dataset
posted on 2023-03-31, 22:50 authored by Kit I. Tong, Sharon Yoon, Keren Isaev, Mehran Bakhtiari, Tracy Lackraj, Michael Y. He, Jesse Joynt, Anjali Silva, Maria C. Xu, Gilbert G. Privé, Housheng Hansen He, Rodger E. Tiedemann, Elizabeth A. Chavez, Lauren C. Chong, Merrill Boyle, David W. Scott, Christian Steidl, Robert Kridel Pathway analysis of RNA-seq results (Gene Ontology, Reactome and WikiPathways).
Funding
Canadian Hematology Society
Leukemia and Lymphoma Society of Canada
Princess Margaret Cancer Foundation
Gilead Sciences Research Scholars Program
Terry Fox Research Institute
BC Cancer Foundation
Natural Sciences and Engineering Research Council of Canada
Canadian Institutes of Health Research
History
ARTICLE ABSTRACT
The efficacy of EZH2 inhibition has been modest in the initial clinical exploration of diffuse large B-cell lymphoma (DLBCL), yet EZH2 inhibitors are well tolerated. Herein, we aimed to uncover genetic and pharmacologic opportunities to enhance the clinical efficacy of EZH2 inhibitors in DLBCL.
We conducted a genome-wide sensitizing CRISPR/Cas9 screen with tazemetostat, a catalytic inhibitor of EZH2. The sensitizing effect of IKZF1 loss of function was then validated and leveraged for combination treatment with lenalidomide. RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing analyses were performed to elucidate transcriptomic and epigenetic changes underlying synergy.
We identified IKZF1 knockout as the top candidate for sensitizing DLBCL cells to tazemetostat. Treating cells with tazemetostat and lenalidomide, an immunomodulatory drug that selectively degrades IKAROS and AIOLOS, phenocopied the effects of the CRISPR/Cas9 screen. The combined drug treatment triggered either cell-cycle arrest or apoptosis in a broad range of DLBCL cell lines, regardless of EZH2 mutational status. Cell-line–based xenografts also showed slower tumor growth and prolonged survival in the combination treatment group. RNA-seq analysis revealed strong upregulation of interferon signaling and antiviral immune response signatures. Gene expression of key immune response factors such as IRF7 and DDX58 were induced in cells treated with lenalidomide and tazemetostat, with a concomitant increase of H3K27 acetylation at their promoters. Furthermore, transcriptome analysis demonstrated derepression of endogenous retroviruses after combination treatment.
Our data underscore the synergistic interplay between IKAROS degradation and EZH2 inhibition on modulating epigenetic changes and ultimately enhancing antitumor effects in DLBCL.
