Four simple rules that are sufficient to generate the mammalian blastocyst

The primitive endoderm supports lineage plasticity to enable regulative development

Mammalian blastocyst formation involves the specification of the trophectoderm followed by the differentiation of the inner cell mass into embryonic epiblast and extra-embryonic primitive endoderm (PrE). During this time, the embryo maintains a window of plasticity and can redirect its cellular fate when challenged experimentally. In this context, we found that the PrE alone was sufficient to regenerate a complete blastocyst and continue post-implantation development. We identify an in vitro population similar to the early PrE in vivo that exhibits the same embryonic and extra-embryonic potency and can form complete stem cell-based embryo models, termed blastoids. Commitment in the PrE is suppressed by JAK/STAT signaling, collaborating with OCT4 and the sustained expression of a subset of pluripotency-related transcription factors that safeguard an enhancer landscape permissive for multi-lineage differentiation. Our observations support the notion that transcription factor persistence underlies plasticity in regulative development and highlight the importance of the PrE in perturbed development.

Effective mechanical potential of cell-cell interaction in tissues harboring cavity and in cell sheet toward morphogenesis

Measuring mechanical forces of cell-cell interactions is important for studying morphogenesis in multicellular organisms. We previously reported an image-based statistical method for inferring effective mechanical potentials of pairwise cell-cell interactions by fitting cell tracking data with a theoretical model. However, whether this method is applicable to tissues with non-cellular components such as cavities remains elusive. Here we evaluated the applicability of the method to cavity-harboring tissues. Using synthetic data generated by simulations, we found that the effect of expanding cavities was added to the pregiven potentials used in the simulations, resulting in the inferred effective potentials having an additional repulsive component derived from the expanding cavities. Interestingly, simulations by using the effective potentials reproduced the cavity-harboring structures. Then, we applied our method to the mouse blastocysts, and found that the inferred effective potentials can reproduce the cavity-harboring structures. Pairwise potentials with additional repulsive components were also detected in two-dimensional cell sheets, by which curved sheets including tubes and cups were simulated. We conclude that our inference method is applicable to tissues harboring cavities and cell sheets, and the resultant effective potentials are useful to simulate the morphologies.

A geometrical model of cell fate specification in the mouse blastocyst

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'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.

Contributions of cell behavior to geometric order in embryonic cartilage

During early development, cartilage provides shape and stability to the embryo while serving as a precursor for the skeleton. Correct formation of embryonic cartilage is hence essential for healthy development. In vertebrate cranial cartilage, it has been observed that a flat and laterally extended macroscopic geometry is linked to regular microscopic structure consisting of tightly packed, short, transversal clonar columns. However, it remains an ongoing challenge to identify how individual cells coordinate to successfully shape the tissue, and more precisely which mechanical interactions and cell behaviors contribute to the generation and maintenance of this columnar cartilage geometry during embryogenesis. Here, we apply a three-dimensional cell-based computational model to investigate mechanical principles contributing to column formation. The model accounts for clonal expansion, anisotropic proliferation and the geometrical arrangement of progenitor cells in space. We confirm that oriented cell divisions and repulsive mechanical interactions between cells are key drivers of column formation. In addition, the model suggests that column formation benefits from the spatial gaps created by the extracellular matrix in the initial configuration, and that column maintenance is facilitated by sequential proliferative phases. Our model thus correctly predicts the dependence of local order on division orientation and tissue thickness. The present study presents the first cell-based simulations of cell mechanics during cranial cartilage formation and we anticipate that it will be useful in future studies on the formation and growth of other cartilage geometries.

A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation

Cooperative DNA binding of transcription factors (TFs) integrates the cellular context to support cell specification during development. Naive mouse embryonic stem cells are derived from early development and can sustain their pluripotent identity indefinitely. Here, we ask whether TFs associated with pluripotency evolved to directly support this state or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is absent, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB allows quantitative titration of this differentiation, and in silico modeling of bipartite ESRRB activity suggests it safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of immortal stem cells. A record of this paper's transparent peer review process is included in the supplemental information.

Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing

During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular signaling. We present an analytically tractable mathematical model based on signaling that reliably generates different cell type patterns with specified proportions. Employing statistical mechanics, We derived a cell fate decision model for two cell types. A detailed steady state analysis on the resulting dynamical system yielded necessary conditions to generate spatially heterogeneous patterns. This allows the cell type proportions to be controlled by a single model parameter. Cell-cell communication is realized by local and global signaling mechanisms. These result in different cell type patterns. A nearest neighbor signal yields checkerboard patterns. Increasing the signal dispersion, cell fate clusters and an engulfing pattern can be generated. Altogether, the presented model allows us to reliably generate heterogeneous cell type patterns of different kinds as well as desired proportions.

Effective mechanical potential of cell-cell interaction explains three-dimensional morphologies during early embryogenesis

Mechanical forces are critical for the emergence of diverse three-dimensional morphologies of multicellular systems. However, it remains unclear what kind of mechanical parameters at cellular level substantially contribute to tissue morphologies. This is largely due to technical limitations of live measurements of cellular forces. Here we developed a framework for inferring and modeling mechanical forces of cell-cell interactions. First, by analogy to coarse-grained models in molecular and colloidal sciences, we approximated cells as particles, where mean forces (i.e. effective forces) of pairwise cell-cell interactions are considered. Then, the forces were statistically inferred by fitting the mathematical model to cell tracking data. This method was validated by using synthetic cell tracking data resembling various in vivo situations. Application of our method to the cells in the early embryos of mice and the nematode Caenorhabditis elegans revealed that cell-cell interaction forces can be written as a pairwise potential energy in a manner dependent on cell-cell distances. Importantly, the profiles of the pairwise potentials were quantitatively different among species and embryonic stages, and the quantitative differences correctly described the differences of their morphological features such as spherical vs. distorted cell aggregates, and tightly vs. non-tightly assembled aggregates. We conclude that the effective pairwise potential of cell-cell interactions is a live measurable parameter whose quantitative differences can be a parameter describing three-dimensional tissue morphologies.

Biophysical models of early mammalian embryogenesis

Embryo development is a critical and fascinating stage in the life cycle of many organisms. Despite decades of research, the earliest stages of mammalian embryogenesis are still poorly understood, caused by a scarcity of high-resolution spatial and temporal data, the use of only a few model organisms, and a paucity of truly multidisciplinary approaches that combine biological research with biophysical modeling and computational simulation. Here, we explain the theoretical frameworks and biophysical processes that are best suited to modeling the early mammalian embryo, review a comprehensive list of previous models, and discuss the most promising avenues for future work.

Seven challenges in the multiscale modeling of multicellular tissues

The growth and dynamics of multicellular tissues involve tightly regulated and coordinated morphogenetic cell behaviors, such as shape changes, movement, and division, which are governed by subcellular machinery and involve coupling through short- and long-range signals. A key challenge in the fields of developmental biology, tissue engineering and regenerative medicine is to understand how relationships between scales produce emergent tissue-scale behaviors. Recent advances in molecular biology, live-imaging and ex vivo techniques have revolutionized our ability to study these processes experimentally. To fully leverage these techniques and obtain a more comprehensive understanding of the causal relationships underlying tissue dynamics, computational modeling approaches are increasingly spanning multiple spatial and temporal scales, and are coupling cell shape, growth, mechanics, and signaling. Yet such models remain challenging: modeling at each scale requires different areas of technical skills, while integration across scales necessitates the solution to novel mathematical and computational problems. This review aims to summarize recent progress in multiscale modeling of multicellular tissues and to highlight ongoing challenges associated with the construction, implementation, interrogation, and validation of such models. This article is categorized under: Reproductive System Diseases > Computational Models Metabolic Diseases > Computational Models Cancer > Computational Models.

The effects of embryo splitting on Cdx2, Sox2, Oct4, and Nanog gene expression in mouse blastocysts

Background

Embryo splitting is utilized in reproduction biotechnology. The blastomeres resulting from the splitting of an embryo in two-, four- or eight-cell stages can develop into separate embryos that are genetically similar to the other blastomeres.

