Chiral forces organize left-right patterning in C. elegans by uncoupling midline and anteroposterior axis

Cell lineage-resolved embryonic morphological map reveals signaling associated with cell fate and size asymmetry

How cells change shape is crucial for the development of tissues, organs and embryos. However, studying these shape changes in detail is challenging. Here we present a comprehensive real-time cellular map that covers over 95% of the cells formed during Caenorhabditis elegans embryogenesis, featuring nearly 400,000 3D cell regions. This map includes information on each cell's identity, lineage, fate, shape, volume, surface area, contact area, and gene expression profiles, all accessible through our user-friendly software and website. Our map allows for detailed analysis of key developmental processes, including dorsal intercalation, intestinal formation, and muscle assembly. We show how Notch and Wnt signaling pathways, along with mechanical forces from cell interactions, regulate cell fate decisions and size asymmetries. Our findings suggest that repeated Notch signaling drives size disparities in the large excretory cell, which functions like a kidney. This work sets the stage for in-depth studies of the mechanisms controlling cell fate differentiation and morphogenesis.

Homochirality in the Vicsek model: Fluctuations and potential implications for cellular flocks

Chirality is a feature of many biological systems, and much research has been focused on understanding the origin and implications of this property. Famously, sugars and amino acids found in nature are homochiral, i.e., chiral symmetry is broken and only one of the two possible chiral states is ever observed. Certain types of cells show chiral behavior, too. Understanding the origin of cellular chirality and its effect on tissues and cellular dynamics is still an open problem and subject to much (recent) research, e.g., in the context of drosophila morphogenesis. Here, we develop a simple model to describe the possible origin of homochirality in cells. Combining the Vicsek model for collective behavior with the model of Jafarpour et al. [Phys. Rev. Lett. 115, 158101 (2015)0031-900710.1103/PhysRevLett.115.158101], developed to describe the emergence of molecular homochirality, we investigate how a homochiral state might have evolved in cells from an initially symmetric state without any mechanisms that explicitly break chiral symmetry. We investigate the transition to homochirality and show how the "openness" of the system as well as noise determine if and when a globally homochiral state is reached. While hypothetical and explorative in nature, our analysis may serve as a starting point for more realistic models of chirality in flocking multicellular systems.

Image-based force inference by biomechanical simulation

During morphogenesis, cells precisely generate forces that drive cell shape changes and cellular motion. These forces predominantly arise from contractility of the actomyosin cortex, allowing for cortical tension, protrusion formation, and cell division. Image-based force inference can derive such forces from microscopy images, without complicated and time-consuming experimental set-ups. However, current methods do not account for common effects, such as physical confinement and local force generation. Here we propose a force-inference method based on a biophysical model of cell shape, and assess relative cellular surface tension, adhesive tension between cells, as well as cytokinesis and protrusion formation. We applied our method on fluorescent microscopy images of the early C. elegans embryo. Predictions for cell surface tension at the 7-cell stage were validated by measurements using cortical laser ablation. Our non-invasive method facilitates the accurate tracking of force generation, and offers many new perspectives for studying morphogenesis.

Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes

The shape of a cell as defined by its membrane can be closely associated with its physiological state. For example, the irregular shapes of cancerous cells and elongated shapes of neuron cells often reflect specific functions, such as cell motility and cell communication. However, it remains unclear whether and which cell shape descriptors can characterize different cellular physiological states. In this study, 12 geometric shape descriptors for a three-dimensional (3D) object were collected from the previous literature and tested with a public dataset of ~400,000 independent 3D cell regions segmented based on fluorescent labeling of the cell membranes in Caenorhabditis elegans embryos. It is revealed that those shape descriptors can faithfully characterize cellular physiological states, including (1) cell division (cytokinesis), along with an abrupt increase in the elongation ratio; (2) a negative correlation of cell migration speed with cell sphericity; (3) cell lineage specification with symmetrically patterned cell shape changes; and (4) cell fate specification with differential gene expression and differential cell shapes. The descriptors established may be used to identify and predict the diverse physiological states in numerous cells, which could be used for not only studying developmental morphogenesis but also diagnosing human disease (e.g., the rapid detection of abnormal cells).

Mechanisms of lineage specification in Caenorhabditis elegans

The studies of cell fate and lineage specification are fundamental to our understanding of the development of multicellular organisms. Caenorhabditis elegans has been one of the premiere systems for studying cell fate specification mechanisms at single cell resolution, due to its transparent nature, the invariant cell lineage, and fixed number of somatic cells. We discuss the general themes and regulatory mechanisms that have emerged from these studies, with a focus on somatic lineages and cell fates. We next review the key factors and pathways that regulate the specification of discrete cells and lineages during embryogenesis and postembryonic development; we focus on transcription factors and include numerous lineage diagrams that depict the expression of key factors that specify embryonic founder cells and postembryonic blast cells, and the diverse somatic cell fates they generate. We end by discussing some future perspectives in cell and lineage specification.

