Single-cell Transcriptomics reveals multi-step adaptations to endocrine therapy

Abstract

Resistant tumours are thought to arise from the action of Darwinian selection on genetically heterogenous cancer cell populations. However, simple clonal selection is inadequate to describe the late relapses often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. Partially, this is due to our limited understanding on the effect of ET at the single cell level. In the present study, we dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. Using single-cell RNA-sequencing and imaging we disentangle the transcriptional variability of plastic cells and define a rare sub-population of pre-adapted (PA) cells which undergoes further transcriptomic reprogramming and copy number changes to acquire full resistance. PA cells show reduced oestrogen receptor α activity but increased features of quiescence and migration. We find evidence for sub-clonal expression of this PA signature in primary tumours and for dominant expression in clustered circulating tumour cells. We propose a multi-step model for ET resistance development and advocate the use of stage-specific biomarkers.

Single cell transcriptomic heterogeneity in invasive ductal and lobular breast cancer cells

“…We examined genetic heterogeneity in cell lines using CNA inferred from scRNA-seq, a method described in multiple previous studies 18,29 . To test robustness and accuracy of this method, we incorporated two external 10X scRNA-seq datasets, which investigated the same cell lines (MCF7 and T47D cells cultured in standard media 29 , plus three different MCF7 strains 21 ). Different strains of the same cell type exhibited high resemblance to each other, as shown by coclustering of T47D CDH1 WT and KO cells with the external T47D dataset ( Fig.…”

Genetic Heterogeneity of Single Circulating Tumour Cells in Colorectal Carcinoma

“…The genetic characterisation of enriched CTCs could exhibit the global molecular portrait of the metastatic microenvironment [ 11 , 12 , 13 , 14 ]. However, it is unlikely to reveal the role of individual cancer cells due to the presence of other contaminated blood cells [ 1 , 10 ].…”

“…Besides, single-cell analysis requires a highly sensitive workflow to isolate the single CTCs from millions of lymphocytes and subsequent downstream experiments. Previous studies have shown that genetic profiles of single CTCs could display a comprehensive landscape of the molecular aberrations in the different signalling pathways and pinpoint new therapeutic targets [ 11 , 12 , 14 ]. Moreover, single-cell analysis of CTCs can exhibit discrepancies in the gene expression in different patients and within individual patient.…”

Intratumor heterogeneity: A new perspective on colorectal cancer research

“…They can also evolve into new subclones which transform the original sensitive group into a resistant colony after treatment. 76 This also provides an explanation for the emergence of novel subclones carrying KRAS mutations in liver metastases from wild-type RAS CRC patients treated with chemotherapy. 7 Apart from providing more resistant subclones by heterogeneous tumors in the face of selection, the interaction between subclones will also lead to stronger drug resistance.…”