Abstract 2361: Identification and analysis of gene fusion and splice variant events in the NCI sarcoma cell line panel

Abstract

Abstract Sarcomas represent approximately 7% of newly diagnosed childhood cancers in the United States per year. A rare form of cancer but one that is highly variable and predominantly characterized by specific chromosomal translocations in pediatric occurrences. Sarcoma tumors can progress through several cellular pathways and are highly dependent on the function of the genes involved in the fusion event. Therefore, the identification of novel fusion candidates or altered genomic functions from splice variation is essential for understanding genomic heterogeneity among sarcomas and for the development of sarcoma specific therapeutic protocols. Within the Division of Cancer Treatment and Diagnosis (NCI) we developed a cell line panel of 67 human sarcoma and measured exon expression using the Affymetrix Exon 1.0 ST arrays. These data have been used to generate gene expression profiles for all the cell lines while the probe coverage across all exons of these genes facilitates identification of putative splice variants and fusion gene candidates. In order to predict gene fusions in these cell lines, we implemented computational prediction algorithms such as generalized linear models and separately random forest procedures training on features determined only from the EWSR1-FLI1 exon expression profiles. These resulted in 83% accuracy and 90% coverage of potential EWSR1-FLI1 fusions and the ability to identify 60% of the known individual sarcoma fusion gene partners, as annotated by the COSMIC database, within all 67 sarcoma cell lines. Specifically, the ASPSCR1-TFE3 fusion gene in alveolar soft part sarcoma is captured in the ASPS-1 cell line; currently the only ASPS cell line known. We also find the alveolar rhabdomyosarcoma PAX3-FOXO1, PAX7-FOXO1 fusion genes and the Ewing's sarcoma EWSR1's C-terminal fusion partners DDIT3, ERG, ETV1 and ETV4, in addition to FLI1. Next, splice variant analysis in all sarcoma cell lines based on exon arrays was performed using the FIRMA algorithm and the computational package AltAnalyze. Using individual gene-exon expression profiles we successfully segregated the sarcoma cell lines based on sarcoma type. Among theses clustering profiles, differential inclusion exon expression was exclusively observed in the gene DMKN (dermokine) primarily in the adult sarcoma types such as chondrosarcoma, fibrosarcoma, leiomyosarcoma and uterine sarcoma and may suggest tissue and sarcoma type alternate splice variations. Additionally, the enzyme phosphatidylserine synthase 1 (PTDSS1) showed exon specific variation in 6 of 8 rhabdomyosarcoma (both ARMS and ERMS) examined but not in other types of sarcoma. Therefore, our computational analysis and discovery of putative gene fusion and splice variant events is 67 sarcoma cell lines has further identified points of heterogeneity within sarcoma subtypes and can potentially be exploited to better identify and treat sarcoma patients based on their tumor profiles. Citation Format: Kazimierz O. Wrzeszczynski, Eric C. Polley, Curtis Hose, Anne Monks, Beverly A. Teicher. Identification and analysis of gene fusion and splice variant events in the NCI sarcoma cell line panel. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2361. doi:10.1158/1538-7445.AM2014-2361