Uncovering transcriptional changesrelated to cisplatin treatment andmixing of TNBC subclones usingsingle-cell RNA sequencing

Triple negative breast cancer (TNBC) has long been characterized by having a high degree of intratumoral heterogeneity. While significant contributions have been made in understanding the components of TNBC tumors, examining the dynamics of interaction between subclones in TNBC is relatively unexplored. By using single-cell RNA sequencing (scRNA-seq)technology, this study aims to focus on understanding changes in gene expression of two TNBC subclones: the cisplatin-resistant subclone (A50) and cisplatin-sensitive subclone (B), when co-cultured in 3D organoids in the presence and absence of cisplatin. We hypothesized that there will be significant differentially expressed genes (DEGs) due to various concentrations of cisplatin and mixing effect. We found DEGs (ACTB, FOS, EIF5, BRD2, MAFG, SF3B4, ID1,MGMT, DDIT4 and LPP) due to treatment with cisplatin in both subclones, with the largest clear effect present at a high concentration of cisplatin. Additionally, the network analysis showed that cisplatin was an upstream regulator for 11 DEGs. Even though, gene expression changes due to mixing are much more subtle than effects due to treatment, we saw some DEGs caused by the mixing effect like MT1X which is related to cisplatin resistance. Taken together, the findings of this project will help in future studies when deducing which genes to target in TNBC chemotherapy treatments based on predictive molecular biomarkers