Abstract B023: ConFusion: The unexpected presence of non-coding RNA fusions in fusion-positive soft tissue sarcomas

Abstract Chromosomal translocations are commonly harbored in rare mesenchymal cancers known as soft tissue sarcomas (STS). These translocations often result in functional oncogenic fusion proteins which are pathognomonic for some STS. To study the transcriptional consequences of these aberrant chimeras across STS, we performed deep RNA sequencing on 39 patent samples with suspected fusion oncoproteins. Samples are representative of Ewing sarcoma, extraskeletal myxoid chondrosarcoma, clear cell sarcoma, myxoid/round cell liposarcoma, endometrial stromal sarcoma, and synovial sarcoma. Unexpectedly, we identified many unique and shared chimeric RNA across all samples including pathognomonic EWSR1 containing fusions as expected for specific subtypes. In Ewing sarcoma (EwS), EWSR1-FLI1 is the most common diagnostic fusion, which can occur via a balanced or complex translocation. Where a balanced translocation occurs, expression of both the canonical fusion (EWSR1-FLI1) and the reciprocal fusion (FLI1-EWSR1) may be seen. However, relatively little is known about the reciprocal fusion. Upon induction of a reciprocal construct in the EwS cell line A673, we identified differential gene expression of the noncoding RNAs including RN7SK, RN7SL1, RN7SL2, and RPPH1. RN7SK is a small nuclear RNA that regulates gene transcription by interacting with the positive transcription elongation factor b (P-TEFb) and plays a role in stem cell proliferation, differentiation, senescence, and apoptosis. Interestingly, noncoding RNA fusions with RN7SK chimera involving RNA pol III transcripts were the most abundant fusions identified across all STS tumors, though a functional role for these aberrant transcripts has not been defined. Wild type EWSR1 plays a role in RNA splicing, and these data suggest that EwS and EwS fusions may play a role in the regulation of ncRNA fusions and subsequently the disruption of normal RN7SK regulatory function. We aim to evaluate whether ncRNA fusions can also be identified in non-fusion driven sarcomas, at what point such ncRNA fusions may be arising in the central dogma, and what their function may be in sarcomagenesis. Further study regarding the function and consequences of these RNA fusions is required to understand their importance in disease initiation and progression. Citation Format: Emily Isenhart, Sarah Gawlak, Kristen Humphrey, Michalis Mastri, Scott Olejniczak, Miranda L. Lynch, Joyce Ohm. ConFusion: The unexpected presence of non-coding RNA fusions in fusion-positive soft tissue sarcomas [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Fusion-Positive Cancer: From Discovery to Therapy; 2026 Jan 13-15; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(1_Suppl):Abstract nr B023.