Dissecting Persistent Cell Populations in Rhabdomyoscaroma

PROJECT SUMMARY Children with unresectable or metastatic solid tumors have continued to have poor outcomes and high recurrence rates. For example, in pediatric rhabdomyosarcoma (RMS), the most common childhood soft tissue sarcoma, 70% of patients with metastatic disease experience disease recurrence; after recurrence, 5-year overall survival drops below 20%. In previously published work, Dr. Patel generated a single-nucleus RNA- sequencing atlas of RMS to better clarify the diversity of malignant cell states within both fusion-negative RMS (FN-RMS) and fusion-positive RMS (FP-RMS). RMS tumors recapitulate the hierarchy of muscle cell states within normal embryogenesis. In FN-RMS, rare tumor cells that expressed genes reminiscent of paraxial mesoderm progenitors survive therapy, and these progenitor-like cells are sufficient to propagate FN-RMS tumors in xenografts. As such, progenitor-like cells represent a critical reservoir of therapy-tolerant cells within FN-RMS. Based off these findings, Dr. Patel will combine computational and experimental biology tools to investigate how cell state hierarchy is maintained within FN-RMS. In Aim 1, Dr. Patel will receive training in the application of systems biology computational algorithms to single-cell RNA-sequencing data and in chromatin profiling to dissect the transcriptional and epigenetic determinants of FN-RMS progenitor-like cell identity. In Aim 2, Dr. Patel will receive training in flow cytometric cell sorting and spatial proteomics to test whether progenitor- like cells undergo feedback control and interact with non-malignant cells of the tumor microenvironment. To support and mentor Dr. Patel, he has developed a career development plan that will be overseen by a diverse mentorship team including: his mentor, Dr. Michael Dyer, a distinguished developmental biologist with a long track record of developing patient-derived models of pediatric cancers, and advisors with expertise in epigenomics (Dr. Stephen Mack), systems biology (Dr. Jiyang Yu), clinical sarcoma treatment (Dr. Alberto Pappo), treatment persistence (Dr. Doug Green) and tumor-immune interactions (Dr. Paul Thomas). Additional collaboration from Dr. Jasmine Plummer and the St. Jude Center for Spatial Omics will provide technical support and guidance. This proposal will support Dr. Patel in the transition from mentored research to an independent career as a physician-scientist and will generate preliminary data to support a competitive R01 submission. By completing the plan outlined in this proposal, Dr. Patel will be poised to lead an impactful research program focused on overcoming the challenge of recurrence and drug persistence in pediatric solid tumors.