Integrated transcriptomics uncovers an enhanced association between the prion protein gene expression and vesicle dynamics signatures in glioblastomas

Abstract

Background: Glioblastoma (GBM) is an aggressive brain tumor that exhibits resistance to current treatment, making the identification of novel therapeutic targets essential. In this context, cellular prion protein (PrP^C) stands out as a potential candidate for new therapies. Encoded by the PRNP gene, PrP^C can present increased expression levels in GBM, impacting cell proliferation, growth, migration, invasion and stemness. Nevertheless, the exact molecular mechanisms through which PRNP/PrP^C modulates key aspects of GBM biology remain elusive.

Methods: To elucidate the implications of PRNP/PrP^C in the biology of this cancer, we analyzed publicly available RNA sequencing (RNA-seq) data of patient-derived GBMs from four independent studies. First, we ranked samples profiled by bulk RNA-seq as PRNP^high and PRNP^low and compared their transcriptomic landscape. Then, we analyzed PRNP⁺ and PRNP^- GBM cells profiled by single-cell RNA-seq to further understand the molecular context within which PRNP/PrP^C might function in this tumor. We explored an additional proteomics dataset, applying similar comparative approaches, to corroborate our findings.

Results: Functional profiling revealed that vesicular dynamics signatures are strongly correlated with PRNP/PrP^C levels in GBM. We found a panel of 73 genes, enriched in vesicle-related pathways, whose expression levels are increased in PRNP^high/PRNP⁺ cells across all RNA-seq datasets. Vesicle-associated genes, ANXA1, RAB31, DSTN and SYPL1, were found to be upregulated in vitro in an in-house collection of patient-derived GBM. Moreover, proteome analysis of patient-derived samples reinforces the findings of enhanced vesicle biogenesis, processing and trafficking in PRNP^high/PRNP⁺ GBM cells.

Conclusions: Together, our findings shed light on a novel role for PrP^C as a potential modulator of vesicle biology in GBM, which is pivotal for intercellular communication and cancer maintenance. We also introduce GBMdiscovery, a novel user-friendly tool that allows the investigation of specific genes in GBM biology.

Keywords: Glioblastoma; Intracellular trafficking; Prion protein; Transcriptomics; Vesicle dynamics.