Neveu Group
Systems biology of stem cell differentiation
Molecular cartography of stem cells: miRNA expression classifies pluripotent cells, cancer cells and differentiated cells. This map allows to follow quantitatively changes in cell identity such as differentiation and reprogramming. It reveals that reprogramming goes through a cancer-like behaviour.
Previous and current research
Pluripotent cells have the dual ability to self-renew and differentiate. Therefore, in pluripotent cells, the expression of hundreds of genes should be stable in the self-renewal case but gene expression can also be tipped in a coordinated manner towards particular states upon external signaling cues (lineage commitment towards terminal differentiation). Deciphering this complex problem has garnered much attention at the systems level.
Tackling this problem requires a good characterization of the pluripotent state: indeed the expression of Nanog, a key pluripotency factor, fluctuates over time in mouse embryonic stem cells (ESC) producing cells with a high or low Nanog state and different self-renewal behaviors. . miRNAs are good marker candidates because they are excellent classifiers of tissue types or cellular states. They also play a crucial role in differentiation. By profiling miRNA expression in human cells, we have previously shown that pluripotency emerges surprisingly as a much more diverse state than previously believed: variability in miRNA expression is comparable to the one found in differentiated cells and cancer cells. We have also shown that it is possible to dramatically reduce the complexity of miRNA expression patterns to a few meaningful dimensions. This reductionist approach still allows to quantitatively and robustly distinguish pluripotency, cancer and lineage commitment. More importantly it suggests that complex processes of the stem cell system such as differentiation and reprogramming can be mapped quantitatively.
Currently, we are employing a dynamic approach at the single cell level to resolve the dynamics of differentiation and the different molecular and cellular processes at play during fate determination. Indeed differentiation is intrinsically a dynamic process, where individual cells have to transition from one state to another. Having developed fluorescent reporters to assess miRNA expression in single cells, we are characterizing mouse ESC self-renewal using single cell live imaging.
Future projects and goals
We plan to study the dynamics of differentiation at the single cell level both in vitro in mouse embryonic stem cells and in vivo in zebrafish. The ultimate goal is to dissect the transcriptional regulation and gene networks underlying stem cell differentiation. We are taking an integrated systems biology approach that combines single cell live imaging of miRNA expression, image processing, perturbation approaches and mathematical modeling.
We wish to address the following questions:
- How dynamic is the pluripotent state?
- What are the in vitro dynamics of differentiation of mouse ESCs?
- What are the in vivo dynamics of differentiation during zebrafish development?