Aims

The present work studied the effects of splitting on embryo pluripotent gene expression (Cdx2, Sox2, Oct4, and Nanog) in mice.

Methods

Two-cell embryos were isolated from stimulated mice. The embryos were grouped into "split" and "non-split" groups. The zona pellucida was removed from the split group and the blastomeres were distributed before being co-cultured with mouse embryo fibroblasts to the blastocyst stage. Normal (non-split) blastocysts were co-cultured in the same way. The 3.5-day-old blastomeres were collected as the control group. For molecular evaluation, real-time PCR was conducted to analyze changes in Cdx2, Sox2, Oct4, and Nanog gene expression. Moreover, the blastocyst formation rate, overall blastocyst rate, and the number of newborns were statistically analyzed.

Results

The findings showed that embryo splitting increased blastocyst formation, overall blastocysts, developmental potential embryos, and the number of infants. Furthermore, the split and non-split (control) groups showed equal expression of pluripotent genes (Cdx2, Sox2, Oct4, and Nanog) in the molecular analysis.

Conclusion

It can be concluded that the growth and developmental potency of sister blastocysts derived from split two-cell stage mouse embryos are the same as those of normal blastocysts. So, there are no significant differences in gene expression between the split and non-split groups.

A theoretical understanding of mammalian preimplantation development

The blastocyst has long been a hallmark system of study in developmental biology due to its importance in mammalian development and clinical relevance for assisted reproductive technologies. In recent years, the blastocyst is emerging as a system of study for mathematical modelling. In this review, we compile, to our knowledge, all models describing preimplantation development. Coupled with experiments, these models have provided insight regarding the morphogenesis and cell-fate specification throughout preimplantation development. In the case of cell-fate specification, theoretical models have provided mechanisms explaining how proportion of cell types are established and maintained when confronted to perturbations. For cell-shape based models, they have described quantitatively how mechanical forces sculpt the blastocyst and even predicted how morphogenesis could be manipulated. As theoretical biology develops, we believe the next critical stage in modelling involves an integration of cell fate and mechanics to provide integrative models of development at distinct spatiotemporal scales. We discuss how, building on a balanced base of mechanical and chemical models, the preimplantation embryo will play a key role in integrating these two faces of the same coin.

Human embryo polarization requires PLC signaling to mediate trophectoderm specification

Apico-basal polarization of cells within the embryo is critical for the segregation of distinct lineages during mammalian development. Polarized cells become the trophectoderm (TE), which forms the placenta, and apolar cells become the inner cell mass (ICM), the founding population of the fetus. The cellular and molecular mechanisms leading to polarization of the human embryo and its timing during embryogenesis have remained unknown. Here, we show that human embryo polarization occurs in two steps: it begins with the apical enrichment of F-actin and is followed by the apical accumulation of the PAR complex. This two-step polarization process leads to the formation of an apical domain at the 8-16 cell stage. Using RNA interference, we show that apical domain formation requires Phospholipase C (PLC) signaling, specifically the enzymes PLCB1 and PLCE1, from the eight-cell stage onwards. Finally, we show that although expression of the critical TE differentiation marker GATA3 can be initiated independently of embryo polarization, downregulation of PLCB1 and PLCE1 decreases GATA3 expression through a reduction in the number of polarized cells. Therefore, apical domain formation reinforces a TE fate. The results we present here demonstrate how polarization is triggered to regulate the first lineage segregation in human embryos.

