WEHI Wednesday Seminar hosted by Professor Shalin Naik

Esmaeel Azadian

Research Officer – Naik Laboratory, Immunity division, WEHI

Clonal fitness is destined

Davis Auditorium

Join via SLIDO enter code #WEHIWednesday

Including Q&A session

Not all cell divisions are equal. Even among seemingly transcriptionally identical cells, growth rates of individual cells and their daughters (clones) can differ. In this way, some clones grow more than others, whether in tissues or in a culture flask. The long-standing assumption has been that this “clonal drift” is stochastic. But what if it reflects something more structured? 

I tracked the kinetics of thousands of individual clones over months-long timescales across two biologically distinct systems: normal human foreskin fibroblasts and human breast cancer cells (MDA-MB-231). Through cellular barcoding and clone splitting, some sibling cells were tracked in separate culture flasks in vitro over several months and others underwent single cell RNA seq analysis. The rationale was that if the kinetics of clonal fitness were concordant amongst daughters separated into different flasks, then growth was imprinted in the founder cell and heritable to daughters; if not, variation was stochastic. Across both systems, clonal kinetics were remarkably concordant, demonstrating that growth properties are stable, heritable, and clone-intrinsic.

Computational integration of clonal kinetics with transcriptome profiling of siblings split off early in the culture process then identified hidden gene expression programs (not identifiable through scRNA-seq alone with the clonal fate), which prospectively correlated with clonal fitness. Surprisingly, these were not prototypic cell cycle regulators and many were common between the two highly distinct fibroblast and breast cancer lineages, pointing to a putatively pan-tissue conserved program of fitness.  Through CRISPR activation and deletion experiments in human fibroblasts I then identified genes causative of clonal fitness, and testing cytometric separation of cells by different markers prior to culture found one predictive of future growth across multiple lineages.

These findings challenge the prevailing view that cellular heterogeneity is mere noise. If growth fate is heritable, a cell population’s trajectory may be destined long before it is observed - making heterogeneity not something to discount, but important structured variation with broad biological implications. By establishing that clonal fitness can be destined this study reveals something that may have been hiding in plain sight across decades of cell biology. 

All welcome!