Abstract 2355: Intratumoral translocation positive heterogeneity in pediatric alveolar rhabdomyosarcoma tumors correlates to changes in genes predicted to inhibit the immunological response

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Abstract Alveolar rhabdomyosarcoma (ARMS) is characterized by one of three translocation states: t(2;13)(q35;q14) producing PAX3-FOXO1, t(1;13)(p36;q14) producing PAX7-FOXO1, or translocation-negative. Tumors with t(2;13) are associated with greater disease severity and mortality than t(1;13) positive or translocation negative patients. We demonstrated that ARMS tumor samples contain intratumoral genetic heterogeneity with respect to the presence of t(2;13). Further, we demonstrated that this heterogeneity had an inverse correlation with tumor aggressiveness, with tumors containing higher translocation positivity having lower failure-free survival of patients. However, it is not yet known whether a correlation exists between percent t(2;13) positivity and changes in gene expression, in particular genes whose function contributes to immune invasion in the tumor microenvironment. Of fifty-five rhabdomyosarcoma patient tumor samples received from Children’s Hospital in New Orleans, nine were confirmed to contain t(2;13) ranging from 16 - 98% cells positive for the translocation. We used aged-matched normal muscle tissue derived from autopsies as a control. RNA was isolated from whole tissue samples and analyzed using the Nanostring nCounter®️ PanCancer IO 360™ Panel. This panel contains 770 genes that specifically analyze tumor immunogenicity, tumor sensitivity to immune attack, inhibitory immune mechanisms, stromal factors, inhibitory metabolism, anti-tumor immune activity, inhibitory immune signaling, immune cell population and abundance, and tumor inflammation. We found 487 genes have an average change in expression ≥ 1.5-fold relative to the control. Of these genes 31 (6.4%) have a statistically significant positive correlation and nearly 25% (114 genes) had a statistically significant negative correlation to percent intratumoral translocation positivity. A closer examination indicated that genes with a negative correlation had biological functions that target a variety of different immunological processes. These include the recognition of antigen by T cells; the activation, maturation, and differentiation of lymphocytes and myeloid cells; adhesion of immune responsive cells; promotion of the inflammatory response; and activation of the innate immune response. These results suggest that increased intratumoral t(2;13) positivity negatively impacts the immunological response thereby increasing the ability for immune evasion of the tumors with higher levels of the translocation, a result consistent with our previously published work. Citation Format: Andrew D. Hollenbach, Matthew Stark, Jovanny Zabaleta, Fern Tsien. Intratumoral translocation positive heterogeneity in pediatric alveolar rhabdomyosarcoma tumors correlates to changes in genes predicted to inhibit the immunological response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2355.