Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas
Yaniv Kazansky, Helen S. Mueller, Daniel Cameron, Phillip Demarest, Nadia Zaffaroni, Noemi Arrighetti, Valentina Zuco, Prabhjot S. Mundi, Yasumichi Kuwahara, Romel Somwar, Rui Qu, Andrea Califano, Elisa de Stanchina, Filemon S. Dela Cruz, Andrew L. Kung, Mrinal M. Gounder, Alex Kentsis
Yaniv Kazansky, Helen S. Mueller, Daniel Cameron, Phillip Demarest, Nadia Zaffaroni, Noemi Arrighetti, Valentina Zuco, Prabhjot S. Mundi, Yasumichi Kuwahara, Romel Somwar, Rui Qu, Andrea Califano, Elisa de Stanchina, Filemon S. Dela Cruz, Andrew L. Kung, Mrinal M. Gounder, Alex Kentsis
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Research Article Cell biology Oncology

Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas

Abstract

Despite the potential of targeted epigenetic therapies, most cancers do not respond to current epigenetic drugs. The polycomb repressive complex EZH2 inhibitor tazemetostat was recently approved for the treatment of SMARCB1-deficient epithelioid sarcomas, based on the functional antagonism between PRC2 and SMARCB1. Through the analysis of tumors of patients treated with tazemetostat, we recently defined key principles of their response and resistance to EZH2 epigenetic therapy. Here, using transcriptomic inference from SMARCB1-deficient tumor cells, we nominate the DNA damage repair kinase ATR as a target for rational EZH2 combination epigenetic therapy. We showed that EZH2 inhibition promotes DNA damage in epithelioid and rhabdoid tumor cells, at least in part via its induction of piggyBac transposable element derived 5 (PGBD5). We leveraged this collateral synthetic lethal dependency to target PGBD5-dependent DNA damage by inhibition of ATR, but not CHK1, using the ATR inhibitor elimusertib. Consequently, combined EZH2 and ATR inhibition improved therapeutic responses in diverse patient-derived epithelioid and rhabdoid tumors in vivo. This advances a combination epigenetic therapy based on EZH2-PGBD5 synthetic lethal dependency suitable for immediate translation to clinical trials for patients.

Authors

Yaniv Kazansky, Helen S. Mueller, Daniel Cameron, Phillip Demarest, Nadia Zaffaroni, Noemi Arrighetti, Valentina Zuco, Prabhjot S. Mundi, Yasumichi Kuwahara, Romel Somwar, Rui Qu, Andrea Califano, Elisa de Stanchina, Filemon S. Dela Cruz, Andrew L. Kung, Mrinal M. Gounder, Alex Kentsis

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Figure 3

CHK1 inhibition does not induce replication stress or synergize with tazemetostat.

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CHK1 inhibition does not induce replication stress or synergize with taz...
(A) DESeq2-normalized read counts of cells treated with 10 μM TAZ versus equivalent volume of DMSO for 11 days. n = 3 biological replicates per condition. P = 0.0035, 0.032, and 0.0041 by 2-sided Student’s t test for DMSO versus TAZ-treated RB1WT, RB1del E1, and RB1del F2 cells, respectively. (B) Cells treated with 10 μM TAZ or DMSO for 11 days do not express MYCN protein. MYCN-amplified neuroblastoma cell line IMR5 was used as a positive control for MYCN expression. (C) Western blot assaying replication stress as measured by RPA32 phosphorylation at S4/8 and T21. Camptothecin treatment (1.5 μM) for 2 hours was used as a positive control for replication stress. Total RPA32 was used to control for RPA32 protein levels, and autophosphorylation of CHK1 at S296 was used to confirm CHK1 inhibition. Cells were pretreated with 10 μM TAZ or DMSO for 9 days. Cells were then split and additionally treated with SRA737 (3 μM) or equivalent volume of DMSO for 2 days. (D) Dose-response curves of G401 cells treated with the CHK1 inhibitor SRA737 for 9 days. (E) Dose-response curves of the indicated G401 cells treated with SRA737 for 9 days in combination with the indicated (0, 0.2, or 2.0 μM) TAZ concentration. Experiments in D and E were repeated 3 times; representative experiments are shown. *P < 0.05, ***P < 0.001.