Abstract 4087: Large intergenic noncoding RNAs associated with Ewing sarcoma family of tumors
Authors: Wai Daniel H. , Wu Dai-Ying , Wing Michele R. , Arceci Robert J. , Reynolds C Patrick , Sorensen Poul H. , Reamon Gregory H. , Milos Patrice M. , Lawlor Elizabeth R. , Buckley Jonathan D. , Kapranov Philipp , Triche Timothy J. 
Published: February 2011

Abstract
BACKGROUND: Ewing sarcoma family of tumors (EFT) represents the second most common primary malignant bone tumor in children and adolescents. The majority of EFTs harbor a translocation (t11;22)(q24;q12) resulting in the expression of the EWS-FLI1 chimeric oncoprotein. We hypothesized that microarray gene expression profiling, in combination with next-generation sequencing technology, could be used to identify EFT-specific genes and transcripts including large intergenic noncoding (linc)RNAs. Next-generation sequencing, coupled with target enrichment for validation, can also identify driver mutations of metastasis and treatment resistance in high-risk cases.
RESULTS: Genome-wide expression profiles of childhood sarcoma and normal tissues were analyzed using both Partek Genomics Suite as well as our own customized software, Genetrix. These are compared with Helicos single molecule sequencing data. The results show that both known genes and candidate lincRNAs strongly associate with EFT and can be used to distinguish EFT from other childhood tumors. Moreover, many lincRNAs are seen on both the poly-A selected track and on the random hexamer primed total RNA expression profile, indicating that the transcripts are multi-exonic and poly-adenylated. Importantly, regions of EFT-associated lincRNA expression may indicate regions that are deregulated by EWS-FLI1 in these tumors. We also focused on lincRNAs with differential expression in an EFT cell line pair (CHLA-9 and −10) derived, respectively, from patient-matched primary and metastatic tumors. RNA-seq determined ∼160,000 regions representing ∼16MB of genomic sequence as being at least 3-fold differentially expressed between the two cell lines. A higher threshold of at least 10-fold expression difference still revealed ∼20,000 regions representing ∼2MB of genomic sequence. In addition, the proportion of differentially-expressed intergenic transcripts was higher in CHLA-9 (18.1%) versus CHLA-10 (11.2%). Annotated transcripts with at least 10-fold expression in CHLA-10 are enriched in plasma membrane and adhesion-related functions, and this is consistent with metastatic behavior. Genes most highly expressed in CHLA-10 include ANXA5, FABP3, and HIST1H1A, whereas genes with much lower expression include CXCL14, MCTP2, and TRIM22. These genes, along with lincRNAs, may play important roles in disease progression and drug resistance.
CONCLUSIONS: We have identified several large intergenic noncoding (linc)RNAs that are highly and differentially expressed by EFT. We hypothesize that these lincRNAs may be novel therapeutic targets in EFT.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4087.