Research Article

Cell competition during reprogramming gives rise to dominant clones

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Science  26 Apr 2019:
Vol. 364, Issue 6438, eaan0925
DOI: 10.1126/science.aan0925

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Domination in the stem cell world

A Nobel Prize–winning discovery showed that specialized cells can be genetically reprogrammed into stem cells, thus gaining the ability to become any cell type in the body. But what happens during reprogramming is not completely understood. Shakiba et al. used experimental and mathematical approaches to show that skin cells compete during reprogramming, eliminating one another as the population progresses toward the stem cell state (see the Perspective by Wolff and Purvis). The “winners” are a special class of skin cells originating from the neural crest. Cells of this type normally emerge during embryonic development and migrate into various tissues, including the skin, muscle, and nervous system.

Science, this issue p. eaan0925; see also p. 330

Structured Abstract

INTRODUCTION

Recent advances in lineage tracking using DNA-based barcoding technologies have provided new insights into the developmental dynamics of cell populations. Nevertheless, the mechanisms that govern these dynamics and their relation to clonal dominance remain unclear. Understanding the factors that determine the appearance and disappearance of individual clones and their derivatives in dynamic, heterogeneous systems has broad implications for normal and aberrant tissue development, providing a new lens with which to understand emergent behaviors in multicellular systems.

The process of reprogramming, whereby somatic cells are converted to induced pluripotent stem cells (iPSCs) through the overexpression of key transcription factors, serves as a tractable model to probe the connection between intrinsic and extrinsic factors influencing cell population dynamics. The field of reprogramming has largely accepted the “clonal equipotency” paradigm, in which somatic cells have an equal potential to attain an iPSC state; however, it remains unclear whether inequalities between the fitness of reprogramming cells drive non-neutral clonal drift.

RATIONALE

This study aimed to quantitatively explore the impact of competitive interactions in driving clonal dynamics within a reprogramming population. A cellular barcoding strategy, whereby heritable DNA tags are inserted into the genome of mouse embryonic fibroblasts (MEFs), was used to track the relative contribution of clonal derivatives to the reprogramming population. Mathematical modeling was used to decouple the effect of stochastic reprogramming latencies on clonal dynamics, enabling the identification of non-neutral clonal dominance. Finally, a mouse model was developed to trace the developmental origins of the heterogeneous MEF compartment and investigate the mechanism of cell fitness inequalities in reprogramming.

RESULTS

Population reprogramming promoted highly selective clonal dynamics, leading to the elimination of up to 80% of clones after a week of reprogramming. Single-cell reprogramming studies, on the other hand, suggested that all MEF-derived clones had a propensity to reprogram when cultured in isolation. Furthermore, an elite subset of dominating clones was found to drive the dynamics and composition of the bulk reprogramming pool. Early dominating clones that emerged after a week of reprogramming exhibited a robust and predictable propensity to overtake the culture and contribute to the final successfully reprogrammed iPSC pool. Our modeling results reveal that neutral effects did not capture the evolution of clone size distributions. Indeed, parallel reprogramming cultures grown from a common pool of barcoded MEFs demonstrated a correlation in clonal outcomes, driven by a subset of reprogramming MEFs. This subset of MEFs exhibited an a priori propensity for reprogramming and dominance. Lineage tracing revealed that these MEFs arise during embryonic development from a Wnt1-expressing population associable with the neural crest compartment.

CONCLUSION

This study reveals cell competition as an important parameter that arises in the population context as a result of genetically encoded inequalities in cell fitness. Competition serves as a mechanism by which otherwise hidden cells with context-specific eliteness emerge to occupy and dominate the reprogramming niche. Given the propensity for a small subset of clones to overtake the population, it is likely that bulk measurements of the reprogramming process represent a biased view of the reprogramming trajectory. The findings of this study reveal that cell competition may be a generalizable and controllable parameter for understanding and controlling the dynamics of multicellular developmental and disease systems in a quantified manner.

Competition during reprogramming results in dominant clones derived from elite cells.

(Top) During reprogramming, when MEFs transition to pluripotency, competition between cells leads to clonal selection and dominance. Numbered circles represent individual reprogramming clones; circle size indicates the relative abundance of cells derived from a clone in the overall population. (Bottom) Mathematical modeling reveals that clonal dynamics are not driven by stochastic reprogramming latencies, but rather by a subset of elite MEFs derived from the neural crest (NC) that have an enhanced a priori reprogramming propensity.

Abstract

The ability to generate induced pluripotent stem cells from differentiated cell types has enabled researchers to engineer cell states. Although studies have identified molecular networks that reprogram cells to pluripotency, the cellular dynamics of these processes remain poorly understood. Here, by combining cellular barcoding, mathematical modeling, and lineage tracing approaches, we demonstrate that reprogramming dynamics in heterogeneous populations are driven by dominant “elite” clones. Clones arise a priori from a population of poised mouse embryonic fibroblasts derived from Wnt1-expressing cells that may represent a neural crest–derived population. This work highlights the importance of cellular dynamics in fate programming outcomes and uncovers cell competition as a mechanism by which cells with eliteness emerge to occupy and dominate the reprogramming niche.

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