Investigating the mechanism of action of the chemical probe QC6352

Abstract

Glioblastoma, despite being the most aggressive form of brain cancer, has seen no significant advancement in patient survival rates since the introduction of the Stupp protocol in 2005. The stagnation in therapeutic progress highlights the complex challenges inherent to glioblastoma treatment, namely, a highly heterogeneous tumour population, an immunosuppressive microenvironment, and the restrictive blood-brain barrier. These challenges are compounded by a critical lack of robust data in preclinical studies, leading to suboptimal drug candidates that ultimately fail in clinical trials.

In a comprehensive systematic review, we assessed the adherence to expert-recommended practices in the use of chemical probes. Our findings revealed that only 4% of the analysed publications complied with the established guidelines. Improper use of chemical probes results in biased conclusions about the importance of certain proteins in disease models, embedding inaccurate information as the foundation for further drug development studies.

The chemical probe QC6352, a known KDM4 inhibitor, was identified through phenotypic screening of a library of epigenetic inhibitors to have potent antiproliferative efficacy in glioblastoma cells. While validating the anti-proliferative efficacy of QC6352 in glioblastoma, discrepancies arose regarding the importance of KDM4 in QC6352’s mechanism of action. By integrating diverse state-of-the-art investigations at the genomic, transcriptomic, and proteomic levels, a phenotype reflecting an activated MAPK pathway was identified and considered to result from the inhibition of PP5 by QC6352.

This PhD thesis highlights the critical need to follow best practice guidelines for preclinical mechanistic studies to establish robust findings and eliminate biased and potentially incorrect conclusions. To obtain improved glioblastoma therapies, the foundational research surrounding the novel target must be derived from robust and well-controlled experiments.