A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development

During early mammalian embryo development, a small number of cells make robust fate decisions at particular spatial locations in a tight time window to form inner cell mass (ICM), and later epiblast (Epi) and primitive endoderm (PE). While recent single-cell transcriptomics data allows scrutinization of heterogeneity of individual cells, consistent spatial and temporal mechanisms the early embryo utilize to robustly form the Epi/PE layers from ICM remain elusive. Here we build a multiscale three-dimensional model for mammalian embryo to recapitulate the observed patterning process from zygote to late blastocyst. By integrating the spatiotemporal information reconstructed from multiple single-cell transcriptomic datasets, the data-informed modeling analysis suggests two major processes critical to the formation of Epi/PE layers: a selective cell-cell adhesion mechanism (via EphA4/EphrinB2) for fate-location coordination and a temporal attenuation mechanism of cell signaling (via Fgf). Spatial imaging data and distinct subsets of single-cell gene expression data are then used to validate the predictions. Together, our study provides a multiscale framework that incorporates single-cell gene expression datasets to analyze gene regulations, cell-cell communications, and physical interactions among cells in complex geometries at single-cell resolution, with direct application to late-stage development of embryogenesis.

Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach

During the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first decision, the trophectoderm and the inner cell mass are formed. Subsequently, the inner cell mass segregates into the epiblast and the primitive endoderm. Inner cell mass organoids represent an experimental model system, mimicking the second cell fate decision. It has been shown that cells of the same fate tend to cluster stronger than expected for random cell fate decisions. Three major processes are hypothesised to contribute to the cell fate arrangements: (1) chemical signalling; (2) cell sorting; and (3) cell proliferation. In order to quantify the influence of cell proliferation on the observed cell lineage type clustering, we developed an agent-based model accounting for mechanical cell-cell interaction, i.e. adhesion and repulsion, cell division, stochastic cell fate decision and cell fate heredity. The model supports the hypothesis that initial cell fate acquisition is a stochastically driven process, taking place in the early development of inner cell mass organoids. Further, we show that the observed neighbourhood structures can emerge solely due to cell fate heredity during cell division.

Measuring and Modeling Single-Cell Heterogeneity and Fate Decision in Mouse Embryos

Cellular heterogeneity is a property of any living system; however, its relationship with cellular fate decision remains an open question. Recent technological advances have enabled valuable insights, especially in complex systems such as the mouse embryo. In this review, we discuss recent studies that characterize cellular heterogeneity at different levels during mouse development, from the two-cell stage up to gastrulation. In addition to key experimental findings, we review mathematical modeling approaches that help researchers interpret these findings. Disentangling the role of heterogeneity in cell fate decision will likely rely on the refined integration of experiments, large-scale omics data, and mathematical modeling, complemented by the use of synthetic embryos and gastruloids as promising in vitro models.

Coordination between patterning and morphogenesis ensures robustness during mouse development

The mammalian preimplantation embryo is a highly tractable, self-organizing developmental system in which three cell types are consistently specified without the need for maternal factors or external signals. Studies in the mouse over the past decades have greatly improved our understanding of the cues that trigger symmetry breaking in the embryo, the transcription factors that control lineage specification and commitment, and the mechanical forces that drive morphogenesis and inform cell fate decisions. These studies have also uncovered how these multiple inputs are integrated to allocate the right number of cells to each lineage despite inherent biological noise, and as a response to perturbations. In this review, we summarize our current understanding of how these processes are coordinated to ensure a robust and precise developmental outcome during early mouse development. This article is part of a discussion meeting issue 'Contemporary morphogenesis'.

Direct analysis of brain phenotypes via neural blastocyst complementation

We provide a protocol for generating forebrain structures in vivo from mouse embryonic stem cells (ESCs) via neural blastocyst complementation (NBC). We developed this protocol for studies of development and function of specific forebrain regions, including the cerebral cortex and hippocampus. We describe a complete workflow, from methods for modifying a given genomic locus in ESCs via CRISPR-Cas9-mediated editing to the generation of mouse chimeras with ESC-reconstituted forebrain regions that can be directly analyzed. The procedure begins with genetic editing of mouse ESCs via CRISPR-Cas9, which can be accomplished in ~4-8 weeks. We provide protocols to achieve fluorescent labeling of ESCs in ~2-3 weeks, which allows tracing of the injected, ESC-derived donor cells in chimeras generated via NBC. Once modified ESCs are ready, NBC chimeras are generated in ~3 weeks via injection of ESCs into genetically programmed blastocysts that are subsequently transferred into pseudo-pregnant fosters. Our in vivo brain organogenesis platform is efficient, allowing functional and systematic analysis of genes and other genomic factors in as little as 3 months, in the context of a whole organism.

