VRK3 depletion induces cell cycle arrest and metabolic reprogramming of pontine diffuse midline glioma - H3K27 altered cells

Virginie Menez; Thomas Kergrohen; Tal Shasha; Claudia Silva-Evangelista; Ludivine Le Dret; Lucie Auffret; Chloé Subecz; Manon Lancien; Yassine Ajlil; Irma Segoviano Vilchis; Kévin Beccaria; Thomas Blauwblomme; Estelle Oberlin; Jacques Grill; David Castel; Marie-Anne Debily

doi:10.3389/fonc.2023.1229312

VRK3 depletion induces cell cycle arrest and metabolic reprogramming of pontine diffuse midline glioma - H3K27 altered cells

Front Oncol. 2023 Oct 10:13:1229312. doi: 10.3389/fonc.2023.1229312. eCollection 2023.

Authors

Virginie Menez¹, Thomas Kergrohen¹, Tal Shasha¹, Claudia Silva-Evangelista¹, Ludivine Le Dret¹, Lucie Auffret¹, Chloé Subecz¹, Manon Lancien¹, Yassine Ajlil¹, Irma Segoviano Vilchis¹, Kévin Beccaria^{1

2}, Thomas Blauwblomme², Estelle Oberlin³, Jacques Grill^{1

4}, David Castel¹, Marie-Anne Debily^{1

5}

Affiliations

¹ U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, INSERM, Gustave Roussy, Université Paris-Saclay, Villejuif, France.
² Department of Pediatric Neurosurgery, Necker Enfants Malades, Paris, France.
³ Inserm UMRS-MD 1197, Université Paris-Saclay, Villejuif, France.
⁴ Département de Cancérologie de l'Enfant et de l'Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France.
⁵ Univ Evry, Université Paris-Saclay, Evry, France.

Abstract

We previously identified VRK3 as a specific vulnerability in DMG-H3K27M cells in a synthetic lethality screen targeting the whole kinome. The aim of the present study was to elucidate the mechanisms by which VRK3 depletion impact DMG-H3K27M cell fitness. Gene expression studies after VRK3 knockdown emphasized the inhibition of genes involved in G1/S transition of the cell cycle resulting in growth arrest in G1. Additionally, a massive modulation of genes involved in chromosome segregation was observed, concomitantly with a reduction in the level of phosphorylation of serine 10 and serine 28 of histone H3 supporting the regulation of chromatin condensation during cell division. This last effect could be partly due to a concomitant decrease of the chromatin kinase VRK1 in DMG following VRK3 knockdown. Furthermore, a metabolic switch specific to VRK3 function was observed towards increased oxidative phosphorylation without change in mitochondria content, that we hypothesized would represent a cell rescue mechanism. This study further explored the vulnerability of DMG-H3K27M cells to VRK3 depletion suggesting potential therapeutic combinations, e.g. with the mitochondrial ClpP protease activator ONC201.

Keywords: VRK3; cell cycle arrest; diffuse midline glioma H3 K27-altered; oxidative phosphorylation (OXPHOS); pediatric glioma.

Grants and funding

DC, JG, and M-AD acknowledge financial support from charities Lisa For Ever, l’Etoile de Martin and La marche de l’Ecureuil. We acknowledge the use of the bioresources of the PRB Tumorothèque Necker and Necker Imagine DNA biobank (BB-033-00065). The authors are grateful to the Necker hospital tumor and DNA banks and the Necker operating room nurses/assistants for their technical assistance. TK was supported by the charity “Imagine for Margo” and by the Fondation Gustave Roussy “Guérir Les Cancers des Enfants au XXIe siècle (GLCE)”. This project was supported by grant “ Taxe d’apprentissage Gustave Roussy – 2018 - CE”.