Targeting Osteosarcoma heterogeneity to improve therapeutic response

Abstract

Intra tumor heterogeneity complicates cancer therapy by providing tumors with the ability to alter their phenotypes and become more therapy resistant. Here, we tested the hypothesis that identifying and modulating expression of key state-specific transcription factors could be used as a strategy for driving cells to a more therapy-sensitive state. Recent single-cell studies have explored the inter and intra tumoral heterogeneity of osteosarcoma and identified gene pathways enriched in specific cell states. For example, metastatic tumors are characterized by an expression of genes in the TNF-, PI3K, TGF{beta} and mTOR pathways. We identified similar profiles in osteosarcoma patient-derived xenograft-derived cell lines and potential transcription factor drivers of these states. We then used perturb-seq to downregulate expression of key transcription factors and evaluated the effect of these modulations on single cell RNA profiles and drug responses. Knockdown of NFE2L3 or NR0B1 increased the proportion of cells sensitive to targeted therapy. This approach, which could potentially be applied to other cancers, could be used as a strategy to increase the response to targeted therapies by increasing the proportion of cells in a drug-sensitive state. HighlightsO_LIDistinct transcriptomic states were identified in osteosarcoma cell lines using single-cell RNA sequencing. C_LIO_LILineage tracing identified states with differential sensitivity to therapy. C_LIO_LIUsing perturb-seq, we identified transcription factors that drive cells towards a more sensitive state. C_LIO_LIThe transcription factor NFE2L3 was identified as targets capable of reprogramming cells to a sensitive state. C_LI