Association of genomically unstable Ewing sarcoma tumors with HOTAIR overexpression and clinical outcome.

Abstract

11035 Background: Ewing sarcoma (ES) is the second most common bone cancer in children, characterized by the EWS-FLI1 fusion protein. Like most translocation-driven pediatric cancers, ES is a genomically “quiet” cancer with a low mutational burden and strong epigenetic regulation. However, recurring copy number alterations (CNAs) still arise in some ES tumors (e.g., chromosome 1q gain, 8 gain, 12 gain, and 16q loss) while other ES tumors completely lack genomic CNAs. We hypothesized that clinical, molecular, and epigenetic differences exist between these two unstable vs. stable genomic subtypes of ES. Methods: We performed CNA analysis on over 200 ES FFPE tumors. 30% of ES tumors had stable genomes while 60% had one or more CNAs across the genome. We performed gene expression and methylation microarray analyses on 24 ES FFPE tumors (11 stable, 13 unstable). Expression and methylation signatures were compared between stable vs. unstable ES and combined with clinical outcome. Results: Patients with unstable vs. stable ES tumors revealed worse 5-year overall (OS) and event-free survival (EFS) (38% vs. 67% EFS, p = 0.005; 58% vs. 84% OS, p = 0.0016). The subtypes had distinct expression and methylation signatures and clustered by methylation patterns. We identified differentially expressed and methylated genes, including upregulation (p = 0.0005) and unmethylation (p = 0.0009) of the long non-coding RNA HOTAIR in unstable vs. stable ES tumors. HOTAIR expression is higher in metastatic ES tumors compared to primary ES tumors (p = 0.02). Per the Cancer Cell Line Encyclopedia (Broad), ES cell lines have increased HOTAIR expression compared to 36 other cancers. Conclusions: ES genomic profiling through copy number, gene expression, and methylation identified at least two subtypes of ES (stable and unstable) that differ in outcome, gene expression and methylation. This data suggests HOTAIR’s involvement in ES pathogenesis, particularly in unstable tumors that have worse prognosis. Investigation is ongoing for HOTAIR expression as a prognostic and therapeutic target for ES, including a marker for LSD-inhibitor response.