Lineage tracing in rhabdoid tumor organoids and orthotopic xenografts reveals convergent transcriptional states

Malignant rhabdoid tumors (MRTs) are aggressive pediatric malignancies driven by loss of a single SWI/SNF subunit in an otherwise near-silent genome, yet they display extensive transcriptional heterogeneity. Whether this heterogeneity reflects the outgrowth of transcriptionally distinct clones, or states adopted independently of lineage, is unknown. Here we combined lentiviral lineage barcoding with single-cell RNA sequencing in two patient-derived renal MRT organoid models, followed through long-term in vitro culture and in a novel orthotopic xenograft setting. In both modalities, tumors and cultures became progressively restricted to a small number of lineages, and the clones that expanded were transcriptionally distinct from one another. Decomposing into gene expression programs showed that some transcriptional states were used broadly across lineages while others were confined to a few, and that lineages expanding independently, in separate cultures and separate animals, converged on the same restricted states. Individual lineages generally maintained their transcriptional identity across passaging and across anatomical sites, including in metastases, which arose from clones already expanded in the matched primary tumor. Which lineages came to dominate, however, differed between animals given the same starting population. Clonal outcome is therefore variable while the transcriptional states available to a tumor are drawn from a constrained and recurring repertoire.