Decoding gene expression heterogeneity in Triple Negative Breast Cancer [scRNA-seq]

In this study, we have employed both bulk RNA- and sc-RNA-seq to investigate the transcriptional status of TNBC cells, grown as 2D or 3D cultures, prior and after development of resistance to two widely used chemotherapeutic drugs, paclitaxel and doxorubicin. Our aim was to uncover the gene expression programs that support drug tolerance in treatment-naïve cells and drug resistance in heterogeneous chemoresistant populations. Analysis of the data from the two techniques yielded similar results to a large degree, yet several low abundance gene expression changes in the chemoresistant cells were detected only by scRNA-seq. Overall design: Targeted single cell RNA-seq experiments using the BD Rhapsody Onco-BC Panel and SUM159 attached or speroid cells untreated or chemoresistant to paclitaxel or doxorubicin, for a total of six populations. No replicates are provided. The BD Single-Cell multiplexing Ki SampleTags 1,2,3 are assigned to SUM159 attached untreated, paclitaxel or doxorubicin resistant respectively. The BD Single-Cell multiplexing Ki SampleTags 4,6,8 are assigned to SUM159 spheroid untreated, paclitaxel or doxorubicin resistant respectively.