Single-cell allelic transcriptomic analysis unravels intratumoral gene expression heterogeneity linked to TNBC pathogenesis

Abstract

Triple-negative breast cancer (TNBC) is the most aggressive subclass of breast cancer, which exhibits high intratumoral heterogeneity. Intratumoral heterogeneity often drives the evolution of drug resistance towards tumour therapy in TNBC. However, the contributing factors and mechanisms behind the intratumoral heterogeneity in TNBC remain poorly understood. It has been implicated that copy number variations (CNVs) often create allelic imbalance and thereby contribute to intratumoral gene expression heterogeneity. However, other processes, such as epigenetic and transcriptional processes, can also contribute to allelic expression heterogeneity in tumour cells. Here, we have investigated how allelic expression heterogeneity contributes to intratumoral heterogeneity in TNBC by performing genome-wide allelic gene expression analysis, excluding most of the CNVs, using single-cell RNA-sequencing datasets. We found widespread monoallelic expression of many genes across different cell types of TNBC. Notably, we found a profound heterogeneity of allelic expression patterns of many genes within TNBC epithelial cells, creating distinct subpopulations of epithelial cells. Importantly, we show that these genes with allelic expression pattern heterogeneity between subpopulations are linked to TNBC immune-surveillance and drug-resistance related pathways, thereby overall shaping the pathogenesis outcomes. Finally, we show that the promoter regions of these genes with profound monoallelic expression are often hypermethylated in TNBC patients. Altogether, our findings reveal that heterogeneous allelic expression patterns contribute to intratumoral heterogeneity and are linked to TNBC pathogenesis.