From pluripotency to totipotency: an experimentalist's guide to cellular potency

Embryonic stem cells (ESCs) are derived from the pre-implantation mammalian blastocyst. At this point in time, the newly formed embryo is concerned with the generation and expansion of both the embryonic lineages required to build the embryo and the extra-embryonic lineages that support development. When used in grafting experiments, embryonic cells from early developmental stages can contribute to both embryonic and extra-embryonic lineages, but it is generally accepted that ESCs can give rise to only embryonic lineages. As a result, they are referred to as pluripotent, rather than totipotent. Here, we consider the experimental potential of various ESC populations and a number of recently identified in vitro culture systems producing states beyond pluripotency and reminiscent of those observed during pre-implantation development. We also consider the nature of totipotency and the extent to which cell populations in these culture systems exhibit this property.

Growth-factor-mediated coupling between lineage size and cell fate choice underlies robustness of mammalian development

Precise control and maintenance of population size is fundamental for organismal development and homeostasis. The three cell types of the mammalian blastocyst are generated in precise proportions over a short time, suggesting a mechanism to ensure a reproducible outcome. We developed a minimal mathematical model demonstrating growth factor signaling is sufficient to guarantee this robustness and which anticipates an embryo's response to perturbations in lineage composition. Addition of lineage-restricted cells both in vivo and in silico, causes a shift of the fate of progenitors away from the supernumerary cell type, while eliminating cells using laser ablation biases the specification of progenitors toward the targeted cell type. Finally, FGF4 couples fate decisions to lineage composition through changes in local growth factor concentration, providing a basis for the regulative abilities of the early mammalian embryo whereby fate decisions are coordinated at the population level to robustly generate tissues in the right proportions.

Why and how the nematode's early embryogenesis can be precise and robust: a mechanical perspective

The early embryogenesis in the nematode Caenorhabditis elegans is well-known for its stereotypic precision of cell arrangements and their lineage relationship. Much research has been focused on how biochemical processes achieve the highly reproducible cell lineage tree. However, the origin of the robustness in the cell arrangements is poorly understood. Here, we set out to provide a mechanistic explanation of how combining mechanical forces with the order and orientation of cell division ensures a robust arrangement of cells. We used a simplified mechanical model to simulate the arrangement of cells in the face of different disturbances. As a result, we revealed three fail-safe principles for cell self-organization in early nematode embryogenesis: ordering, simultaneity, and the division orientation of cell division events. Our work provides insight into the developmental strategy and contributes to the understanding of how robust or variable the cell arrangement can be in developing embryos.

Self-Similar Dynamics of Nuclear Packing in the Early Drosophila Embryo

Embryonic development starts with cleavages, a rapid sequence of reductive divisions that result in an exponential increase of cell number without changing the overall size of the embryo. In Drosophila, the final four rounds of cleavages occur at the surface of the embryo and give rise to ∼6000 nuclei under a common plasma membrane. We use live imaging to study the dynamics of this process and to characterize the emergent nuclear packing in this system. We show that the characteristic length scale of the internuclear interaction scales with the density, which allows the densifying embryo to sustain the level of structural order at progressively smaller length scales. This is different from nonliving materials, which typically undergo disorder-order transition upon compression. To explain this dynamics, we use a particle-based model that accounts for density-dependent nuclear interactions and synchronous divisions. We reproduce the pair statistics of the disordered packings observed in embryos and recover the scaling relation between the characteristic length scale and the density both in real and reciprocal space. This result reveals how the embryo can robustly preserve the nuclear-packing structure while being densified. In addition to providing quantitative description of self-similar dynamics of nuclear packings, this model generates dynamic meshes for the computational analysis of pattern formation and tissue morphogenesis.

