Transcriptomic Analysis Identifies the PVT1-miR-34a Axis as a Novel Non-Coding RNA Therapeutic Target in Diffuse Intrinsic Pontine Glioma

Abstract

Objective: Diffuse intrinsic pontine glioma (DIPG) is a lethal paediatric brainstem tumour with a median survival under one year and no effective therapy. Although non-coding RNAs (ncRNAs) regulate tumour progression, their regulatory networks in DIPG remain poorly characterised. This study aimed to identify dysregulated lncRNA– miRNA–mRNA axes in DIPG through integrated transcriptomic analysis, computationally validate these networks, and investigate their downstream impact on cancer-related pathways to reveal novel therapeutic targets for RNAbased precision medicine.

Methods: This study was conducted at the Precision Medicine Lab, National Centre in Big Data and Cloud Computing (NCBC), Peshawar, from 1st July to 22nd August 2025. RNA-seq datasets comprising 25 DIPG and 45 normal brain samples were obtained from GEO. Following normalization and differential expression analysis (padj < 0.05, |log2FC| > 2), dysregulated lncRNAs, miRNAs, and mRNAs were integrated into a ceRNA network using LncBase and miRTarBase. KEGG pathway enrichment, STRING protein–protein interaction analysis, Cytoscape network visualization, and Spearman correlation analysis were performed to identify and validate functionally relevant regulatory interactions.

Results: PCA demonstrated clear separation between DIPG and control transcriptomes. PVT1 was significantly upregulated (log2FC = 3.44), whereas miR-34a was downregulated (log2FC = -3.66). Eleven oncogenic mRNAs, including NOTCH1, PDGFRA, CDK4, SOX2, and MYC, were identified as predicted targets and formed a highly connected STRING interaction network. KEGG enrichment highlighted "MicroRNAs in cancer," while correlation analysis supported an inverse PVT1-miR-34a relationship and positive associations with these oncogenes, consistent with a ceRNA regulatory mechanism.

Conclusion: The PVT1-miR-34a axis appears to promote oncogenic pathways in DIPG. Targetting PVT1 or restoring miR-34a may represent potential RNA-based therapeutic strategies, warranting further experimental validation through reporter and knockdown assays.