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Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations

Fernandez, E. C.; Tomassoni, L.; Zhang, X.; Wang, J.; Obradovic, A.; Laise, P.; Griffin, A. T.; Vlahos, L.; Minns, H. E.; Morales, D. V.; Simmons, C.; Gallitto, M.; Wei, H.-J.; Martins, T. J.; Becker, P. S.; Crawford, J. R.; Tzaridis, T.; Wechsler-Reya, R. J.; Garvin, J.; Gartrell, R. D.; Szalontay, L.; Zacharoulis, S.; Wu, C.-C.; Zhang, Z.; Califano, A.; Pavisic, J.

2024-03-17 systems biology
10.1101/2024.03.17.585370 bioRxiv
Show abstract

Diffuse Midline Gliomas (DMGs) are universally fatal, primarily pediatric malignancies affecting the midline structures of the central nervous system. Despite decades of clinical trials, treatment remains limited to palliative radiation therapy. A major challenge is the coexistence of molecularly distinct malignant cell states with potentially orthogonal drug sensitivities. To address this challenge, we leveraged established network-based methodologies to elucidate Master Regulator (MR) proteins representing mechanistic, non-oncogene dependencies of seven coexisting subpopulations identified by single-cell analysis--whose enrichment in essential genes was validated by pooled CRISPR/Cas9 screens. Perturbational profiles of 372 clinically relevant drugs helped identify those able to invert the activity of subpopulation-specific MRs for follow-up in vivo validation. While individual drugs predicted to target individual subpopulations--including avapritinib, larotrectinib, and ruxolitinib--produced only modest tumor growth reduction in orthotopic models, systemic co-administration induced significant survival extension, making this approach a valuable contribution to the rational design of combination therapy.

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