Reversal of Cancer Gene Expression Identifies Repurposed Drugs for Diffuse Intrinsic Pontine Glioma

Diffuse Intrinsic Pontine Glioma (DIPG) is an aggressive incurable pediatric brainstem cancer. Due to its inoperable tumor location and resistance to conventional chemotherapy agents such as temozolomide, radiotherapy is the current standard treatment. This study aimed to identify potential therapeutic agents for DIPG treatment using a computational drug screening pipeline. We hypothesized that drugs that can reverse a disease gene signature can be potential drug candidates for that disease. Because of lack of normal brain samples as control for creating disease signature, we implemented a deep learning autoencoder to select reference control samples. Using a systematic computational approach with publicly available gene expression databases for DIPG signature and gene expression data of pre and post drug treated cancer cell lines, we identified drug hits with potential to reverse a DIPG gene signature to one that matches normal tissue background. We then tested the identified drugs at their IC50 concentration for 24 hours on patient-derived DIPG4 cell lines. Overall Design: mRNA profiles of DIPG4 cell lines treated with Triptolide (TPL), Triamterene(TRIAM), Mycophenolate mofetil (MMF) and DMSO as control Overall design: We setup three sets of experiments with DMSO, TPL, TRIAM and MMF treated DIPG4 cells. RNA was extracted using the RNeasy plus mini kit (Qiagen). Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit; prepared libraries were quality controlled and quantified using a Qubit and Labchip Bioanalyzer. Libraries were pooled and run on a Illumina NovaSeq 6000 instrument. Sequencing was performed by 2 × 150 bp paired-end read format.