Single cell transcriptomic profiling identifies tumor-acquired and therapy-resistant cell states in pediatric rhabdomyosarcoma

Abstract

Rhabdomyosarcoma (RMS) is a pediatric tumor that resembles undifferentiated muscle cells; yet the extent to which cell state heterogeneity and molecular features are shared with human development have not been fully ascribed. Here, we report a single-cell/nucleus RNA sequencing atlas derived from 72 datasets that includes patient tumors, patient-derived xenografts, primary in vitro cultures, and established cell lines. We report four dominant muscle-lineage cell states in RMS: progenitors, proliferative, differentiated, and ground cells. We stratify these RMS cells along the continuum of human muscle development and show that RMS cells share expression patterns with fetal/embryonal myogenic precursors rather than postnatal satellite cells. Indeed, fusion-negative RMS (FN-RMS) have a discrete stem cell hierarchy that faithfully recapitulates fetal muscle development. We also identify therapy-resistant FN-RMS progenitor cells that share transcriptomic similarity with bipotent skeletal mesenchymal cells, while a subset of fusion-positive (FP) RMS have tumor-acquired cells states, including a neuronal cell state, that are not found in development. Chemotherapy induced upregulation of progenitor signatures in FN-RMS while the neuronal gene programs were retained after therapy in FP-RMS. Taken together, this work identifies new cell state heterogeneity including unique treatment-resistant and tumor-acquired cell states that differ across RMS subtypes.

Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo

“…Neuronal populations were also distinctly identified in FP-RMS patient and orthotopic patient-derived xenograft tumor samples from single-cell RNA-sequencing 53 . Critically, upon chemotherapeutic treatment in these xenograft models, this neuronal population was transcriptionally enriched, which would support a hypothesis that neural pathways drive FP-RMS therapeutic resistance 52 .…”

“…Single-cell RNA-sequencing of cell lines, orthotopic patient-derived xenograft models, and patient samples have shown that fusion-positive rhabdomyosarcoma consists of various cellular populations, including differentiated, ground, neuronal, progenitor, and proliferative [52][53][54][55][56] . To assess which transcriptional tumor cell populations PAX3::FOXO1 is initially activating, we completed gene set enrichment analysis to the markers of each of these cell populations.…”