The Myogenesis Program Drives Clonal Selection and Drug Resistance in Rhabdomyosarcoma

Abstract

Rhabdomyosarcoma (RMS) is a pediatric cancer with features of skeletal muscle; patients with unresectable or metastatic RMS fare poorly due to high rates of disease recurrence. Here, we use single cell and single nucleus RNA-sequencing to show that RMS tumors recapitulate the spectrum of embryonal myogenesis. Using matched patient samples from a clinical trial and orthotopic patient-derived xenografts (O-PDXs), we show chemotherapy eliminates the most proliferative component with features of myoblasts; after treatment, the quiescent immature population with features of paraxial mesoderm expands to reconstitute the developmental hierarchy of the original tumor. We discovered that this paraxial mesoderm population is dependent on EGFR signaling and is sensitive to EGFR inhibitors. Taken together, this data serves as a proof-of-concept that targeting each developmental state in RMS is an effective strategy for improving outcomes by preventing disease recurrence.

Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma

“…As such, targeting this interaction could represent an opportunity to sensitize FP RMS tumours to immune-mediated killing through blocking of the TIGIT receptor, an approach which is currently being clinically evaluated for other tumour types 33 . Overall, we observed a higher proportion of T/NK cells, relative to myeloid cells (∼1:1), than has been previously described in studies utilizing immunohistochemistry 31,32 or scRNA-seq 28 . Additionally, beyond endothelial cells, we were unable to detect any other non-immune cell types in the TME, such as cancer associated fibroblasts (CAFs) or non-malignant skeletal muscle cells.…”

“…3b). These patterns were corroborated using a dataset from a recently published independent single-nucleus RNA-seq cohort of RMS tumours 28 (Extended Data Fig. 5b).…”

“…Notably, our proposed model of differentiation trajectories in RMS differs from that recently put forth by Patel et al 28 . In their analysis, a single trajectory explains both FN and FP RMS, whereby cells resembling paraxial mesoderm ( MEOX2 +, found mainly in FN tumours) connect to highly proliferative myoblast-like cells which in turn may give rise to (or derive from) a more differentiated myocyte-like state.…”

“…b , Scatter plot depicting the satellite cell-like (x-axis), myogenic (y-axis) and proliferative (colour) meta-program scores calculated in the data from Patel et. al (malignant FP cells) 28 . Vertical and horizontal lines depict the discrete cell-state cut-offs used in Fig.…”

Neuroblastoma: When differentiation goes awry

“…While those studies were useful in elucidating the clonal architecture of tumors before and after treatment, they provided little insight into the underlying phenotypes of the cells that survive treatment and contribute to clonal selection and disease recurrence (Figure 4). However, when combined with sc/ snRNA-seq analyses or other methods, researchers can begin to understand the properties of the cells that survive treatment and how they may change during clonal selection and evolution (Patel et al, 2022). This is particularly relevant for neuroblastoma because of the observation that ADR and MES cells can interconvert and have differential sensitivity to chemotherapy (Figures 4A and 4B).…”