Effect of doxorubicin exposure in breast cancer on single-cell level by scRNA-seq analysis

Abstract: Doxorubicin is a highly effective chemotherapeutic agent against a variety of cancers; however, the exact mechanisms responsible for the effects of doxorubicin on cancer are not widely understood and have not been studied on a single-cell level. Single-cell RNA sequencing analysis is a recent technology that enables the assessment of transcriptional similarities and differences within a population of cells. This thesis aims to study the effects of doxorubicin in breast cancer on a single-cell level and see if there are differently affected subpopulations of cells. A single-cell RNA sequencing pipeline was developed in R and used to analyse breast cancer single-cells treated with doxorubicin. Quality control, filtering, cell-clustering, differently expression gene analysis, pathways analysis and cell type identification were performed. The results identified seven different subpopulations that demonstrated a differential expression of genes and expression-level of pathways such as NEIL3-mediated resolution of induced interstrand crosslinks related with the effect of doxorubicin on cancer cells. The analysis also suggests that two subpopulations of cells could consist of specific cell types potentially treatment-resistant. These findings reinforce the relation of doxorubicin effect on cancer with some important genes and pathways, as well as reaffirming the heterogeneity of breast cancer. As a novel contribution, the results show that different subpopulations of cells could be affected differently by doxorubicin exposure, but future studies with more samples should be performed to see if the analysis leads to similar results