Architecture of the cortical actomyosin network driving apical constriction in C. elegans

Apical constriction is a cell shape change that drives key morphogenetic events during development, including gastrulation and neural tube formation. The forces driving apical constriction are primarily generated through the contraction of apicolateral and/or medioapical actomyosin networks. In the Drosophila ventral furrow, the medioapical actomyosin network has a sarcomere-like architecture, with radially polarized actin filaments and centrally enriched non-muscle myosin II and myosin activating kinase. To determine if this is a broadly conserved actin architecture driving apical constriction, we examined actomyosin architecture during C. elegans gastrulation, in which two endodermal precursor cells internalize from the surface of the embryo. Quantification of protein localization showed that neither the non-muscle myosin II NMY-2 nor the myosin-activating kinase MRCK-1 is enriched at the center of the apex. Further, visualization of barbed- and pointed-end capping proteins revealed that actin filaments do not exhibit radial polarization at the apex. Our results demonstrate that C. elegans endodermal precursor cells apically constrict using a mixed-polarity actin filament network and with myosin and a myosin activator distributed throughout the network. Taken together with observations made in other organisms, our results demonstrate that diverse actomyosin architectures are used in animal cells to accomplish apical constriction.

Stability of asymmetric cell division: A deformable cell model of cytokinesis applied to C. elegans

Cell division during early embryogenesis is linked to key morphogenic events such as embryo symmetry breaking and tissue patterning. It is thought that the physical surrounding of cells together with cell intrinsic cues act as a mechanical "mold," guiding cell division to ensure these events are robust. To quantify how cell division is affected by the mechanical and geometrical environment, we present a novel computational mechanical model of cytokinesis, the final phase of cell division. Simulations with the model reproduced experimentally observed furrow dynamics and describe the volume ratio of daughter cells in asymmetric cell divisions, based on the position and orientation of the mitotic spindle. For dividing cells in geometrically confined environments, we show how the orientation of confinement relative to the division axis modulates the volume ratio in asymmetric cell division. Further, we quantified how cortex viscosity and surface tension determine the shape of a dividing cell and govern bubble-instabilities in asymmetric cell division. Finally, we simulated the formation of the three body axes via sequential (a)symmetric divisions up until the six-cell stage of early C. elegans development, which proceeds within the confines of an eggshell. We demonstrate how model input parameters spindle position and orientation provide sufficient information to reliably predict the volume ratio of daughter cells during the cleavage phase of development. However, for egg geometries perturbed by compression, the model predicts that a change in confinement alone is insufficient to explain experimentally observed differences in cell volume. This points to an effect of the compression on the spindle positioning mechanism. Additionally, the model predicts that confinement stabilizes asymmetric cell divisions against bubble-instabilities.

A compound PCP scheme underlies sequential rosettes-based cell intercalation

The formation of sequential rosettes is a type of collective cell behavior recently discovered in the Caenorhabditis elegans embryo that mediates directional cell migration through sequential formation and resolution of multicellular rosettes involving the migrating cell and its neighboring cells along the way. Here, we show that a planar cell polarity (PCP)-based polarity scheme regulates sequential rosettes, which is distinct from the known mode of PCP regulation in multicellular rosettes during the process of convergent extension. Specifically, non-muscle myosin (NMY) localization and edge contraction are perpendicular to that of Van Gogh as opposed to colocalizing with Van Gogh. Further analyses suggest a two-component polarity scheme: one being the canonical PCP pathway with MIG-1/Frizzled and VANG-1/Van Gogh localized to the vertical edges, the other being MIG-1/Frizzled and NMY-2 localized to the midline/contracting edges. The NMY-2 localization and contraction of the midline edges also required LAT-1/Latrophilin, an adhesion G protein-coupled receptor that has not been shown to regulate multicellular rosettes. Our results establish a distinct mode of PCP-mediated cell intercalation and shed light on the versatile nature of the PCP pathway.

