Abstract B011: Two epigenetically distinct cellular states in osteosarcoma are regulated by a cluster-specific set of pioneer transcription factors

Abstract

Abstract The Osteosarcoma (OS) genome is characterized by aneuploidy and dramatic structural rearrangements often leading to copy number gain and loss. There is significant heterogeneity between patients. Additionally, there is less known regarding the epigenetic heterogeneity within osteosarcoma and how this may impact critical phenotypes such as therapy response and metastasis. To characterize the osteosarcoma epigenome, we integrated ATAC-seq and RNA-seq across a unique set of patient samples, PDXs and PDX-derived cell lines obtained across the disease continuum and including biopsies, resections, and metastases. Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) analysis revealed the presence of two distinct epigenetic cell states. Differential chromatin accessibility between the clusters showed ~3000 unique open regions per cluster. Using GREAT to associate the differential genomic regions to genes, the enriched pathways of Cluster 1 (C1) are related to mesenchymal cell proliferation, skeletal system morphogenesis, osteoblast differentiation, and Wnt signaling pathway, whereas Cluster 2 (C2) enriched pathways are related to cell motility and migration, extracellular matrix organization and regulation of protein serine/threonine kinase activity. Accessible regions in the chromatin were enriched for a unique set of transcription factor binding sites. C1 accessible regions are enriched with transcription factor binding motifs (TFBM) related to development including RUNX2/3, MEOX2, HOXA2/5, VAX1/2, MEF, VSX and DLX; whereas members of AP1 complex including FOSL1/2, c-FOS, JUN are TFBM enriched in open regions in C2. This is correlated with high protein expression of these transcription factors in a cluster-specific manner and differential binding to chromatin. As expected, gene expression showed a positive correlation with accessible regions in promoters. RUNX2 plays a major role in chromatin remodeling in C1, modifying the chromatin accessibility of 5300 regions, most located in <1kb from the promoters. In conclusion, we uncovered two epigenetically cell states regulated by a cluster-specific set of transcription factors which are able to remodel the chromatin. Citation Format: Eunice Lopez Fuentes, Andrew Clugston, Leanne C. Sayles, E. Alejandro Sweet-Cordero. Two epigenetically distinct cellular states in osteosarcoma are regulated by a cluster-specific set of pioneer transcription factors [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B011.