Transcriptome Profiling of Ewing Sarcomas - Treatment Resistance Pathways and IGF-Dependency

Background: Ewing sarcoma (ES) are aggressive sarcomas driven by EWS-fusion genes. We sought to investigate if whole-transcriptome sequencing (RNA-seq) could be used to detect patterns associated with chemotherapy response or tumor progression after first-line treatment. Methods: Transcriptome sequencing (RNA-seq) was done for 13 consecutive cases of ES. As we identified IGF2 expression as a potential driver for chemotherapy response and progression, we investigated the effect of IGF2 on proliferation, radioresistance, apoptosis and transcriptome in four ES cell lines and IGF2 expression in a validation series of 14 patients. Findings: Transcriptome analysis identified differentially expressed genes (adj. p < 0.005) and pathways associated with chemotherapy response (285 genes), short overall-survival (662 genes) and progression after treatment (447 genes). Imprinting independent promoter-P3 mediated IGF2 expression was identified in a subset of cases with aggressive clinical course. In ES cell lines IGF2 induced proliferation, but only promoted radioresistance in the CADO cells. High IGF2 expression was also significantly associated with shorter overall-survival in clinical ES. Interpretation: Transcriptome analysis of the clinical samples and the cell lines revealed a IGF-dependent signature, potentially related to a stem cell like phenotype. Transcriptome analysis is potentially a powerful complementary tool to predict the clinical behavior of ES and may be utilized for clinical trial stratification strategies and personalized oncology. We herein describe gene signatures coupled to biological functions that could be important for clinical ES behavior, including IGF2 expression. Finally, IGF-inhibition may be more successful in conjunction with conventional radio-chemotherapy for a subset of patients. Funding Statement: This study was supported by grants from the Swedish Childhood Cancer Foundation, the Swedish Cancer Society, the Cancer Society in Stockholm, Stockholm County Council and Karolinska Institutet. Declaration of Interests: The authors declare no conflicts of interest. Ethics Approval Statement: The study and collection of patients’ samples were approved by the local ethics committee (The Regional Ethics Committee in Stockholm), reference number 2013 1979-31. All patients had given oral and written consent prior to sample collection. Normal tissue controls were anonymized in accordance to the Swedish Biobank Law.