Published OnlineFirst April 29, 2020; DOI: 10.1158/2159-8290.CD-19-0789 RESEARCH ARTICLE EZH2 -Defi cient T-cell Acute Lymphoblastic Leukemia Is Sensitized to CHK1 Inhibition through Enhanced Replication Stress Theresa E. León 1 , Tanya Rapoz-D’Silva 1 , Cosetta Bertoli 2 , Sunniyat Rahman 1 , Michael Magnussen 1 , Brian Philip1 , Nadine Farah 1 , Simon E. Richardson 1 , Sara Ahrabi 1 , José Afonso Guerra-Assunção 3 , Rajeev Gupta4 , Elisabeth P. Nacheva 5 , Stephen Henderson 3 , Javier Herrero 3 , David C. Linch 1 , Robertus A.M. de Bruin2 , and Marc R. Mansour 1 Downloaded from cancerdiscovery.aacrjournals.org on September 30, 2021. © 2020 American Association for Cancer Research. Published OnlineFirst April 29, 2020; DOI: 10.1158/2159-8290.CD-19-0789 ABSTRACT Loss-of-function mutations of EZH2 , the enzymatic component of PRC2, have been associated with poor outcome and chemotherapy resistance in T-cell acute lymphoblastic leukemia (T-ALL). Using isogenic T-ALL cells, with and without CRISPR/Cas9–induced EZH2-inactivating mutations, we performed a cell-based synthetic lethal drug screen. EZH2-defi cient cells exhibited increased sensitivity to structurally diverse inhibitors of CHK1, an interaction that could be validated genetically. Furthermore, small-molecule inhibition of CHK1 had effi cacy in delaying tumor progression in isogenic EZH2-defi cient, but not EZH2 wild-type, T-ALL cellsin vivo , as well as in a pri- mary cell model of PRC2-mutant ALL. Mechanistically, EZH2 defi ciency resulted in a gene-expression signature of immature T-ALL cells, marked transcriptional upregulation of MYCN , increased replication stress, and enhanced dependency on CHK1 for cell survival. Finally, we demonstrate this phenotype is mediated through derepression of a distal PRC2-regulated MYCN enhancer. In conclusion, we highlight a novel and clinically exploitable pathway in high-risk EZH2-mutated T-ALL. SIGNIFICANCE: Loss-of-function mutations of PRC2 genes are associated with chemotherapy resist- ance in T-ALL, yet no specifi c therapy for this aggressive subtype is currently clinically available. Our work demonstrates that loss of EZH2 activity leads to MYCN-driven replication stress, resulting in increased sensitivity to CHK1 inhibition, a fi nding with immediate clinical relevance. INTRODUCTION (8–10 ), emphasizing the need to develop novel therapies for this high-risk subgroup of patients. Loss-of-function mutations and deletions of Enhancer of Synthetic lethal screening has shown great promise in iden- Zeste (Drosophila) homolog 2 (EZH2 ), the enzymatic compo- tifying novel therapeutic targets in tumors defi cient in a vari- nent of polycomb repressor complex 2 (PRC2), are recurrently ety of tumor suppressors ( 11 ). Perhaps the best-characterized found in T-cell acute lymphoblastic leukemia (T-ALL) and synthetic lethal interaction, targeting the DNA repair path- have been strongly associated with disease pathogenesis ( 1, way with PARP inhibitors in BRCA2-defi cient cells ( 12, 13 ), 2 ). Alterations of the core components of PRC2, including has translated into clinically meaningful benefi ts in patients EZH2, EED , and SUZ12 , are particularly frequent in the early with breast and ovarian cancers ( 14, 15 ). Identifi cation of syn- T-cell precursor ALL subtype (ETP-ALL; refs. 1, 3 ), a subgroup thetic lethal interactions arising from epigenetic defi ciencies characterized by aberrant expression of myeloid and stem cell in cancer cells also offers promising therapeutic possibilities, markers ( 4 ). such as the sensitization to WEE1 inhibition observed in EZH2 catalyzes the trimethylation of histone H3 on Lys27 tumors with SETD2 loss ( 16 ). (H3K27me3), an epigenetic mark associated with transcrip- We hypothesized that EZH2 defi ciency would render T-ALL tional repression of genes involved in differentiation and cells dependent on distinct survival pathways that could be development ( 5 ). Importantly, work in mice has shown that exploited to provide a novel, less toxic, and more effi cacious EZH2 is required for normal B- and T-cell maturation ( 6 ), and therapeutic strategy for high-risk T-ALL. Through a targeted biallelic deletion of EZH2 leads to highly penetrant spontane- drug screen in isogenic T-ALL cells, we discovered that EZH2- ous T-ALL ( 7 ). Moreover, recent work associates loss of EZH2 defi cient T-ALL cells are highly sensitive to inhibition of with poor prognosis in T-ALL and acute myeloid leukemia the replication stress checkpoint kinase CHK1. Mechanisti- (AML), mediated through an increase in chemoresistance cally, loss of EZH2 was associated with marked upregulation of MYCN, a signifi cant increase in replication stress, and dependency on CHK1 for cell survival. 