Background Rhabdomyosarcoma (RMS) is the most common type of soft tissue sarcoma in the pediatric population. Outcomes for patients diagnosed with high-risk disease are dismal, yet therapeutic interventions have not changed in decades. Trials of immunotherapy have been unsuccessful in treating patients with RMS, but the reasons behind this failure are poorly explored and deep immune profiling of specimens from patients in trials was never performed. We aim to characterize the tumor immune microenvironment of RMS specimens to understand this failure of the immune system in RMS patients.

Methods Tumor specimens harvested from patients diagnosed with RMS at Johns Hopkins Hospital (surgery/biopsy for RMS tumors) were collected and divided so that one piece was fixed in formalin for immunohistochemistry experiments, one piece was used for generating single-cell suspensions containing tumor and immune cells for flow cytometry and single-cell RNA sequencing experiments, and one piece was frozen in RNAlater for transcriptome studies.

Results We immune profiled 51 human embryonal and alveolar rhabdomyosarcoma specimens via immunohistochemistry for CD3, CD20, CD4, CD8, CD21, Peripheral Node Addressin (PNAd), PD1, PD-L1, CD163 and demonstrated that within the tumor beds of RMS, chronic inflammatory signals lead to T and B-cell interactions to generate highly organized structures called tertiary lymphoid structures (TLS). These structures have been associated with better prognosis and better response to immunotherapy in different solid cancers. We then performed multiparameter flow cytometry analysis of immune cells from 15 RMS specimens and confirmed the presence of B and T-follicular helper cells along with the expression of prototypic TLS homeostatic chemokines including CXCR5 and CXCL13. Single-cell RNA sequencing (coupled with BCR and TCR sequencing) of 56,045 immune and tumor cells also validated the presence of a TLS signature and revealed oligoclonal expansion of B- and T-cells in the TME of RMS tumors. Most importantly, we performed Kaplan-Meier survival analysis and Cox-proportional hazards regression analysis of 30 RMS patients and showed that the presence of TLS correlates with better overall survival of RMS patients.

Conclusions Our data suggest that the presence of TLS could potentially be used in better evaluating the prognosis of RMS patients. It is of utmost importance to understand the mechanisms involved in TLS formation and their role in the immune response to tumor antigens, since understanding this mechanism could lead to elaboration of therapeutic interventions aimed at inducing TLS formation.