Visualizing Phagocytic Cargo In Vivo from Engulfment to Resolution in Caenorhabditis elegans

The nematode Caenorhabditis elegans offers many experimental advantages to study conserved mechanisms of phagocytosis and phagocytic clearance. These include the stereotyped timing of phagocytic events in vivo for time-lapse imaging, the availability of transgenic reporters labeling molecules involved in different steps of phagocytosis, and the transparency of the animal for fluorescence imaging. Further, the ease of forward and reverse genetics in C. elegans has enabled many of the initial discoveries of proteins involved in phagocytic clearance. In this chapter, we focus on phagocytosis by the large undifferentiated blastomeres of C. elegans embryos, which engulf and eliminate diverse phagocytic cargo from the corpse of the second polar body to cytokinetic midbody remnants. We describe the use of fluorescent time-lapse imaging to observe the distinct steps of phagocytic clearance and methods to normalize this process to distinguish defects in mutant strains. These approaches have enabled us to reveal new insights from the initial signaling to induce phagocytosis up until the final resolution of phagocytic cargo in phagolysosomes.

Delineating the mechanisms and design principles of Caenorhabditis elegans embryogenesis using in toto high-resolution imaging data and computational modeling

The nematode (roundworm) Caenorhabditis elegans is one of the most popular animal models for the study of developmental biology, as its invariant development and transparent body enable in toto cellular-resolution fluorescence microscopy imaging of developmental processes at 1-min intervals. This has led to the development of various computational tools for the systematic and automated analysis of imaging data to delineate the molecular and cellular processes throughout the embryogenesis of C. elegans, such as those associated with cell lineage, cell migration, cell morphology, and gene activity. In this review, we first introduce C. elegans embryogenesis and the development of techniques for tracking cell lineage and reconstructing cell morphology during this process. We then contrast the developmental modes of C. elegans and the customized technologies used for studying them with the ones of other animal models, highlighting its advantage for studying embryogenesis with exceptional spatial and temporal resolution. This is followed by an examination of the physical models that have been devised-based on accurate determinations of developmental processes afforded by analyses of imaging data-to interpret the early embryonic development of C. elegans from subcellular to intercellular levels of multiple cells, which focus on two key processes: cell polarization and morphogenesis. We subsequently discuss how quantitative data-based theoretical modeling has improved our understanding of the mechanisms of C. elegans embryogenesis. We conclude by summarizing the challenges associated with the acquisition of C. elegans embryogenesis data, the construction of algorithms to analyze them, and the theoretical interpretation.

Visualizing and quantifying molecular and cellular processes in C. elegans using light microscopy

Light microscopes are the cell and developmental biologists' "best friend", providing a means to see structures and follow dynamics from the protein to the organism level. A huge advantage of C. elegans as a model organism is its transparency, which coupled with its small size means that nearly every biological process can be observed and measured with the appropriate probe and light microscope. Continuous improvement in microscope technologies along with novel genome editing techniques to create transgenic probes have facilitated the development and implementation of a dizzying array of methods for imaging worm embryos, larvae and adults. In this review we provide an overview of the molecular and cellular processes that can be visualized in living worms using light microscopy. A partial inventory of fluorescent probes and techniques successfully used in worms to image the dynamics of cells, organelles, DNA, and protein localization and activity is followed by a practical guide to choosing between various imaging modalities, including widefield, confocal, lightsheet, and structured illumination microscopy. Finally, we discuss the available tools and approaches, including machine learning, for quantitative image analysis tasks, such as colocalization, segmentation, object tracking, and lineage tracing. Hopefully, this review will inspire worm researchers who have not yet imaged their worms to begin, and push those who are imaging to go faster, finer, and longer.

Imaging Epidermal Cell Rearrangement in the C. elegans Embryo

The Caenorhabditis elegans embryo is well suited for analysis of directed cell rearrangement via modern microscopy, due to its simple organization, short generation time, transparency, invariant lineage, and the ability to generate engineered embryos expressing various fluorescent proteins. This chapter provides an overview of routine microscopy techniques for imaging dorsal intercalation, a convergent extension-like morphogenetic movement in the embryonic epidermis of C. elegans, including making agar mounts, low-cost four-dimensional (4D) Nomarski microscopy, laser microsurgery, and 4D fluorescence microscopy using actin and junctional fusion proteins, as well as tissue-specific promoters useful for studying dorsal intercalation.

Computable early Caenorhabditis elegans embryo with a phase field model

Morphogenesis is a precise and robust dynamic process during metazoan embryogenesis, consisting of both cell proliferation and cell migration. Despite the fact that much is known about specific regulations at molecular level, how cell proliferation and migration together drive the morphogenesis at cellular and organismic levels is not well understood. Using Caenorhabditis elegans as the model animal, we present a phase field model to compute early embryonic morphogenesis within a confined eggshell. With physical information about cell division obtained from three-dimensional time-lapse cellular imaging experiments, the model can precisely reproduce the early morphogenesis process as seen in vivo, including time evolution of location and morphology of each cell. Furthermore, the model can be used to reveal key cell-cell attractions critical to the development of C. elegans embryo. Our work demonstrates how genetic programming and physical forces collaborate to drive morphogenesis and provides a predictive model to decipher the underlying mechanism.

