Epigenetic determinants of cell plasticity and therapeutic response in osteosarcoma

Osteosarcoma is a genomically complex tumor characterized by structural rearrangements, aneuploidy, and large-scale chromosomal alterations. This complexity leads to widespread intertumoral heterogeneity, which has restricted clinical classification of osteosarcoma to mostly histopathological considerations and limited treatment options to chemotherapy. To discover molecular features for classification and treatment of this genomically complex tumor, we used epigenetic profiling (ATAC-seq and H3K27ac) and single-cell multiome analysis, which revealed two distinct cellular subtypes in osteosarcoma, i.e. “early osteoblast derived” (EOD), which exhibited upregulation of transcription factors associated with early bone development, and “late osteoblast derived” (LOD), which upregulates genes involved in late bone development. By integrating ATAC-seq with H3K27ac analysis, we defined critical superenhancers for these subtypes and defined core regulatory circuits (CRCs) that govern the underlying gene expression programs. We used a panel of PDX-derived cell lines to identify subtype-specific targeted therapies and found differential responses dependent on these cellular states. Taken together, we identified two epigenetically distinct subtypes of osteosarcoma that are controlled by state-specific transcription factors, and exhibit distinct drug responses. These findings create opportunities for exploiting targeted therapy strategies for osteosarcoma treatment and underscore the importance of defining epigenetic subtypes in cancers that are highly genomically complex.