Overcoming clinical resistance to EZH2 inhibition using rational epigenetic combination therapy

Abstract

Essential epigenetic dependencies have become evident in many cancers. Based on functional antagonism between BAF/SWI/SNF and PRC2 in SMARCB1-deficient sarcomas, we and colleagues recently completed the clinical trial of the EZH2 inhibitor tazemetostat, leading to its FDA approval. However, the principles of tumor response to epigenetic therapy in general, and tazemetostat in particular, remain unknown. Using functional genomics of patient tumors and diverse experimental models, we define molecular mechanisms of tazemetostat resistance in SMARCB1-deficient sarcomas and rhabdoid tumors. We found distinct classes of acquired mutations that converge on the RB1/E2F axis and decouple EZH2-dependent differentiation and cell cycle control. This allows tumor cells to escape tazemetostat-induced G1 arrest despite EZH2 inhibition, and suggests a general mechanism for effective EZH2 therapy. Thus, we develop combination strategies to circumvent tazemetostat resistance using cell cycle bypass and synthetic lethal targeting, and provide prospective biomarkers for therapy stratification. This offers a paradigm for rational epigenetic combination therapy suitable for immediate translation to clinical trials for epithelioid sarcomas, rhabdoid tumors, and other epigenetically dysregulated cancers.

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

“…). Using CRISPR gene editing, we generated isogenic RB1 wild-type and RB1 del mutant G401 cells and confirmed correct biallelic RB1 inactivating mutations and consequent loss of RB1 protein expression, using the AAVS1 safe harbor as a negative control (8). In prior work, we found that defects in the RB1/E2F axis, including mutations of RB1, cause TAZ resistance (8).…”

“…We found that in addition to the expected upregulation of Polycomb gene sets, EZH2 inhibition in G401 rhabdoid tumor cells with TAZ for 11 days also caused a significant increase in the expression of PGBD5 (mean fold-increase of 6.6 and Student’s t-test p = 1.2E-7; Figure 1D ). Using CRISPR gene editing, we generated isogenic RB1 wild-type and RB1 del mutant G401 cells and confirmed correct biallelic RB1 inactivating mutations and consequent loss of RB1 protein expression, using the AAVS1 safe harbor as a negative control (8). In prior work, we found that defects in the RB1/E2F axis, including mutations of RB1 , cause TAZ resistance (8).…”

“…Prior studies showed that inhibition of EZH2 methyltransferase activity using tazemetostat is insufficient to induce durable tumor regressions in most patients with epithelioid and rhabdoid tumors (8). Our recent functional genetic studies of patient tumors before and after clinical TAZ therapy led to a specific model of effective epigenetic therapy, including rational combinations to overcome RB1/E2F pathway defects that were observed in 43% of tumors with primary or acquired TAZ resistance (8). Here, we further advanced this approach by identifying a collateral synthetic lethal dependency between EZH2 and PGBD5 in rhabdoid and epithelioid sarcomas that confers a susceptibility to combined epigenetic therapy using EZH2 and ATR inhibition.…”

“…Thus, effective targeting of DNA damage repair must leverage tumor-specific mutational and repair processes, providing a rationale for combining epigenetic and DNA repair inhibitors. In the case of rhabdoid and epithelioid sarcomas with SMARCB1 deficiency, the epigenetic antagonism between the chromatin remodeling activities of BAF and PRC2 contributes to the dependency of tumor cells on EZH2 activity (5), whose inhibition promotes the expression of tumor suppressors otherwise repressed by PRC2 (8, 33). This epigenetic reprogramming also appears to increase the expression of PGBD5, with the associated DNA damage and requirement for its ATR-dependent repair.…”

“…All mouse experiments were carried out in accordance with institutionally approved animal use protocols (8). To generate PDXs, tumor specimens were collected under approved IRB protocol Therapeutic studies used female and male NSG mice obtained from the Jackson Laboratory.…”