Embryonic development is a precise process involving cell division, cell-cell interaction, and cell migration. During the process, how each cell reaches its supposed location and be in contact with the right neighbors, and what roles genetic factors and physical forces play are important and fascinating questions. Using the worm Caenorhabditis elegans as a model system, we build a phase field model to simulate early morphogenesis. With a few physical inputs, the model can precisely reproduce the early morphological development of the worm. Such an accurate simulator can not only teach us how physical forces work together with genetic factors to shape up the complex process of development, but also make predictions, such as key cell-cell attractions critical in the process.

Symmetry-breaking of animal cytokinesis

Cytokinesis is a mechanism that separates dividing cells via constriction of a supramolecular structure, the contractile ring. In animal cells, three modes of symmetry-breaking of cytokinesis result in unilateral cytokinesis, asymmetric cell division, and oriented cell division. Each mode of cytokinesis plays a significant role in tissue patterning and morphogenesis by the mechanisms that control the orientation and position of the contractile ring relative to the body axis. Despite its significance, the mechanisms involved in the symmetry-breaking of cytokinesis remain unclear in many cell types. Classical embryologists have identified that the geometric relationship between the mitotic spindle and cell cortex induces cytokinesis asymmetry; however, emerging evidence suggests that a concerted flow of compressional cell-cortex materials (cortical flow) is a spindle-independent driving force in spatial cytokinesis control. This review provides an overview of both classical and emerging mechanisms of cytokinesis asymmetry and their roles in animal development.

PDZD-8 and TEX-2 regulate endosomal PI(4,5)P2 homeostasis via lipid transport to promote embryogenesis in C. elegans

Different types of cellular membranes have unique lipid compositions that are important for their functional identity. PI(4,5)P2 is enriched in the plasma membrane where it contributes to local activation of key cellular events, including actomyosin contraction and cytokinesis. However, how cells prevent PI(4,5)P2 from accumulating in intracellular membrane compartments, despite constant intermixing and exchange of lipid membranes, is poorly understood. Using the C. elegans early embryo as our model system, we show that the evolutionarily conserved lipid transfer proteins, PDZD-8 and TEX-2, act together with the PI(4,5)P2 phosphatases, OCRL-1 and UNC-26/synaptojanin, to prevent the build-up of PI(4,5)P2 on endosomal membranes. In the absence of these four proteins, large amounts of PI(4,5)P2 accumulate on endosomes, leading to embryonic lethality due to ectopic recruitment of proteins involved in actomyosin contractility. PDZD-8 localizes to the endoplasmic reticulum and regulates endosomal PI(4,5)P2 levels via its lipid harboring SMP domain. Accumulation of PI(4,5)P2 on endosomes is accompanied by impairment of their degradative capacity. Thus, cells use multiple redundant systems to maintain endosomal PI(4,5)P2 homeostasis.

Wnt Signaling Induces Asymmetric Dynamics in the Actomyosin Cortex of the C. elegans Endomesodermal Precursor Cell

During asymmetrical division of the endomesodermal precursor cell EMS, a cortical flow arises, and the daughter cells, endodermal precursor E and mesodermal precursor MS, have an enduring difference in the levels of F-actin and non-muscular myosin. Ablation of the cell cortex suggests that these observed differences lead to differences in cortical tension. The higher F-actin and myosin levels in the MS daughter coincide with cell shape changes and relatively lower tension, indicating a soft, actively moving cell, whereas the lower signal in the E daughter cell is associated with higher tension and a more rigid, spherical shape. The cortical flow is under control of the Wnt signaling pathway. Perturbing the pathway removes the asymmetry arising during EMS division and induces subtle defects in the cellular movements at the eight-cell stage. The perturbed cellular movement appears to be associated with an asymmetric distribution of E-cadherin across the EMS cytokinesis groove. ABpl forms a lamellipodium which preferentially adheres to MS by the E-cadherin HMR-1. The HMR-1 asymmetry across the groove is complete just at the moment cytokinesis completes. Perturbing Wnt signaling equalizes the HMR-1 distribution across the lamellipodium. We conclude that Wnt signaling induces a cortical flow during EMS division, which results in a transition in the cortical contractile network for the daughter cells, as well as an asymmetric distribution of E-cadherin.

