RNA therapeutics for the Treatment of Brain Cancer

Abstract

Individuals diagnosed with glioblastoma multiforme (GBM) have a short life expectancy of 12–15 months. Current strategies are often limited by the blood-brain barrier. This project is to develop therapies to bypass challenges to effective and continuous drug delivery to the brain, targeting cancer-driving genes. Tumor blood vessel formation depends on vascular endothelial growth factor receptor 2 (VEGFR2), while tumor cell proliferation is stimulated by epidermal growth factor receptor (EGFR). Both are important for tumor cell survival. In our lab, we are developing an innovative therapy that can bypass the blood brain barrier by developing RNA therapies to alter the splicing mechanism of the VEGFR2 and EGFR genes to reduce or block their activation, thus stop tumor cell angiogenesis and growth. Our approach uses an adeno-associated virus gene transfer vector encoding RNA therapeutics targeting critical elements of the EGFR and VEGFR2 pre-mRNA transcript. The ‘pre-mRNA structurome’ can be used to uncover and determine the accessibility of targetable regions. Our approach has the potential to deliver one single dose of gene therapy directly to the GBM tumor environment and block the production of EGFR and VEGFR2 and activate the expression of a stable therapeutic isoform of the two genes. To advance our therapeutic strategy, we have analyzed the secondary structure of the two genes using selective 2’ hydroxyl acylation and primer extension followed by mutational profiling (SHAPE-MaP). SHAPE-MaP reactivity profiles were generated revealing the structure of splicing and cryptic polyadenylation signal (PAS) elements within the targeted region. We identified enhancer binding motifs surrounding the 5’ splice site and hidden elements of the cryptic PAS. Based on these structural profiles, we generated RNA therapies to unravel the hidden PAS to activate expression of the short therapeutic isoform.