Transitions in cell potency during early mouse development are driven by Notch

The Notch signalling pathway plays fundamental roles in diverse developmental processes in metazoans, where it is important in driving cell fate and directing differentiation of various cell types. However, we still have limited knowledge about the role of Notch in early preimplantation stages of mammalian development, or how it interacts with other signalling pathways active at these stages such as Hippo. By using genetic and pharmacological tools in vivo, together with image analysis of single embryos and pluripotent cell culture, we have found that Notch is active from the 4-cell stage. Transcriptomic analysis in single morula identified novel Notch targets, such as early naïve pluripotency markers or transcriptional repressors such as TLE4. Our results reveal a previously undescribed role for Notch in driving transitions during the gradual loss of potency that takes place in the early mouse embryo prior to the first lineage decisions.

We start life as a single cell, which immediately begins to divide to form an embryo that will eventually contain all the different kinds of cells found in the adult body. During the first few rounds of cell division, embryonic cells can become any type of adult cells, but also form the placenta, the organ that sustains the embryo while in the womb. As cells keep on dividing, they lose this ability, called potency, and they take on more specific and inflexible roles.

The first choice embryonic cells must make is whether to become part of the placenta or part of the future body. These types of decisions are controlled by molecular cascades known as signalling pathways, which relay information from the cells surface to its control centre. There, specific genes get turned on or off in response to an outside signal.

Previous research showed that two signalling pathways, Hippo and Notch, help separate placenta cells from those that will form the rest of the body. However, it was not known whether the two pathways worked independently, or if they were overlapping. Menchero et al. therefore wanted to find out when exactly the Notch pathway started to be active, and examine how it helped cells to either become the placenta or part of the future body.

Experiments with developing mouse embryos showed that the Notch pathway was activated after the very first two cell divisions, when the embryo consists of only four cells. Genetic manipulations combined with drug treatments that changed the activity of the Notch pathway confirmed that Notch and Hippo acted independently at this stage. Further, larger-scale analysis of gene activity in these embryos also revealed that Notch signalling was working in a previously unknown way: it turned off the genes that maintain potency, pushing the cells to become more specialised.

Ultimately, identifying this new mode of action for the Notch pathway in the early embryo may help to understand how the signalling cascade acts in other types of processes. This knowledge could be useful, for example, to push embryonic cells grown in the laboratory towards a desired fate.

Agent-based modeling of morphogenetic systems: Advantages and challenges

The complexity of morphogenesis poses a fundamental challenge to understanding the mechanisms governing the formation of biological patterns and structures. Over the past century, numerous processes have been identified as critically contributing to morphogenetic events, but the interplay between the various components and aspects of pattern formation have been much harder to grasp. The combination of traditional biology with mathematical and computational methods has had a profound effect on our current understanding of morphogenesis and led to significant insights and advancements in the field. In particular, the theoretical concepts of reaction–diffusion systems and positional information, proposed by Alan Turing and Lewis Wolpert, respectively, dramatically influenced our general view of morphogenesis, although typically in isolation from one another. In recent years, agent-based modeling has been emerging as a consolidation and implementation of the two theories within a single framework. Agent-based models (ABMs) are unique in their ability to integrate combinations of heterogeneous processes and investigate their respective dynamics, especially in the context of spatial phenomena. In this review, we highlight the benefits and technical challenges associated with ABMs as tools for examining morphogenetic events. These models display unparalleled flexibility for studying various morphogenetic phenomena at multiple levels and have the important advantage of informing future experimental work, including the targeted engineering of tissues and organs.

Theoretical tool bridging cell polarities with development of robust morphologies

Despite continual renewal and damages, a multicellular organism is able to maintain its complex morphology. How is this stability compatible with the complexity and diversity of living forms? Looking for answers at protein level may be limiting as diverging protein sequences can result in similar morphologies. Inspired by the progressive role of apical-basal and planar cell polarity in development, we propose that stability, complexity, and diversity are emergent properties in populations of proliferating polarized cells. We support our hypothesis by a theoretical approach, developed to effectively capture both types of polar cell adhesions. When applied to specific cases of development – gastrulation and the origins of folds and tubes – our theoretical tool suggests experimentally testable predictions pointing to the strength of polar adhesion, restricted directions of cell polarities, and the rate of cell proliferation to be major determinants of morphological diversity and stability.

