Abstract 2851: Characterization of neogenes in desmoplastic small round cell tumors

Abstract Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, soft tissue sarcoma caused by the EWS: : WT1 fusion protein (FP). The FP acts as an aberrant transcription factor with oncogenic properties. Recently, oncogenic chimeric transcription factors (OCTF), such as EWS: : WT1, were discovered to induce the expression of novel transcripts in otherwise silent genomic regions. These neogenes (NGs) are highly specific to each OCTF and not detected in normal tissue. 37 NGs were found to be associated with the EWS: : WT1 FP. We explored the NGs to characterize their expression and regulation in a cohort of MD Anderson Cancer Center patients. We annotated and counted the NGs from the bulk RNA-seq data of 37 specimens. After fusion detection, only 22/37 specimens harbored the EWS: : WT1 FP. We found that only the same 22 specimens robustly expressed DSRCT-specific NGs. Interestingly the NGs were heterogeneously expressed, suggesting that there may be patient-specific differences. Single-nucleus RNA-sequencing (snRNA-seq) of Ewing sarcoma (ES), CIC: : DUX4 sarcoma (CDS), DSRCT, and osteosarcoma revealed that only the three sarcomas driven by an OCTF robustly expressed NGs. Notably, the DSRCT-specific NGs were only expressed in DSRCT. Similarly, ES and CDS only expressed their subtype-specific NGs. Given the robust expression of the DSRCT-specific NGs in DSRCT, we asked if the EWS: : WT1 FP regulated the expression of the NGs. Knockdown (KD) of the EWS: : WT1 FP in four DSRCT cell lines showed a consistent reduction in DSRCT-specific NGs. While there was variability in NG expression and EWS: : WT1 FP KD sensitivity, we identified seven NGs decreased by at least 75% in all four cell lines and an additional eight NGs with 75% reduction across three cell lines. BOD-DSRCT and SK-DSRCT2 had the largest number of NGs reduced after KD, with 25/37 and 20/37 NGs with 75% expression reduction, respectively. EWS: : WT1 FP has two known isoforms generated by alternative splicing in the WT1 domain that includes or excludes three amino acids, lysine, threonine, and serine (KTS) between zinc fingers 3 and 4, producing E+KTS and E-KTS isoforms. By transducing one or both isoforms into the mesothelial cell line LP9, we found 3/37 NGs were induced by the E+KTS isoform and 17/37 were induced by the E-KTS isoform, suggesting that the E-KTS isoform is primarily responsible for NG expression. Current work is underway investigating the relationship between EWS: : WT1 FP binding and NG expression and the potential for NG to produce novel peptides that could serve as DSRCT immunotherapy targets. Citation Format: Danh Truong, Justin Magrath, Sean Lee, Joseph Ludwig. Characterization of neogenes in desmoplastic small round cell tumors abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts) ; 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84 (6Suppl): Abstract nr 2851.