Single-Cell Transcriptomic Heterogeneity in Invasive Ductal and Lobular Breast Cancer Cells

Abstract

Invasive lobular breast carcinoma (ILC), one of the major breast cancer histological subtypes, exhibits unique clinical and molecular features compared to the other well-studied ductal cancer subtype (IDC). The pathognomonic feature of ILC is loss of E-cadherin, mainly caused by inactivating mutations within the CDH1 gene, but the extent of contribution of this genetic alteration to ILC-specific molecular characteristics remains largely understudied. To profile these features transcriptionally, we conducted single cell RNA sequencing on a panel of IDC and ILC cell lines, as well as an IDC cell line (T47D) with CRISPR-Cas9-mediated knock out (KO) of CDH1. Inspection of intra-cell line heterogeneity illustrated genetically and transcriptionally distinct subpopulations in multiple cell lines and highlighted rare populations of MCF7 cells highly expressing an apoptosis-related signature, positively correlated with a pre-adaptation signature to estrogen deprivation. Investigation of CDH1 KO-induced alterations showed transcriptomic membranous systems remodeling, elevated resemblance to ILCs in regulon activation, and suggests IRF1 as a potential mediator of reduced proliferation and increased cytokine-mediated immune-reactivity in ILCs..

Inferring Cell Subtypes and LncRNA Function by a Cell-Specific CeRNA Network in Breast Cancer

“…The scRNA-seq technique has become a powerful tool for the elucidation of intra-tumor and intra-cell line heterogeneity in breast cancer (2,23). Estrogen regulation generally involves not only individual molecules but also molecular networks.…”

“…The transcriptional regulation of estrogen receptor (ER) is an intricate network of signaling and functional processes that is still largely unknown at the single cell level. Recently, the intra-cell line heterogeneity of breast cancer has been comprehensively characterized through single-cell RNA sequencing (scRNA-seq), revealing transcriptomic subpopulations within cell lines (2). Therefore, investigating the heterogeneity of estrogen regulation at the single cell level could shed more light on estrogen mechanisms and potential breast cancer therapeutics.…”

Atlas of Lobular Breast Cancer Models: Challenges and Strategic Directions

“…Therefore, silencing or knockout of CDH1 in non-ILC cells has been considered a reasonable alternative to model ILC mechanistically. E-cadherin-null isogenic partners have been generated for human ER + NST lines MCF7 [90], T47D, and MDA-MB-468, the murine 4T1 cells [99], as well from the non-malignant breast epithelial MCF10A cells and primary cells isolated from normal breast tissue [100][101][102][103][104][105]. Interestingly, E-cadherin deficiency in non-ILC cells is insufficient to induce an EMT [100].…”

Subclonal heterogeneity and evolution in breast cancer

“…Interestingly, single-cell sequencing highlighted that these pre-adapted cells that display features of dormancy and mixed epithelial and mesenchymal traits are able to survive upon short-term endocrine therapy, however, these pathways are not seen in fully resistant cells, suggesting that the cells undergo further transcriptomic reprogramming to become fully resistant to endocrine therapy and to generate subsequent metastasis 79 . Additionally, single-cell sequencing of ER + cell lines has identified genetically and transcriptionally distinct subpopulations including rare populations of MCF7 cells highly expressing an apoptosis-related signature, positively correlated with a pre-adaptation signature to oestrogen deprivation 88 . These results suggest a multi-step mechanism of drug resistance to endocrine therapy where both genetic and nongenetic alterations contribute to this phenotype.…”