Cells have the power to organise themselves to form complex and stable structures, whether it is to create a fully shaped baby from a single egg, or to allow adult salamanders to grow a new limb after losing a leg. This ability has been scrutinised at many different levels. For example, researchers have looked at the chemical messages exchanged by cells, or they have recorded the different shapes an embryo goes through during development. However, it is still difficult to reconcile the information from these approaches into a description that makes sense at multiple scales.

When an embryo develops, sheets of cells fold and unfold to create complex 3D shapes, like the tubes that make our lungs. Moulding sheets into tubes relies on interactions between cells that are not the same in all directions. In fact, two types of asymmetry (or polarity) guide these interactions. Apical-basal polarity runs across a sheet of cells, which means that the top surface of the sheet differs from the bottom. Planar cell polarity runs along the sheet and distinguishes one end from the other. For instance, apical-basal polarity marks the inner and outer surfaces of our skin, while planar cell polarity controls the direction in which our hair grows.

Nissen et al. set out to investigate how these polarities help cells in an embryo organise themselves to form complicated folds and tubes. To do this, simple mathematical representations of both apical-basal and planar cell polarities were designed. The representations were then combined to create computer simulations of groups of cells as these divide and interact with each other.

Simulations of ‘cells’ with only apical-basal polarity were able to generate different shapes in the ‘tissues’ produced, including many found in living organisms. External conditions, such as how cells were arranged to start with, determined the resulting shape. With both apical-basal and planar cell polarities, the simulations reproduced an important change that occurs during early development. They also replicated how the tubes that transport nutrients and oxygen form.

These results show that simple properties of individual cells, such as polarities, can produce different shapes in developing tissues and organs, without the need for a complicated overarching program. Abnormal changes in cell polarity are also associated with diseases such as cancer. The mathematical model developed by Nissen et al. could therefore be a useful tool to study these events.

Genetic Control of Early Cell Lineages in the Mammalian Embryo

Establishing the different lineages of the early mammalian embryo takes place over several days and several rounds of cell divisions from the fertilized egg. The resulting blastocyst contains the pluripotent cells of the epiblast, from which embryonic stem cells can be derived, as well as the extraembryonic lineages required for a mammalian embryo to survive in the uterine environment. The dynamics of the cellular and genetic interactions controlling the initiation and maintenance of these lineages in the mouse embryo are increasingly well understood through application of the tools of single-cell genomics, gene editing, and in vivo imaging. Exploring the similarities and differences between mouse and human development will be essential for translation of these findings into new insights into human biology, derivation of stem cells, and improvements in fertility treatments.

Mouse ICM Organoids Reveal Three-Dimensional Cell Fate Clustering

During mammalian preimplantation, cells of the inner cell mass (ICM) adopt either an embryonic or an extraembryonic fate. This process is tightly regulated in space and time and has been studied previously in mouse embryos and embryonic stem cell models. Current research suggests that cell fates are arranged in a salt-and-pepper pattern of random cell positioning or a spatially alternating pattern. However, the details of the three-dimensional patterns of cell fate specification have not been investigated in the embryo nor in in vitro systems. We developed ICM organoids as a, to our knowledge, novel three-dimensional in vitro stem cell system to model mechanisms of fate decisions that occur in the ICM. ICM organoids show similarities to the in vivo system that arise regardless of the differences in geometry and total cell number. Inspecting ICM organoids and mouse embryos, we describe a so far unknown local clustering of cells with identical fates in both systems. These findings are based on the three-dimensional quantitative analysis of spatiotemporal patterns of NANOG and GATA6 expression in combination with computational rule-based modeling. The pattern identified by our analysis is distinct from the current view of a salt-and-pepper pattern. Our investigation of the spatial distributions both in vivo and in vitro dissects the contributions of the different parts of the embryo to cell fate specifications. In perspective, our combination of quantitative in vivo and in vitro analyses can be extended to other mammalian organisms and thus creates a powerful approach to study embryogenesis.

