ATRX is a multifunctional protein that is tightly regulated by and implicated in transcriptional regulation and chromatin remodeling. Numerous studies have shown that genetic alterations in ATRX play a significant role in gliomas. This study aims to further determine the relationship between ATRX and glioma prognosis and identify possible mechanisms for exploring the biological significance of ATRX using large data sets.

We used The Cancer Genome Atlas (TCGA) database and 130 immunohistochemical results to confirm the difference in ATRX mutations in high- and low-grade gliomas. An online analysis of the TCGA glioma datasets using the cBioPortal platform was performed to study the relationship between ATRX mutations and IDH1, TP53, CDKN2A and CDKN2B mutations in the corresponding TCGA glioma dataset. In combination with clinical pathology data, the biological significance of the relationships were analyzed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses and annotations of all adjacent genes in the network were performedin the Database for Annotation, Visualization and Integrated Discovery (DAVID) and R language. A protein-protein interaction (PPI) network was constructed, and the interactions of all adjacent nodes were analyzed by the String database and using Cytoscape software.

In the selected TCGA glioma datasets, a total of 2,228 patients were queried, 21% of whom had ATRX alterations, which co-occurred frequently with TP53 and IDH1 mutations. ATRX alterations are associated with multiple critical molecular events, which results in a significantly improved overall survival (OS) rate. In low-grade gliomas, ATRX mutations are significantly associated with multiple important molecular events, such as ZNF274 and FDXR at mRNA and protein levels. A functional cluster analysis revealed that these genes played a role in chromatin binding and P53, and a link was observed between ATRX and IDH1 and TP53 in the interaction network. ATRX and TP53 are important nodes in the network and have potential links with the blood oxygen imbalance.

ATRX mutations have clinical implications for the molecular diagnosis of gliomas and can provide diagnostic and prognostic information for gliomas. ATRX is expected to serve as a new therapeutic target.

Mesenchymal subtype of glioblastoma (mesGBM) is a refractory disease condition characterized by therapeutic failure and tumor recurrence. Hyperactive transforming growth factor-β (TGF-β) signaling could be a signature event in mesGBM, which leads to dysregulation of downstream targets and contribute to malignant transformation. In this study we aimed to investigate the hyperactive TGFβ signaling-mediated pathogenesis and possible downstream targets for the development of novel therapeutic interventions for mesGBM.

GBM-BioDP is an online resource for accessing and displaying interactive views of the TCGA GBM data set. Transcriptomic sequencing followed by bioinformatic analysis was performed to identify dysregulated microRNAs. Target prediction by MR-microT and dual luciferase reporter assay were utilized to confirm the predicted target of novel_miR56. CCK-8 assays was used to assesse cell viability. The miRNA manipulation was proceeded by cell transfection and lentivirus delivery. A plasmid expressing GFP-LC3 was introduced to visualize the formation of autophagosomes. Orthotopic GBM model was constructed for in vivo study.

TGFβ1 and TGFβ receptor type Ⅱ (TβRII) were exclusively upregulated in mesGBM (P < 0.01). Dysregulated miRNAs were identified after LY2109761 (a TβRI/Ⅱ inhibitor) treatment in a mesGBM-derived cell line, and novel_miR56 was selected as a promising candidate for further functional verification. Novel_miR56 was found to potentially bind to PRAS40 via seed region complementarity in the 3′ untranslated region, and we also confirmed that PRAS40 is a direct target of novel_miR56 in glioma cells. In vitro, over expression of novel_miR56 in tumor cells significantly promoted proliferation and inhibited autophagy (P < 0.05). The expression levels of P62/SQSTM was significantly increased accompanied by the decrease of BECN1 and LC3B-Ⅱ/Ⅰ, which indicated that autophagic activity was reduced after novel_miR56 treatment. In addition, over expression of novel_miR56 also promoted tumor growth and inhibited autophagy in vivo, which is associated with worse prognosis (P < 0.05).

In summary, we provide novel insight into TGFβ signaling-mediated pathogenesis in mesGBM and TGFβ signaling-induced novel_miR56 may be a novel target for mesGBM management.