Mapping the Single-cell Differentiation Landscape of Osteosarcoma

Abstract

AbstractThe genetic and intratumoral heterogeneity observed in human osteosarcomas (OS) poses challenges for drug development and the study of cell fate, plasticity, and differentiation, processes linked to tumor grade, cell metastasis, and survival. To pinpoint errors in OS differentiation, we transcriptionally profiled 31,527 cells from a tissue-engineered model that directs MSCs toward adipogenic and osteoblastic fates. Incorporating pre-existing chondrocyte data, we applied trajectory analysis and non-negative matrix factorization (NMF) to generate the first human mesenchymal differentiation atlas. This ‘roadmap’ served as a reference to delineate the cellular composition of morphologically complex OS tumors and quantify each cell’s lineage commitment. Projecting these signatures onto a bulk RNA-seq OS dataset unveiled a correlation between a stem-like transcriptomic phenotype and poorer survival outcomes. Our study takes the critical first step in accurately quantifying OS differentiation and lineage, a prerequisite to better understanding global differentiation bottlenecks that might someday be targeted therapeutically.Statement of SignificanceOS treatment kills proliferating cells without addressing the root cause: dysregulated differentiation. By deconvolving OS tumors by cell type and differentiation archetype, we identified core gene sets linked to cell fate and patient survival. The ability to quantify, and eventually modulate, such archetypes facilitate a novel OS-specific drug-screening strategy.