Modeling unveils sex differences of signaling networks in mouse embryonic stem cells

For a short period during early development of mammalian embryos, both X chromosomes in females are active, before dosage compensation is ensured through X‐chromosome inactivation. In female mouse embryonic stem cells (mESCs), which carry two active X chromosomes, increased X‐dosage affects cell signaling and impairs differentiation. The underlying mechanisms, however, remain poorly understood. To dissect X‐dosage effects on the signaling network in mESCs, we combine systematic perturbation experiments with mathematical modeling. We quantify the response to a variety of inhibitors and growth factors for cells with one (XO) or two X chromosomes (XX). We then build models of the signaling networks in XX and XO cells through a semi‐quantitative modeling approach based on modular response analysis. We identify a novel negative feedback in the PI3K/AKT pathway through GSK3. Moreover, the presence of a single active X makes mESCs more sensitive to the differentiation‐promoting Activin A signal and leads to a stronger RAF1‐mediated negative feedback in the FGF‐triggered MAPK pathway. The differential response to these differentiation‐promoting pathways can explain the impaired differentiation propensity of female mESCs.