Subclonal heterogeneity and evolution in breast cancer

Abstract

Subclonal heterogeneity and evolution are characteristics of breast cancer that play a fundamental role in tumour development, progression and resistance to current therapies. In this review, we focus on the recent advances in understanding the epigenetic and transcriptomic changes that occur within breast cancer and their importance in terms of cancer development, progression and therapy resistance with a particular focus on alterations at the single-cell level. Furthermore, we highlight the utility of using single-cell tracing and molecular barcoding methodologies in preclinical models to assess disease evolution and response to therapy. We discuss how the integration of single-cell profiling from patient samples can be used in conjunction with results from preclinical models to untangle the complexities of this disease and identify biomarkers of disease progression, including measures of intra-tumour heterogeneity themselves, and how enhancing this understanding has the potential to uncover new targetable vulnerabilities in breast cancer.

Fig. 1. Pre-existing and acquired mechanisms of resistance to therapy in a model of clonal selection.

a Tumours consist of genetically and phenotypically diverse clones (represented in different colours). Selective pressure such as therapy will eliminate a percentage of sensitive clones leaving behind some pre-existing resistant clones with particular genomic aberrations. These clones are able to survive and expand leading to drug resistance mediated through the selection of pre-exitsing clones (represented as gene A–D). New genomic aberrations may also arise due to the selective pressures of therapy leading to acquired drug resistance (represented as gene E). Remaining clones that are resistant to therapy may also be due to additional unknown resistance mechanisms and they may be pre-existing and/or acquired. b Pre-existing and/or acquired drug resistance may be due to transcriptional and epigenetic mechanisms affecting gene expression or the communication of tumour cells with the microenvironment. This figure was created with BioRender.com and is adapted in part from the template 'tumour microenvironment 2'.

Fig. 2. Models tackling intra-TH in breast cancer.

Once the primary tumour is removed from a patient, the tumour sample is used for (1) initial clinical assessment and characterisation, followed by (2) PDX (patient material grown in mice) and (3) PDO (patient material directly grown ex vivo) establishment for research purposes and compared to the primary tumour sample. The remaining tumour is (4) dissociated to single cells, barcoded and (5) injected into the mammary glands of mice. Primary and matched metastatic tumours are removed from mice and subjected to (6) single-cell RNA sequencing, DNA sequencing and high throughput drug screenings thus (7) identifying the genetic, non-genetic make-up and evolution of these tumours at a single-cell level as well as identifying novel therapeutic strategies and biomarkers. This is then linked back into the analysis of patient samples in clinical trials. This figure was created with BioRender.com.