elucidating divergent regulatory underpinnings in MB molecular subtypes, the hidden oncogenic signaling drivers with minimal differential expression remain obscure. Here, we leveraged two bulk RNA-seq datasets involving 1055 patients to construct pediatric MB specific co-expression profiles and regulatory networks, unveiling unique attributes of the ribosome pathway in different molecular subtypes. NPM1, a pivotal ribosome regulator, was pinpointed as a promising targetable driver for MB by integrating differentially expressed candidates and reported drug targets. To assess the role of NPM1 in MB progression, we employed NETBID2 gene activity algorithm, Kaplan–Meier survival curves, single-cell RNA-seq (scRNA-seq) analysis, and functional validations in MB cell lines. Our findings highlighted substantial correlations between the activity values of NPM1 and the prognosis of MB patients, eclipsing the significance of its expression levels. Furthermore, NPM1 was extensively and highly expressed in early SOX2 positive neural stem cells and tumor cells. Deficiency of NPM1 impeded MB cell growth, triggered apoptosis and led to a reduction of c-Myc levels. Our findings provide new approaches for exploring underlying pathways and underscore the clinical transformation value of NPM1 as a master regulator for MB.