Many cancer cells display vast cell-to-cell variability, but the processes that underlie how this clonal diversity is established, maintained, and inherited remain unclear. The cell surface phenotype, CD44+/CD24-, can be used to isolate aggressive, “stem-like” tumour cells that possess enhanced drug resistance and metastatic abilities in various models of cancer. Here, we show that distinct phenotypic equilibriums in the proportions of these aggressive cells exist across breast, ovarian, prostate and lung cancer cell lines. This baseline phenotypic equilibrium is re-established when subpopulations are sorted and replated, indicating cancer cells can transition through these different cellular states. In contrast, when individual cells are sorted and expanded as single-cell subclones, they display a spectrum of phenotypes. These phenotypic clonal biases are due to cell-intrinsic processes and are stable for more than 100 days in culture
In breast cancer cell lines, the diverse clonal phenotypes are paralleled by distinct molecular and functional properties. Transcriptional and chromatin accessibility profiling demonstrated that the clonal heterogeneity extends beyond the cell surface markers used for initial characterisation, and hundreds of genes are differentially regulated across clones. In vitro, the spectra of clones show distinct differences in cell size, growth rate and tumoursphere forming ability. In vivo, the clones have dramatic differences in their tumour initiating and metastatic capabilities. Interestingly, while the CD44/CD24 phenotype can predict in vivo tumour growth for some clones, others behave unexpectedly, suggesting another axis of clonal heterogeneity determines in vivo behaviour.
Our findings give insight into the dynamics of clonal memory and inheritance of clonal phenotypes in cancer. Ongoing efforts are centred on using this tractable model to identify novel mediators that regulate and maintain cells in this aggressive stem-like state, with the aim of identifying novel druggable targets that can be therapeutically leveraged to manipulate cellular phenotypes in cancer.