RNA-seq differential expression analysis of GBM-derived extracellular vesicle cargos in patient-derived xenograft models
Glioblastoma (GBM) is the most aggressive tumor and lethal disease of the central nervous system. Gliomas have a poor prognosis, as delayed diagnosis is common and standard treatment approaches are unable to cope with the tumor’s heterogeneity, mutagenesis and invasiveness. Previous studies have identified extracellular vesicles (EVs) as an integral part of tumor growth and resistance, and EVs are a possible reporter of gliomas’ pharmacodynamics. The purpose of this study is to explore the possibility of using a patient’s blood sample to see if a drug has reached the tumor. This would be transformative as a minimally invasive and more feasible alternative, compared to the existing option of a tumor biopsy. RNA-seq data was analyzed across various conditions, including several cell lines with varying drug sensitivities, drug treatments, drug concentrations, and time periods post-treatment. Sequence data revealed condition-dependent alterations in the RNA cargos of glioma-derived EVs. Based on these changes, together with gene ontology and differential gene analysis, we were able to consistently determine when a given drug had bypassed the blood-brain barrier to reach the target tumor. We also found that differentially expressed genes were commonly upregulated or downregulated when a given test condition was held constant. Most differentially expressed genes observed to be commonly upregulated were found to be long non-coding RNA with possible regulatory functions over oncogenes. A negative correlation was found between the TMZ concentration and the expression level of Y RNA, a DNA replication initiator in tumors. Under decreased TMZ concentrations, differentially expressed genes were overrepresented in biological processes such as cytoplasmic translation and cellular macromolecule biosynthesis. Across both different TMZ and MLN concentrations, differentially expressed genes were overrepresented in other molecular mechanisms, such as G protein-coupled receptors: a possible therapeutic target for GBM. These discoveries support the potential utility of plasma EVs in diagnostic roles, providing both pharmacodynamic information and indications of tumor response to drug treatment.