Bulk RNA Sequencing of SUM159PT cells grown in 2D or from tumors formed in NOD mice. Bulk RNA Sequencing of SUM159PT cells grown in 2D or from tumors formed in NOD mice

Cancer is a heterogeneous disease, where multiple, phenotypically distinct subpopulations co-exist. Tumor evolution is a result of a complex interplay of genetic and epigenetic factors. To predict the molecular drivers of distinct cancer responses, we apply single-cell lineage tracing (scRNA-Seq of barcoded cells) on a triple-negative breast cancer model. We propose GALILEO, a framework providing lineage tracing, transcriptomic, and chromatin accessibility information simultaneously at single-cell resolution (Multiome ATAC + gene expression on barcoded cells). The combination of single-cell lineage tracing with phenotypic assays allows to link a cell state with its fate. Overall design: SUM159PT cells were cultivated in 2D dishes (N=6) or transplanted (100k cells) in vivo in the mammary fat pad of NOD mice and collected when the tumors (N=5) reached 1.2 cm (with a typical latency of 30 days). Bulk RNA-seq was used to compare the transcriptome of SUM159 derived tumors compared to cells grown in 2D