Mapping the Single-cell Differentiation Landscape of Osteosarcoma

Abstract

The genetic 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 cells lineage commitment. Projecting a bulk RNA-seq OS dataset onto this roadmap 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 disease cause: dysregulated differentiation. Constructing a roadmap of mesenchymal differentiation enabled us to identify gene modules linked to OS cell fate and patient survival. This ability to characterize and quantify cancer cell fate enables a novel, differentiation-based drug-screening strategy.