Ewing sarcoma (EWS) is a rare pediatric tumor predominantly occurring in children of European ancestry and is characterized by the pathognomonic EWSR1-FLI1 fusion oncogene. To identify germline susceptibility loci associated with EWS risk, we performed a genome-wide association study (GWAS) meta-analysis of 749 EWS cases and 1,378 unaffected individuals of European ancestry from sample collections within the Institut Curie, National Cancer Institute and the Childhood Cancer Survivor Study. Our study replicated previously reported susceptibility loci at 1p36.22, 10q21.3 and 15q15.1 as well as identified novel loci at 6p25.1, 8q24.23, 20p11.22 and 20p11.23 (P-values<5×10-8). These seven EWS susceptibility loci discovered in only 749 cases make EWS one of the most productive GWAS studied cancers when considering a locus to case discovery ratio. All estimated effect estimates were high for cancer GWAS with odds ratios in excess of 1.7 observed. These high per allele effects among relatively common germline variants are striking in light of the rarity of EWS cases and lack of evidence of EWS as part of a familial cancer syndrome and therefore suggest a distinctive genetic architecture for EWS. Interestingly, in silico bioinformatics analysis identified that most EWS susceptibility loci reside near GGAA nucleotide repeat sequences where binding of the EWSR1-FLI1 fusion protein occurs. ChIP-seq analyses confirmed in vivo binding of EWSR1-FLI1, suggesting germline variation in these regions could alter EWSR1-FLI1 binding and potentially deregulate neighboring genes. To identify genes with allele specific expression differences, we carried out expression quantitative trait locus (eQTL) analyses at each identified EWS susceptibility locus. We identified eQTLs for plausible candidate genes at 6p25.1 with RREB1, a RAS-responsive element, and at 20p11.23 with KIZ, a centrosomal stabilization protein. We also noted the 20p11.22 locus is near NKX2-2, a highly overexpressed gene in EWS, although no eQTL was observed in our expression data. Furthermore, knockdown of EWSR1-FLI1 in EWS cell lines indicated a more than 2-fold difference in expression of RREB1 and NKX2-2, further supporting the role of specific regulation of these genes by EWSR1-FLI1 and suggesting RREB1 and NKX2-2 may be transcription factors involved in core regulatory circuitries of EWS. Overall, our study suggests a distinctive underlying genetic architecture for EWS in which moderate risk common germline variants interact with EWSR1-FLI1 binding to alter expression of nearby target genes.

Citation Format: Mitchell J. Machiela, Thomas G. Grünewald, Didier Surdez, Stephanie Reynaud, Olivier Mirabeau, Eric Karlins, Rebeca Alba Rubio, Sakina Zaidi, Sandrine Grossetete-Lalami, Stelly Ballet, Eve Lapouble, Valérie Laurence, Jean Michon, Gaelle Pierron, Heinrich Kovar, Nathalie Gaspar, Udo Kontny, Anna González-Neira, Piero Picci, Javier Alonso, Ana Patino-Garcia, Nadège Corradini, Neal D. Freedman, Nathaniel Rothman, Casey L. Dagnall, Laurie Burdette, Kristine Jones, Michelle Manning, Kathleen Wyatt, Weiyin Zhou, Meredith Yeager, David G. Cox, Robert N. Hoover, Javed Khan, Gregory T. Armstrong, Wendy M. Leisenring, Smita Bhatia, Leslie L. Robison, Uta Dirksen, Markus Metzler, Wolfgang Hartmann, Konstantin Strauch, Thomas Kirchner, Andreas E. Kulozik, Lindsay M. Morton, Lisa Mirabello, Margaret A. Tucker, Franck Tirode, Stephen J. Chanock, Olivier Delattre. Multiple new susceptibility loci identified in genome-wide association study of Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2970.