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 1

VRK1 is a dependency in glioblastoma, NB, and DMG.

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VRK1 is a dependency in glioblastoma, NB, and DMG. (A) Histogram plots s...
(A) Histogram plots showing VRK1 CERES-corrected dependency scores in over 900 cell lines, representing 25 cancer lineages from the DepMap data set (21Q3). Compared with all other lineages, cell lines in the CNS (P = 2 × 10–12) and PNS (P = 3 × 10–18) lineages were significantly more dependent on VRK1. (B) Differential dependency of gene KO in CNS and PNS cell lines versus all other lineages. Gene effect size is calculated as the difference in average CERES score between lineage groupings, and q value is determined by limma eBayes methodology. The top enriched dependencies in CNS/PNS lineages are annotated. (C) VRK1 protein expression following expression of 4 different sgRNAs in the NB-1 neuroblastoma cell line. The top 3 guides with greatest VRK1 loss were carried forward in subsequent experiments. (D) Population doubling assay following VRK1 KO with 3 separate guides in NB-1 cells. sgCtrl represents a nontargeting control guide (n = 3; mean ± SD). (E) sgVRK1 KO after 14 days in cell lines representing NB (n = 3), GBM (n = 2), and DMG (n = 2) models. (n ≥ 3; mean ± SD plotted.) (F) Time course of CASP3/7 activity, as measured by cleavage of a peptide reporter, following VRK1 KO in LN443 cells (n = 3; mean ± SD). Total reporter fluorescence signal is normalized by cell confluence. Significance at each time point was determined by 2-way ANOVA (treatment × time). *P < 0.05. (G) Quantification of annexin V–positive cells following VRK1 KO with 2 separate guides in 3 cell lines representing NB and DMG lineages after 7 days. (n = 3; mean ± SD; from 2 separate experiments.) *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 (D and G).