@article {142312, title = {A geometrical model of cell fate specification in the mouse blastocyst.}, journal = {Development}, volume = {151}, year = {2024}, month = {2024 Apr 15}, abstract = {

The lineage decision that generates the epiblast and primitive endoderm from the inner cell mass (ICM) is a paradigm for cell fate specification. Recent mathematics has formalized Waddington{\textquoteright}s landscape metaphor and proven that lineage decisions in detailed gene network models must conform to a small list of low-dimensional stereotypic changes called bifurcations. The most plausible bifurcation for the ICM is the so-called heteroclinic flip that we define and elaborate here. Our re-analysis of recent data suggests that there is sufficient cell movement in the ICM so the FGF signal, which drives the lineage decision, can be treated as spatially uniform. We thus extend the bifurcation model for a single cell to the entire ICM by means of a self-consistently defined time-dependent FGF signal. This model is consistent with available data and we propose additional dynamic experiments to test it further. This demonstrates that simplified, quantitative and intuitively transparent descriptions are possible when attention is shifted from specific genes to lineages. The flip bifurcation is a very plausible model for any situation where the embryo needs control over the relative proportions of two fates by a morphogen feedback.

}, keywords = {Animals, Blastocyst, Cell Differentiation, Cell Lineage, Endoderm, Fibroblast Growth Factors, Gene Expression Regulation, Developmental, Germ Layers, Mice, Models, Biological, Signal Transduction}, issn = {1477-9129}, doi = {10.1242/dev.202467}, author = {Raju, Archishman and Siggia, Eric D} } @article {129157, title = {A geometrical perspective on development.}, journal = {Dev Growth Differ}, year = {2023}, month = {2023 May 16}, abstract = {

Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Models of these networks are known to have more parameters than data can determine. Recent work, inspired by Waddington{\textquoteright}s metaphor of a landscape, has instead tried to understand the geometry of gene regulatory networks. Here, we describe recent results on the appropriate mathematical framework for constructing these landscapes. This allows the construction of minimally parameterized models consistent with cell behavior. We review existing examples where geometrical models have been used to fit experimental data on cell fate and describe how spatial interactions between cells can be understood geometrically.

}, issn = {1440-169X}, doi = {10.1111/dgd.12855}, author = {Raju, Archishman and Siggia, Eric D} } @article {99112, title = {Geometry of gene regulatory dynamics.}, journal = {Proc Natl Acad Sci U S A}, volume = {118}, year = {2021}, month = {2021 Sep 21}, abstract = {

Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types that elaborate this complexity results from the activity of gene networks and was likened by Waddington to a flow through a landscape in which valleys represent alternative fates. Geometric methods allow the formal representation of such landscapes and codify the types of behaviors that result from systems of differential equations. Results from Smale and coworkers imply that systems encompassing gene network models can be represented as potential gradients with a Riemann metric, justifying the Waddington metaphor. Here, we extend this representation to include parameter dependence and enumerate all three-way cellular decisions realizable by tuning at most two parameters, which can be generalized to include spatial coordinates in a tissue. All diagrams of cell states vs. model parameters are thereby enumerated. We unify a number of standard models for spatial pattern formation by expressing them in potential form (i.e., as topographic elevation). Turing systems appear nonpotential, yet in suitable variables the dynamics are low dimensional and potential. A time-independent embedding recovers the original variables. Lateral inhibition is described by a saddle point with many unstable directions. A model for the patterning of the eye appears as relaxation in a bistable potential. Geometric reasoning provides intuitive dynamic models for development that are well adapted to fit time-lapse data.

}, issn = {1091-6490}, doi = {10.1073/pnas.2109729118}, author = {Rand, David A and Raju, Archishman and S{\'a}ez, Meritxell and Corson, Francis and Siggia, Eric D} }