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

Abstract

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.