Using single cell RNA-seq to assess heterogeneous subpopulations and optimize therapeutic strategy in triple-negative breast cancer cells

Purpose: Triple Negative Breast Cancer (TNBC) is a particularly aggressive form of breast cancer with high intertumoral and intratumoral heterogeneity. Our overall goal in this study is to investigate the heterogeneity of TNBC, and develop effective combination therapy. Methods: We applied HCC1143 cell line as a representative of aggressive TNBC and performed single cell RNA-seq with 10x genomics platform for cells before and after paclitaxel treatment. Different cell subpopulations were identified with Seurat, and the relationship between different subpoulations were investigated with scEpath. Results: Different subpopulations were detected in TNBC cell populations. Targetable genes were identified and some of them were validated with drug. Overall design: Whole transcriptome profiles of HCC1143 cell populations for vehicle control and treated samples at 24h and 72h.