Possibilities and limitations of three-dimensional reconstruction and simulation techniques to identify patterns, rhythms and functions of apoptosis in the early developing neural tube

The now classical idea that programmed cell death (apoptosis) contributes to a plethora of developmental processes still has lost nothing of its impact. It is, therefore, important to establish effective three-dimensional (3D) reconstruction as well as simulation techniques to decipher the exact patterns and functions of such apoptotic events. The present study focuses on the question whether and how apoptosis promotes neurulation-associated processes in the spinal cord of Tupaia belangeri (Tupaiidae, Scandentia, Mammalia). Our 3D reconstructions demonstrate that at least two craniocaudal waves of apoptosis consecutively pass through the dorsal spinal cord. The first wave appears to be involved in neural fold fusion and/or in selection processes among premigratory neural crest cells. The second one seems to assist in establishing the dorsal signaling center known as the roof plate. In the hindbrain, in contrast, apoptosis among premigratory neural crest cells progresses craniocaudally but discontinuously, in a segment-specific manner. Unlike apoptosis in the spinal cord, these segment-specific apoptotic events, however, precede later ones that seemingly support neural fold fusion and/or postfusion remodeling. Arguing with Whitehead that biological patterns and rhythms differ in that biological rhythms depend "upon the differences involved in each exhibition of the pattern" (Whitehead in An enquiry concerning the principles of natural knowledge. Cambridge University Press, London, 1919, p. 198) we show that 3D reconstruction and simulation techniques can contribute to distinguish between (static) patterns and (dynamic) rhythms of apoptosis. By deciphering novel patterns and rhythms of developmental apoptosis, our reconstructions help to reconcile seemingly inconsistent earlier findings in chick and mouse embryos, and to create rules for computer simulations.

Making lineage decisions with biological noise: Lessons from the early mouse embryo

Understanding how individual cells make fate decisions that lead to the faithful formation and homeostatic maintenance of tissues is a fundamental goal of contemporary developmental and stem cell biology. Seemingly uniform populations of stem cells and multipotent progenitors display a surprising degree of heterogeneity, primarily originating from the inherent stochastic nature of molecular processes underlying gene expression. Despite this heterogeneity, lineage decisions result in tissues of a defined size and with consistent proportions of differentiated cell types. Using the early mouse embryo as a model we review recent developments that have allowed the quantification of molecular intercellular heterogeneity during cell differentiation. We first discuss the relationship between these heterogeneities and developmental cellular potential. We then review recent theoretical approaches that formalize the mechanisms underlying fate decisions in the inner cell mass of the blastocyst stage embryo. These models build on our extensive knowledge of the genetic control of fate decisions in this system and will become essential tools for a rigorous understanding of the connection between noisy molecular processes and reproducible outcomes at the multicellular level. We conclude by suggesting that cell-to-cell communication provides a mechanism to exploit and buffer intercellular variability in a self-organized process that culminates in the reproducible formation of the mature mammalian blastocyst stage embryo that is ready for implantation into the maternal uterus. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Cellular Differentiation Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Gene Expression and Transcriptional Hierarchies > Quantitative Methods and Models.

Modeling-Based Investigation of the Effect of Noise in Cellular Systems

Noise is pervasive in cellular biology and inevitably affects the dynamics of cellular processes. Biological systems have developed regulatory mechanisms to ensure robustness with respect to noise or to take advantage of stochasticity. We review here, through a couple of selected examples, some insights on possible robustness factors and constructive roles of noise provided by computational modeling. In particular, we focus on (1) factors that likely contribute to the robustness of oscillatory processes such as the circadian clocks and the cell cycle, (2) how reliable coding/decoding of calcium-mediated signaling could be achieved in presence of noise and, in some cases, enhanced through stochastic resonance, and (3) how embryonic cell differentiation processes can exploit stochasticity to create heterogeneity in a population of identical cells.