1 Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom. 2 MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom. 3 Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, RESULTS London, United Kingdom. 4 Stem Cell Laboratory, UCL Cancer Institute, The CHK1 Inhibitor MK8776 Selectively Kills University College London, London, United Kingdom. 5 Health Service Lab- oratories LLP, UCL Cancer Institute, London, United Kingdom. EZH2-Defi cient T-ALL Cells Note: Supplementary data for this article are available at Cancer Discovery To investigate synthetic lethal interactions that could be Online (http://cancerdiscovery.aacrjournals.org/). exploited in PRC2 defi cient T-ALL, we generated isogenic Jur- Corresponding Author: Marc R. Mansour, UCL Cancer Institute, London kat T-ALL cells using a double-nicking CRISPR/Cas9 strat- WC1E 6DD, United Kingdom. Phone: +4420-7679-6231; E-mail: m.mansour egy targeting exon 2 of EZH2, an approach that minimizes @ucl.ac.uk off-target effects ( 17 ). We generated two clones with bialellic Cancer Discov 2020;10:998–1017 frameshift mutations in EZH2 (EZH2-KO1 and EZH2-KO2) doi: 10.1158/2159-8290.CD-19-0789 that resulted in loss of EZH2 protein expression and a global © 2020 American Association for Cancer Research. absence of its functional mark H3K27me3 ( Fig. 1A and B ; JULY 2020 CANCER DISCOVERY | 999 Downloaded from cancerdiscovery.aacrjournals.org on September 30, 2021. © 2020 American Association for Cancer Research. Published OnlineFirst April 29, 2020; DOI: 10.1158/2159-8290.CD-19-0789 RESEARCH ARTICLE León et al. A EZH2-WT CD Jurkat 125 T-ALL cell line Unedited EZH2-KO Edited 100 MK8776 0.01 CRISPR/Cas9 D10A P = 0.03 double-nicking strategy 75 WT KO2KO1 value B 50 P 0.1 EZH2 MK8776 25 H3K27me3 cell viability (%) EZH2-KO 0 1 H3 0 25 50 75 100 125 0.0 0.5 1.0 1.5 2.0 EZH2-WT cell viability (%) Relative cell viability (EZH2-KO/WT) ratio EF125 125 EZH2-WT EZH2-WT EZH2-KO1 100 EZH2-KO1 100 EZH2-KO2 EZH2-KO2 75 75 50 IC50 50 IC50 WT 1,777 nmol/L WT 3,164 nmol/L Cell viability (%) KO1 805 nmol/L*** Cell viability (%) KO1 1,374 nmol/L*** 25 25 KO2 825 nmol/L*** KO2 1,513 nmol/L*** 0 0 2.0 2.5 3.0 3.5 2.0 2.5 3.0 3.5 MK8776 log (nmol/L) CCT245737 log (nmol/L) GH125 125 EZH2-WT EZH2-WT EZH2-KO1 EZH2-KO1 100 100 EZH2-KO2 EZH2-KO2 75 75 50 50 IC50 IC50 WT 1,212 nmol/L WT 300 nmol/L Cell viability (%) Cell viability (%) KO1 597 nmol/L*** KO1 180 nmol/L*** 25 25 KO2 600 nmol/L*** KO2 178 nmol/L*** 0 0 2.0 2.5 3.0 3.5 1.5 2.0 2.5 3.0 LY2603618 log (nmol/L) CHIR-124 log (nmol/L) IJDMSO MK8776 Live Annexin V+/Pl+ EZH2-WT WT 100 *** EZH2-KO Q2 Q2 *** Q1 Q1 Q4 Q4 80 *** Q3 Q3 60 *** EZH2-KO 40 Q2 Q2 Cells (%) Q1 Q1 20 Q4 Q4 Q3 Q3 0 Annexin-V 012012 MK8776 (µmol/L) PI 1000 | CANCER DISCOVERY JULY 2020 AACRJournals.org Downloaded from cancerdiscovery.aacrjournals.org on September 30, 2021. © 2020 American Association for Cancer Research. Published OnlineFirst April 29, 2020; DOI: 10.1158/2159-8290.CD-19-0789 CHK1 Inhibition in EZH2-Deficient T-ALL RESEARCH ARTICLE Supplementary Fig. S1A and S1B). EZH2-deficient clones had to MK8776 after preincubation with GSK126, a specific similar growth kinetics to their wild-type (WT) counterparts EZH2 inhibitor (Fig. 2D). Notably, incubation of cells with (Supplementary Fig. S1C, solid lines). GSK126 alone had no appreciable effect on cell growth (Sup- We assessed the relative sensitivity of EZH2-KO (EZH2- plementary Fig. S1C), EZH2 expression, or CHK1 protein KO1 cells, unless specified) and EZH2-WT cells to an in-house levels (Supplementary Fig. S3A). Following seven days of curated library of 219 commercially available compounds tar- EZH2 inhibition, a global decrease in H3K27me3 mark in geting specific chromatin-modifying enzymes, cell cycle, and treated cell lines was confirmed by Western blotting (Fig. 2E). DNA-repair processes, including small-molecule inhibitors Consistent with findings in our EZH2-KO clones, preincuba- that are already in clinical use for the treatment of cancer tion of Jurkat cells with GSK126 significantly increased their (Supplementary Table S1). The majority of drugs had similar sensitivity to CHK1 inhibition when exposed to MK8776 at effects on cell viability in both EZH2-WT and EZH2-KO cells doses corresponding their initial IC50 and IC75 (Fig. 2F; Sup- (Fig. 1C and D; Supplementary Table S2). However, MK8776, plementary Fig. S3B). Similar sensitization to MK8776 upon a CHK1 inhibitor that has been tested in early-phase clinical GSK126 preincubation was observed in PEER, CUTLL1, ALL- trials in solid tumors (18), demonstrated a significant dif- SIL, and PF-382 cell lines (Fig. 2E and F; Supplementary Fig. ferential reduction on cell viability in EZH2-KO cells com- S3B). These data not only support our results in isogenic pared with WT cells (P = 0.03 by two-tailed Student t test; EZH2-KO Jurkat cells, but also confirm that the observed Fig.