Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

Abstract

SummaryTranscription factor fusion proteins can transform cells by inducing global changes of the transcriptome, often creating a state of oncogene addiction. Here, we investigate the role of epigenetic mechanisms in this process, focusing on Ewing sarcoma cells that are dependent on the EWS-FLI1 fusion protein. We established reference epigenome maps comprising DNA methylation, seven histone marks, open chromatin states, and RNA levels, and we analyzed the epigenome dynamics upon downregulation of the driving oncogene. Reduced EWS-FLI1 expression led to widespread epigenetic changes in promoters, enhancers, and super-enhancers, and we identified histone H3K27 acetylation as the most strongly affected mark. Clustering of epigenetic promoter signatures defined classes of EWS-FLI1-regulated genes that responded differently to low-dose treatment with histone deacetylase inhibitors. Furthermore, we observed strong and opposing enrichment patterns for E2F and AP-1 among EWS-FLI1-correlated and anticorrelated genes. Our data describe extensive genome-wide rewiring of epigenetic cell states driven by an oncogenic fusion protein.

Molecular genetics of Ewing sarcoma, model systems and finding novel (immuno-) therapeutic targets

“…The epigenetic profile of EWS has been directly linked to the activity of EWSR1-FLI1 [24,80] . EWSR1-FLI1 preferentially binds to sites with GGAA repeats, and classical ETS binding sites.…”

“…Fusion of the N-terminal region of EWSR1, which contains a strong transcriptional activation domain [21,22] , and these DNA binding domains causes aberrant transcription of a multitude of genes. Additionally, EWSR1-ETS is known to affect epigenetic programs [23,24] , splicing [25,26] , and metabolic activity [27] of EWS. Oncogenic fusions between ETS genes and transcriptional activators are not unique to EWS: in 50%-70% of prostate cancers, similar chromosomal rearrangements are found [28] .…”

DNA Methylation Profiling Opens A New Phase in the Search of Targeted Therapy Against Ewing Sarcoma

“…Now it is possible to clearly perform an ES diagnosis in base of the presence of EWS/FLI1 (or a few functionally identical Editorial Rello-Varona & Tirado gene fusion variants). We know that EWS/FLI1 works as a transcription factor as well as a chromatin remodeler [10]. EWS/FLI1 action reprograms the cells, developing a cancerous phenotype.…”

“…As a tumor entity that, apart from the EWS/FLI1 fusion, rarely shows recurrent mutations, any improvement in the knowledge of its epigenomic landscape becomes an important milestone [10]. In this sense, DNA methylation profiling provides meaningful data [4].…”

SLFN11: Achilles' Heel or Troublemaker

“…As exemplarily demonstrated for EWS-FLI1 and ETS1, the SLFN11 promoter is highly promiscuous for ETS factor binding and activation, and the presented gene expression correlation analysis suggests that various different ETS factors may activate SLFN11 in a cell type-specific manner. A recent Ewing sarcoma epigenome study showed that EWS-FLI1 binding to promoters, in contrast to enhancers, is primarily associated with broadly active and widely expressed genes, where it acts predominantly as an amplifier of preexisting gene expression (4). In fact, in two model systems, human umbilical cord vascular endothelial cells and mouse embryonic superficial zone cells, ectopic expression of EWS-FLI1 led to the replacement of endogenous FLI1, respectively ERG, at ETS-driven promoters (5, 6), whereas knockdown of EWS-FLI1 resulted in its replacement from target promoters by ELF1 and GABPA ETS family members in a Ewing sarcoma cell line (7).…”