A Massachusetts General Hospital (MGH) research team has used epigenome editing tools to investigate how the genetic abnormality that drives Ewing sarcoma – the second most common bone cancer in children and young adults – unleashes tumor growth. In their paper in the journal Genes & Development the researchers show that blocking the fusion protein EWS-FLI1 from binding and activating specific ‘enhancer’ sites in the genome prevents the expression of genes that promote tumor growth.

“We previously showed that binding of EWS-FLI1 to GGAA microsatellite repeats in the genome converts these sites into active enhancers,” says Miguel Rivera, MDMGH Department of Pathology and Center for Cancer Research, co-senior author of the report. “Now we have used new epigenome editing tools to turn off individual microsatellites and demonstrate that they have important functions in controlling the expression of nearby genes that are critical for tumor growth.”

Ewing sarcoma is caused by a genetic alteration known as a chromosomal translocation in which the chromosome 22 gene EWS is fused to the chromosome 11 gene FLI1, leading to generation of the fusion protein EWS-FLI1. A 2014 Cancer Cell study led by Rivera and Bradley Bernstein, MD, PhD, also of MGH Pathology and the Center for Cancer Research, found that EWS-FLI1 had two properties that could lead to tumor growth: conversion of microsatellite repeats – repetitive DNA elements commonly found in the genome – into active enhancers that stimulate the expression of other genes and repression of other factors that regulate gene transcription. In essence, EWS-FLI1 both steps on the gas and takes off the brakes to tumor growth.

The current study was designed to directly test the links between microsatellite activation by EWS-FLI1, the expression of cancer-associated genes and tumor growth. The researchers focused on GGAA microsatellites – repeats of the nucleotides guanine and adenine – that are usually inactive but in Ewing sarcoma are bound and activated by EWS-FLI1.

The investigators used a novel CRISPR-based system to bring a repressor module to sites adjacent to the GGAA microsatellites in Ewing sarcoma cells, which markedly reduced expression of nearby genes believed to stimulate tumor growth. In contrast, repression of GGAA repeats in cancer cells that did not express the fusion protein had no effect on gene expression. Finally, silencing a specific repeat known to regulate expression of SOX2, a transcription factor that acts as an oncogene, led to a significant decrease in the size of Ewing sarcoma tumors in mice.

“Finding regulatory regions such as enhancers in the genome that are specifically utilized in tumors but not in normal cells may point to new therapeutic opportunities,” says Rivera, an assistant professor of Pathology at Harvard Medical School. “We’re now working towards identifying other tumor-specific enhancers that are important for tumor growth in Ewing sarcoma and other types of cancer.”

Ivan Stamenkovic, MD, and Nicolo Riggi, MD, PhD, of the University of Lausanne, Switzerland, are co-senior authors of the Genes & Development paper. The co-lead authors are Gaylor Boulay, PhD, and Angela Volorio, MD, BM, MGH Pathology and Center for Cancer Research (CCR). Additional co-authors are Sowmya Iyer, MGH Pathology/CCR; and Liliane Broye, University of Lausanne. Support for the study includes grants from the V Foundation for Cancer Research, the Charley Davidson Children's Cancer Fund at MassGeneral Hospital for Children, the Medic Foundation, the Swiss Cancer Research Foundation, the Swiss National Science Foundation, the Swiss Cancer League, Oncosuisse and the Botnar Foundation.

Massachusetts General Hospital, founded in 1811, is the original and largest teaching hospital of Harvard Medical School. The MGH Research Institute conducts the largest hospital-based research program in the nation, with an annual research budget of more than $900 million and major research centers in HIV/AIDS, cardiovascular research, cancer, computational and integrative biology, cutaneous biology, genomic medicine, medical imaging, neurodegenerative disorders, regenerative medicine, reproductive biology, systems biology, photomedicine and transplantation biology. The MGH topped the 2015 Nature Index list of health care organizations publishing in leading scientific journals and earned the prestigious 2015 Foster G. McGaw Prize for Excellence in Community Service. In August 2017 the MGH was once again named to the Honor Roll in the U.S. News & World Report list of "America's Best Hospitals."