Spatial mitochondrial lineage tracing uncovers a premetastatic niche and microenvironment programmed fate switching in osteosarcoma

Abstract

Osteosarcoma progression involves complex spatiotemporal dynamics, yet the lineage relationships underlying tumor cell fate decisions remain poorly understood. Here we integrate single cell and spatial transcriptomics and mitochondrial variants-based lineage tracing to map the evolution of a late-stage, non-metastatic osteosarcoma. Single cell pseudotemporal reconstruction of malignant cells reveals a stepwise cascade of transcriptional programs that are associated with bifurcation of COL3A1+ progenitors into ALPL+ osteoblastic and THY+ mesenchymal lineages. Critically, we demonstrate that the metastatic THY1+ mesenchymal cell fate is not governed by cell-autonomous transcriptional programs alone; this pro-tumorigenic state is associated with spatial co-localization with PLVAP+ dysfunctional endothelia to form a pro-metastatic niche (THY1_Endo) enriched for PTN/NOTCH signaling. To distinguish clonal ancestry from microenvironmental plasticity, we leveraged spatially resolved somatic mitochondrial variants as endogenous lineage tracers. A spatial autocorrelation filter confirmed significant clonal spatial coherence (Z = 10.07, p {approx} 4 x 10-24). Phylogenetic reconstruction using a Wright-Fisher drift model coupled with a hidden Markov tree (WF-HMT) identified COL3A1+ cells as the ancestral tumour state with ALPL+ and THY1+ states acquired repeatedly and independently across the phylogeny. We propose a "time-space-lineage" relay model where sequential microenvironmental signals are associated with tumor cell fate and pre-metastatic niche assembly through clonal commitment. This multi dimensional framework bridges single cell states, spatial organization, temporal dynamics, and clonal ancestry - underscoring the power of somatic mitochondrial variants to resolve clonal history and intercept cancer evolution.