VRK1 as a synthetic lethal target in VRK2 promoter–methylated cancers of the nervous system
Jonathan So, … , Mariella G. Filbin, William C. Hahn
Jonathan So, … , Mariella G. Filbin, William C. Hahn
Published August 30, 2022
Citation Information: JCI Insight. 2022;7(19):e158755. https://doi.org/10.1172/jci.insight.158755.
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Research Article Oncology

VRK1 as a synthetic lethal target in VRK2 promoter–methylated cancers of the nervous system

Abstract

Collateral lethality occurs when loss of a gene/protein renders cancer cells dependent on its remaining paralog. Combining genome-scale CRISPR/Cas9 loss-of-function screens with RNA sequencing in over 900 cancer cell lines, we found that cancers of nervous system lineage, including adult and pediatric gliomas and neuroblastomas, required the nuclear kinase vaccinia-related kinase 1 (VRK1) for their survival in vivo. VRK1 dependency was inversely correlated with expression of its paralog VRK2. VRK2 knockout sensitized cells to VRK1 loss, and conversely, VRK2 overexpression increased cell fitness in the setting of VRK1 loss. DNA methylation of the VRK2 promoter was associated with low VRK2 expression in human neuroblastomas and adult and pediatric gliomas. Mechanistically, depletion of VRK1 reduced barrier-to-autointegration factor phosphorylation during mitosis, resulting in DNA damage and apoptosis. Together, these studies identify VRK1 as a synthetic lethal target in VRK2 promoter–methylated adult and pediatric gliomas and neuroblastomas.

Authors

Jonathan So, Nathaniel W. Mabe, Bernhard Englinger, Kin-Hoe Chow, Sydney M. Moyer, Smitha Yerrum, Maria C. Trissal, Joana G. Marques, Jason J. Kwon, Brian Shim, Sangita Pal, Eshini Panditharatna, Thomas Quinn, Daniel A. Schaefer, Daeun Jeong, David L. Mayhew, Justin Hwang, Rameen Beroukhim, Keith L. Ligon, Kimberly Stegmaier, Mariella G. Filbin, William C. Hahn

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Figure 2

VRK1 dependency is correlated with VRK2 expression.

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VRK1 dependency is correlated with VRK2 expression. (A) Whole-genome Pe...
(A) Whole-genome Pearson correlations between gene expression from CCLE (21Q3) and VRK1 dependency in the DepMap database (21Q3) and adjusted P values. (B) Scatterplot showing VRK1 dependency versus VRK2 expression. Extent of VRK2 promoter methylation is indicated by dot size. Red dots represent cell lines of CNS lineage, and blue dots represent PNS lineage. (C) VRK2 promoter methylation status stratified by clinical characteristics across the TCGA GBM-LGG cohort. LGG, low grade glioma; GBM, glioblastoma multiforme. Violin plots with mean (solid line) and first and third quartiles (dashed line). (D) VRK2 promoter methylation in pediatric high-grade gliomas and DMGs with wild-type histone H3 and mutant histone H3 (K27M or G34R). Data from Mackay et al., 2017 (39). Violin plots with mean (solid line) and first and third quartiles (dashed line). (E) Cell viability following 14 days’ KO of VRK1 in VRK2lo LNZ308 and LN443 cell lines and VRK2hi GAMG and SF172 cell lines. (F) Cell viability analysis 14 days following VRK1 KO in VRK2hi GBM cell line (SF172), expressing control CRISPR sgRNA or sgRNA targeting VRK2. (n = 3; mean ± SD.) (G) Immunoblot showing the overexpression of exogenous VRK2WT, VRK1WT, and kinase-inactive VRK1K179E in NB-1 NB cells with or without VRK1 KO. RFP, red fluorescent protein. (H) Cell viability analysis for NB-1 cells in G following 14 days of VRK1 KO in cells overexpressing VRK2WT, VRK1WT, and kinase-inactive VRK1K179E. (n = 3; mean ± SD.) (I) Effect of VRK2WT or VRK2K168E overexpression on LN443 GBM cell viability following 14 days VRK1 KO. (n = 3; mean ± SD.) *P < 0.05, **P < 0.001, ***P < 0.0001; significance was determined by 2-tailed Student’s t test (E) and 1-way ANOVA with Tukey’s test (C, D, F, H, and I).