Mechanics and self-organization in tissue development

Self-organization is an all-important feature of living systems that provides the means to achieve specialization and functionality at distinct spatio-temporal scales. Herein, we review this concept by addressing the packing organization of cells, the sorting/compartmentalization phenomenon of cell populations, and the propagation of organizing cues at the tissue level through traveling waves. We elaborate on how different theoretical models and tools from Topology, Physics, and Dynamical Systems have improved the understanding of self-organization by shedding light on the role played by mechanics as a driver of morphogenesis. Altogether, by providing a historical perspective, we show how ideas and hypotheses in the field have been revisited, developed, and/or rejected and what are the open questions that need to be tackled by future research.

spheresDT/Mpacts-PiCS: Cell Tracking and Shape Retrieval in Membrane-labeled Embryos

Motivation

Uncovering the cellular and mechanical processes that drive embryo formation requires an accurate read out of cell geometries over time. However, automated extraction of 3D cell shapes from time-lapse microscopy remains challenging, especially when only membranes are labeled.

Results

We present an image analysis framework for automated tracking and three-dimensional cell segmentation in confocal time lapses. A sphere clustering approach allows for local thresholding and application of logical rules to facilitate tracking and unseeded segmentation of variable cell shapes. Next, the segmentation is refined by a discrete element method simulation where cell shapes are constrained by a biomechanical cell shape model. We apply the framework on Caenorhabditis elegans embryos in various stages of early development and analyze the geometry of the 7- and 8-cell stage embryo, looking at volume, contact area and shape over time.

Availability and implementation

The Python code for the algorithm and for measuring performance, along with all data needed to recreate the results is freely available at 10.5281/zenodo.5108416 and 10.5281/zenodo.4540092. The most recent version of the software is maintained at https://bitbucket.org/pgmsembryogenesis/sdt-pics.

Supplementary information

Supplementary data are available at Bioinformatics online.

Analyzing signaling activity and function in hematopoietic cells

Cells constantly sense their environment, allowing the adaption of cell behavior to changing needs. Fine-tuned responses to complex inputs are computed by signaling pathways, which are wired in complex connected networks. Their activity is highly context-dependent, dynamic, and heterogeneous even between closely related individual cells. Despite lots of progress, our understanding of the precise implementation, relevance, and possible manipulation of cellular signaling in health and disease therefore remains limited. Here, we discuss the requirements, potential, and limitations of the different current technologies for the analysis of hematopoietic stem and progenitor cell signaling and its effect on cell fates.

CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left-right symmetry breaking

Proper left-right symmetry breaking is essential for animal development, and in many cases, this process is actomyosin-dependent. In Caenorhabditis elegans embryos active torque generation in the actomyosin layer promotes left-right symmetry breaking by driving chiral counterrotating cortical flows. While both Formins and Myosins have been implicated in left-right symmetry breaking and both can rotate actin filaments in vitro, it remains unclear whether active torques in the actomyosin cortex are generated by Formins, Myosins, or both. We combined the strength of C. elegans genetics with quantitative imaging and thin film, chiral active fluid theory to show that, while Non-Muscle Myosin II activity drives cortical actomyosin flows, it is permissive for chiral counterrotation and dispensable for chiral symmetry breaking of cortical flows. Instead, we find that CYK-1/Formin activation in RhoA foci is instructive for chiral counterrotation and promotes in-plane, active torque generation in the actomyosin cortex. Notably, we observe that artificially generated large active RhoA patches undergo rotations with consistent handedness in a CYK-1/Formin-dependent manner. Altogether, we conclude that CYK-1/Formin-dependent active torque generation facilitates chiral symmetry breaking of actomyosin flows and drives organismal left-right symmetry breaking in the nematode worm.

Collective nuclear behavior shapes bilateral nuclear symmetry for subsequent left-right asymmetric morphogenesis in Drosophila

Proper organ development often requires nuclei to move to a specific position within the cell. To determine how nuclear positioning affects left-right (LR) development in the Drosophila anterior midgut (AMG), we developed a surface-modeling method to measure and describe nuclear behavior at stages 13-14, captured in three-dimensional time-lapse movies. We describe the distinctive positioning and a novel collective nuclear behavior by which nuclei align LR symmetrically along the anterior-posterior axis in the visceral muscles that overlie the midgut and are responsible for the LR-asymmetric development of this organ. Wnt4 signaling is crucial for the collective behavior and proper positioning of the nuclei, as are myosin II and the LINC complex, without which the nuclei fail to align LR symmetrically. The LR-symmetric positioning of the nuclei is important for the subsequent LR-asymmetric development of the AMG. We propose that the bilaterally symmetrical positioning of these nuclei may be mechanically coupled with subsequent LR-asymmetric morphogenesis.

Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation

The invariant development and transparent body of the nematode Caenorhabditis elegans enables complete delineation of cell lineages throughout development. Despite extensive studies of cell division, cell migration and cell fate differentiation, cell morphology during development has not yet been systematically characterized in any metazoan, including C. elegans. This knowledge gap substantially hampers many studies in both developmental and cell biology. Here we report an automatic pipeline, CShaper, which combines automated segmentation of fluorescently labeled membranes with automated cell lineage tracing. We apply this pipeline to quantify morphological parameters of densely packed cells in 17 developing C. elegans embryos. Consequently, we generate a time-lapse 3D atlas of cell morphology for the C. elegans embryo from the 4- to 350-cell stages, including cell shape, volume, surface area, migration, nucleus position and cell-cell contact with resolved cell identities. We anticipate that CShaper and the morphological atlas will stimulate and enhance further studies in the fields of developmental biology, cell biology and biomechanics.

Early Committed Clockwise Cell Chirality Upregulates Adipogenic Differentiation of Mesenchymal Stem Cells

Cell chirality is observed with diverse forms and coordinates various left-right (LR) asymmetry in tissue morphogenesis. To give rise to such diversity, cell chirality may be coupled with cell differentiation. Here, using micropatterned human mesenchymal stem cells (hMSCs), an early committed clockwise (CW) cell chirality that can itself upregulate the adipogenic differentiation is reported. hMSC chirality enables a positively tilted chiral orientation on micropatterned stripes. When cultured as single cells on circular micropatterns, an anticlockwise (ACW)-biased nucleus rotation and swirling pattern of actin filament are observed. Interestingly, with adipogenic induction for 3-6 days, such chirality is reversed to negative chiral orientation and CW-biased rotation, which is earlier than the maturation of other differentiation markers, and consistently expressed in terminally differentiated adipocytes. Using latrunculin A (LatA), cytochalasin D (CD), and nocodazole (Noco) that forces a CW-biased actin filament and nucleus rotation resembling the early differentiated chirality upon adipogenic induction, an upregulation of adipogenic differentiation is found. The result demonstrates that the early differentiated chirality may serve as a mechanical precursor to engage the lineage commitment, suggesting a feedback mechanism of chiral actin in regulating cell differentiation and LR morphogenesis.

Cell lineage-dependent chiral actomyosin flows drive cellular rearrangements in early Caenorhabditis elegans development

Proper positioning of cells is essential for many aspects of development. Daughter cell positions can be specified via orienting the cell division axis during cytokinesis. Rotatory actomyosin flows during division have been implied in specifying and reorienting the cell division axis, but how general such reorientation events are, and how they are controlled, remains unclear. We followed the first nine divisions of Caenorhabditis elegans embryo development and demonstrate that chiral counter-rotating flows arise systematically in early AB lineage, but not in early P/EMS lineage cell divisions. Combining our experiments with thin film active chiral fluid theory we identify a mechanism by which chiral counter-rotating actomyosin flows arise in the AB lineage only, and show that they drive lineage-specific spindle skew and cell reorientation events. In conclusion, our work sheds light on the physical processes that underlie chiral morphogenesis in early development.

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.

Systems Properties and Spatiotemporal Regulation of Cell Position Variability during Embryogenesis

An intriguing question in developmental biology is how do developmental processes achieve high reproducibility among individuals? An in-depth analysis of information contained in phenotypic variability provides an important perspective to address this question. In this work, we present a quantitative and functional analysis of cell position variability during Caenorhabditis elegans embryogenesis. We find that cell position variability is highly deterministic and regulated by intrinsic and extrinsic mechanisms. Positional variability is determined by cell lineage identity and is coupled to diverse developmental properties of cells, including embryonic localization, cell contact, and left-right symmetry. Temporal dynamics of cell position variability are highly concordant, and fate specification contributes to a systems-wide reduction of variability that could provide a buffering strategy. Positional variability is stringently regulated throughout embryogenesis and cell-cell junctions function to restrict variability. Our results provide insight into systems properties and spatiotemporal control of cellular variability during development.

Flipping Shells! Unwinding LR Asymmetry in Mirror-Image Molluscs

In seeking to understand the establishment of left-right (LR) asymmetry, a limiting factor is that most animals are ordinarily invariant in their asymmetry, except when manipulated or mutated. It is therefore surprising that the wider scientific field does not appear to fully appreciate the remarkable fact that normal development in molluscs, especially snails, can flip between two chiral types without pathology. Here, I describe recent progress in understanding the evolution, development, and genetics of chiral variation in snails, and place it in context with other animals. I argue that the natural variation of snails is a crucial resource towards understanding the invariance in other animal groups and, ultimately, will be key in revealing the common factors that define cellular and organismal LR asymmetry.

