A non-canonical EZH2 function sensitizes solid tumors to genotoxic stress

Drugs that block the activity of the methyltransferase EZH2 are in clinical development for the treatment of non-Hodgkin lymphomas harboring gain-of-function EZH2 mutations that enhance its polycomb repressive function. In contrast, in castration-resistant prostate cancer (CRPC) we have previously reported that EZH2 plays a non-canonical role as a transcriptional activator. In this setting, we now show that EZH2 inhibitors can also block the non-canonical activity of EZH2 and inhibit the growth of CRPC cells. Gene expression and epigenomic profiling of cells treated with EZH2 inhibitors demonstrated that rather than de-repressing tumor suppressor genes silenced by PRC2, EZH2 inhibitors downregulate a set of DNA repair genes that are directly regulated by EZH2. In addition, genome-wide CRISPR/Cas9-mediated loss-of-function screens in the presence of EZH2 inhibitors identified these DNA repair genes to underlie the growth-inhibitory function of these compounds. Interrogation of public data from diverse solid tumor types expressing wild-type EZH2 showed that expression of DNA damage repair genes is significantly correlated with cellular sensitivity to EZH2 inhibitors. Consistent with these findings, treatment of CRPC cells with EZH2 inhibitors dramatically enhanced their sensitivity to genotoxic stress. These studies reveal a previously unappreciated mechanism of action of EZH2 inhibitors and provide a mechanistic basis for potential new combination cancer therapies.

[1]  P. Nelson,et al.  EZH2 cooperates with gain‐of‐function p53 mutants to promote cancer growth and metastasis , 2019, The EMBO journal.

[2]  Hong Chang,et al.  EZH2 as a therapeutic target for multiple myeloma and other haematological malignancies , 2018, Biomarker Research.

[3]  Myles A Brown,et al.  Transcriptional Regulation in Prostate Cancer. , 2018, Cold Spring Harbor perspectives in medicine.

[4]  Peng Jiang,et al.  Improved design and analysis of CRISPR knockout screens , 2018, Bioinform..

[5]  N. Wajapeyee,et al.  Mechanisms of resistance to EZH2 inhibitors in diffuse large B-cell lymphomas. , 2018, Blood.

[6]  Shane A. Evans,et al.  Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage-and Histone Methylation-Dependent Pathways , 2018, Cell reports.

[7]  W. Béguelin,et al.  Enhancer of zeste homolog 2 (EZH2) inhibitors , 2018, Leukemia & lymphoma.

[8]  I. Tempera,et al.  Poly(ADP-ribose) Polymerase 1, PARP1, modifies EZH2 and inhibits EZH2 histone methyltransferase activity after DNA damage , 2018, Oncotarget.

[9]  Jun Yao,et al.  EZH2 contributes to the response to PARP inhibitors through its PARP-mediated poly-ADP ribosylation in breast cancer , 2017, Oncogene.

[10]  O. Coqueret,et al.  Regulation of senescence escape by the cdk4–EZH2–AP2M1 pathway in response to chemotherapy , 2018, Cell Death & Disease.

[11]  J. Maciejewski,et al.  Mutations in DNMT3A, U2AF1, and EZH2 identify intermediate-risk acute myeloid leukemia patients with poor outcome after CR1 , 2018, Blood Cancer Journal.

[12]  Phillip G. Montgomery,et al.  Defining a Cancer Dependency Map , 2017, Cell.

[13]  Tero Aittokallio,et al.  SynergyFinder: a web application for analyzing drug combination dose–response matrix data , 2017, Bioinform..

[14]  L. Macconaill,et al.  Validation of OncoPanel: A Targeted Next-Generation Sequencing Assay for the Detection of Somatic Variants in Cancer. , 2017, Archives of pathology & laboratory medicine.

[15]  Mingming Jia,et al.  COSMIC: somatic cancer genetics at high-resolution , 2016, Nucleic Acids Res..

[16]  C. Roberts,et al.  Targeting EZH2 in cancer , 2016, Nature Medicine.

[17]  M. Smonskey,et al.  EZH2 inhibition re-sensitizes multidrug resistant B-cell lymphomas to etoposide mediated apoptosis , 2016, Oncoscience.

[18]  Joshua A. Bittker,et al.  Correlating chemical sensitivity and basal gene expression reveals mechanism of action , 2015, Nature chemical biology.

[19]  Jun S. Liu,et al.  Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR , 2015, Genome Biology.

[20]  Shirley X. Liu,et al.  Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression , 2015, Molecular Cancer Research.

