Immune profiling of pleomorphic rhabdomyosarcoma

Pleomorphic rhabdomyosarcoma (PRMS) is a rare soft tissue tumor of the skeletal muscle that occurs predominantly in middle-aged adults. No standard systemic therapy options are available, and surgical resection is the most widely used treatment modality. For these types of rare cancers, obtaining molecular evidence would allow us to justify enrolling patients into basket trials with other sarcomas and tumor-types with similar molecular profiles. Our goal is to fully characterize PRMS at multiple levels: genomic, transcriptomic, epigenomic, and immunologic to build tumor profiles. Initial evidence from seven patients that we profiled at MD Anderson Cancer Center (MDACC) using whole exome and RNA sequencing showed that PRMS has predominantly TP53 and RB1 mutations, confirming the patients’ reported complex karyotypes. Their gene expression profiles cluster with a subset of undifferentiated pleomorphic sarcomas and leiomyosarcomas identified in the TCGA-SARC project. Thus, these features indicate that PRMS has similar prevalent somatic alterations as other pleomorphic and high-grade complex karyotype sarcomas such as leiomyosarcoma and osteosarcoma. Therefore, it may be possible to treat PRMS with similar therapies used for leiomyosarcoma and osteosarcoma. We are now expanding our cohort to PRMS specimens from University College London and Cleveland Clinic and are currently conducting deep whole genome, transcriptome, and methylation array analyses. In this proposal, we will focus on immune profiling the expanded cohort of the project. Immune profiling analyses will include T-cell receptor sequencing and multiplex immunofluorescent staining. T-cell receptor sequencing will determine the level of T-cell activation through the measures of T-cell expansion (clonality), allowing us to gain insights into the number of neoantigens that elicit T-cell responses (diversity). To examine other molecular features, the geographic distribution of T-cell activity, and the state of checkpoint pathways, we will conduct concurrent immunofluorescent staining of multiple immune markers (including two sets of T-cell activation and checkpoint markers) on whole-mount sections. These assays will be done in the MDACC Translational Molecular Pathology Immuno-profiling Lab. The output from these assays will be integrated with data obtained from the other platforms to generate subsets of patients who may benefit from specific types of targeted, immune and, more likely, combination therapies. The knowledge gained from these profiles will be used to both design preclinical models and to enroll patients in current and future immune therapy trials for sarcoma at MDACC.