Aurora B functions at the apical surface after specialized cytokinesis during morphogenesis in C. elegans

Although cytokinesis has been intensely studied, the way it is executed during development is not well understood, despite a long-standing appreciation that various aspects of cytokinesis vary across cell and tissue types. To address this, we investigated cytokinesis during the invariant Caenorhabditis elegans embryonic divisions and found several parameters that are altered at different stages in a reproducible manner. During early divisions, furrow ingression asymmetry and midbody inheritance is consistent, suggesting specific regulation of these events. During morphogenesis, we found several unexpected alterations to cytokinesis, including apical midbody migration in polarizing epithelial cells of the gut, pharynx and sensory neurons. Aurora B kinase, which is essential for several aspects of cytokinesis, remains apically localized in each of these tissues after internalization of midbody ring components. Aurora B inactivation disrupts cytokinesis and causes defects in apical structures, even if inactivated post-mitotically. Therefore, we demonstrate that cytokinesis is implemented in a specialized way during epithelial polarization and that Aurora B has a role in the formation of the apical surface.

Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis

Motivation

Cell movement in the early phase of Caenorhabditis elegans development is regulated by a highly complex process in which a set of rules and connections are formulated at distinct scales. Previous efforts have demonstrated that agent-based, multi-scale modeling systems can integrate physical and biological rules and provide new avenues to study developmental systems. However, the application of these systems to model cell movement is still challenging and requires a comprehensive understanding of regulatory networks at the right scales. Recent developments in deep learning and reinforcement learning provide an unprecedented opportunity to explore cell movement using 3D time-lapse microscopy images.

Results

We present a deep reinforcement learning approach within an agent-based modeling system to characterize cell movement in the embryonic development of C.elegans. Our modeling system captures the complexity of cell movement patterns in the embryo and overcomes the local optimization problem encountered by traditional rule-based, agent-based modeling that uses greedy algorithms. We tested our model with two real developmental processes: the anterior movement of the Cpaaa cell via intercalation and the rearrangement of the superficial left-right asymmetry. In the first case, the model results suggested that Cpaaa's intercalation is an active directional cell movement caused by the continuous effects from a longer distance (farther than the length of two adjacent cells), as opposed to a passive movement caused by neighbor cell movements. In the second case, a leader-follower mechanism well explained the collective cell movement pattern in the asymmetry rearrangement. These results showed that our approach to introduce deep reinforcement learning into agent-based modeling can test regulatory mechanisms by exploring cell migration paths in a reverse engineering perspective. This model opens new doors to explore the large datasets generated by live imaging.

Availability and implementation

Source code is available at https://github.com/zwang84/drl4cellmovement.

Supplementary information

Supplementary data are available at Bioinformatics online.

Mechanical stress induces a scalable switch in cortical flow polarization during cytokinesis

During animal development, cells need to sense and adapt to mechanical forces from their environment. Ultimately, these forces are transduced through the actomyosin cortex. How the cortex simultaneously responds to and creates forces during cytokinesis is not well understood. Here we show that, under mechanical stress, cortical actomyosin flow can switch polarization during cytokinesis in the C. elegans embryo. In unstressed embryos, longitudinal cortical flow contributes to contractile ring formation, while rotational cortical flow is additionally induced in uniaxially loaded embryos, i.e. embryos compressed between two plates. Rotational flow depends on astral microtubule signals and is required for the redistribution of the actomyosin cortex in loaded embryos. Rupture of longitudinally aligned cortical fibers during cortex rotation releases tension, initiates orthogonal longitudinal flow and, thereby, contributes to furrowing in loaded embryos. Moreover, actomyosin regulators involved in RhoA regulation, cortical polarity and chirality are all required for rotational flow, and become essential for cytokinesis under mechanical stress. In sum, our findings extend the current framework of mechanical stress response during cell division and show scaling of orthogonal cortical flows to the amount of mechanical stress.