[21]  J. Pritchard,et al.  Acquisition of a single EZH2 D1 domain mutation confers acquired resistance to EZH2-targeted inhibitors , 2015, Oncotarget.

[22]  Yangchao Chen,et al.  Targeting EZH2 for Cancer Therapy: Progress and Perspective , 2015, Current protein & peptide science.

[23]  Clifford A. Meyer,et al.  Sequence determinants of improved CRISPR sgRNA design , 2015, Genome research.

[24]  Wei Li,et al.  Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer , 2015, The EMBO journal.

[25]  David A. Orlando,et al.  Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. , 2014, Cell reports.

[26]  Samuel H. Wilson,et al.  Base Excision Repair Defects Invoke Hypersensitivity to PARP Inhibition , 2014, Molecular Cancer Research.

[27]  Heather L. Mulder,et al.  The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes , 2014, Nature Communications.

[28]  J. Moffat,et al.  Measuring error rates in genomic perturbation screens: gold standards for human functional genomics , 2014, bioRxiv.

[29]  R. Golsteyn,et al.  Genotoxic Anti-Cancer Agents and Their Relationship to DNA Damage, Mitosis, and Checkpoint Adaptation in Proliferating Cancer Cells , 2014, International journal of molecular sciences.

[30]  S. Gabriel,et al.  Discovery and saturation analysis of cancer genes across 21 tumor types , 2014, Nature.

[31]  E. Chan,et al.  Identification of EZH2 and EZH1 small molecule inhibitors with selective impact on diffuse large B cell lymphoma cell growth. , 2013, Chemistry & biology.

[32]  F. Feng,et al.  A hormone-DNA repair circuit governs the response to genotoxic insult. , 2013, Cancer discovery.

[33]  H. Hieronymus,et al.  Androgen receptor signaling regulates DNA repair in prostate cancers. , 2013, Cancer discovery.

[34]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[35]  G. Poirier,et al.  Polycomb repressive complex 2 contributes to DNA double-strand break repair , 2013, Cell cycle.

[36]  Benjamin J. Raphael,et al.  Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. , 2013, The New England journal of medicine.

[37]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[38]  M. Loda,et al.  EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent , 2012, Science.

[39]  P. Atadja,et al.  Selective inhibition of Ezh2 by a small molecule inhibitor blocks tumor cells proliferation , 2012, Proceedings of the National Academy of Sciences.

[40]  Yan Liu,et al.  EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations , 2012, Nature.

[41]  E. Ren,et al.  Functional Aspects of PARP1 in DNA Repair and Transcription , 2012, Biomolecules.

[42]  Tim J. Wigle,et al.  A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells. , 2012, Nature chemical biology.

[43]  R. Copeland.  Faculty Opinions recommendation of The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. , 2012 .

[44]  Benjamin J. Raphael,et al.  The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer , 2016 .

[45]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[46]  Yong Jiang,et al.  Mutation of A677 in histone methyltransferase EZH2 in human B-cell lymphoma promotes hypertrimethylation of histone H3 on lysine 27 (H3K27) , 2012, Proceedings of the National Academy of Sciences.

[47]  Michel Sadelain,et al.  Safe harbours for the integration of new DNA in the human genome , 2011, Nature Reviews Cancer.

[48]  David G Johnson,et al.  Transcriptional and nontranscriptional functions of E2F1 in response to DNA damage. , 2012, Cancer research.

[49]  Qiang Yu,et al.  Polycomb protein EZH2 regulates cancer cell fate decision in response to DNA damage , 2011, Cell Death and Differentiation.

[50]  N. Curtin,et al.  The role of PARP in DNA repair and its therapeutic exploitation , 2011, British Journal of Cancer.

[51]  Steven J. M. Jones,et al.  Frequent mutation of histone modifying genes in non-Hodgkin lymphoma , 2011, Nature.

[52]  A. Jankowska,et al.  Novel homo- and hemizygous mutations in EZH2 in myeloid malignancies , 2010, Leukemia.

[53]  C. Sander,et al.  Integrative genomic profiling of human prostate cancer. , 2010, Cancer cell.

[54]  Ryan D. Morin,et al.  Somatic mutation of EZH2 (Y641) in Follicular and Diffuse Large B-cell Lymphomas of Germinal Center Origin , 2010, Nature Genetics.

[55]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[56]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[57]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[58]  Hengbin Wang,et al.  Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing , 2002, Science.

[59]  S. Mok,et al.  Altered expression of BRCA1, BRCA2, and a newly identified BRCA2 exon 12 deletion variant in malignant human ovarian, prostate, and breast cancer cell lines , 2000, Molecular carcinogenesis.