Planar Asymmetries in the C. elegans Embryo Emerge by Differential Retention of aPARs at Cell-Cell Contacts

Formation of the anteroposterior and dorsoventral body axis in Caenorhabditis elegans depends on cortical flows and advection of polarity determinants. The role of this patterning mechanism in tissue polarization after formation of cell-cell contacts is not fully understood. Here, we demonstrate that planar asymmetries are established during left-right symmetry breaking: Centripetal cortical flows asymmetrically and differentially advect anterior polarity determinants (aPARs) from contacts to the medial cortex, resulting in their unmixing from apical myosin. Contact localization and advection of PAR-6 requires balanced CDC-42 activation, while asymmetric retention and advection of PAR-3 can occur independently of PAR-6. Concurrent asymmetric retention of PAR-3, E-cadherin/HMR-1 and opposing retention of antagonistic CDC-42 and Wnt pathway components leads to planar asymmetries. The most obvious mark of planar asymmetry, retention of PAR-3 at a single cell-cell contact, is required for proper cytokinetic cell intercalation. Hence, our data uncover how planar polarity is established in a system without the canonical planar cell polarity pathway through planar asymmetric retention of aPARs.

Morphogenetic degeneracies in the actomyosin cortex

One of the great challenges in biology is to understand the mechanisms by which morphogenetic processes arise from molecular activities. We investigated this problem in the context of actomyosin-based cortical flow in C. elegans zygotes, where large-scale flows emerge from the collective action of actomyosin filaments and actin binding proteins (ABPs). Large-scale flow dynamics can be captured by active gel theory by considering force balances and conservation laws in the actomyosin cortex. However, which molecular activities contribute to flow dynamics and large-scale physical properties such as viscosity and active torque is largely unknown. By performing a candidate RNAi screen of ABPs and actomyosin regulators we demonstrate that perturbing distinct molecular processes can lead to similar flow phenotypes. This is indicative for a ‘morphogenetic degeneracy’ where multiple molecular processes contribute to the same large-scale physical property. We speculate that morphogenetic degeneracies contribute to the robustness of bulk biological matter in development.

Cell Contact Gives a Twist to Cell Division

The orientation of cell division is crucial in many developmental processes. In this issue of Developmental Cell, Sugioka and Bowerman (2018) report a myosin-dependent mechanism whereby physical contact between cells influences the division plane, with implications for understanding how cell division orientation is regulated in multicellular contexts.

Combinatorial Contact Cues Specify Cell Division Orientation by Directing Cortical Myosin Flows

Cell division axes during development are specified in different orientations to establish multicellular assemblies, but the mechanisms that generate division axis diversity remain unclear. We show here that patterns of cell contact provide cues that diversify cell division orientation by modulating cortical non-muscle myosin flow. We reconstituted in vivo contact patterns using beads or isolated cells to show two findings. First, we identified three contact-dependent cues that pattern cell division orientation and myosin flow: physical contact, contact asymmetry, and a Wnt signal. Second, we experimentally demonstrated that myosin flow generates forces that trigger plasma membrane movements and propose that their anisotropy drives cell division orientation. Our data suggest that contact-dependent control of myosin specifies the division axes of Caenorhabditis elegans AB, ABa, EMS cells, and the mouse AB cell. The contact pattern-dependent generation of myosin flows, in concert with known microtubule/dynein pathways, may greatly expand division axis diversity during development.

From cytoskeletal dynamics to organ asymmetry: a nonlinear, regulative pathway underlies left-right patterning

Consistent left-right (LR) asymmetry is a fundamental aspect of the bodyplan across phyla, and errors of laterality form an important class of human birth defects. Its molecular underpinning was first discovered as a sequential pathway of left- and right-sided gene expression that controlled positioning of the heart and visceral organs. Recent data have revised this picture in two important ways. First, the physical origin of chirality has been identified; cytoskeletal dynamics underlie the asymmetry of single-cell behaviour and patterning of the LR axis. Second, the pathway is not linear: early disruptions that alter the normal sidedness of upstream asymmetric genes do not necessarily induce defects in the laterality of the downstream genes or in organ situs Thus, the LR pathway is a unique example of two fascinating aspects of biology: the interplay of physics and genetics in establishing large-scale anatomy, and regulative (shape-homeostatic) pathways that correct molecular and anatomical errors over time. Here, we review aspects of asymmetry from its intracellular, cytoplasmic origins to the recently uncovered ability of the LR control circuitry to achieve correct gene expression and morphology despite reversals of key 'determinant' genes. We provide novel functional data, in Xenopus laevis, on conserved elements of the cytoskeleton that drive asymmetry, and comparatively analyse it together with previously published results in the field. Our new observations and meta-analysis demonstrate that despite aberrant expression of upstream regulatory genes, embryos can progressively normalize transcriptional cascades and anatomical outcomes. LR patterning can thus serve as a paradigm of how subcellular physics and gene expression cooperate to achieve developmental robustness of a body axis.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

Cell chirality: its origin and roles in left-right asymmetric development

An item is chiral if it cannot be superimposed on its mirror image. Most biological molecules are chiral. The homochirality of amino acids ensures that proteins are chiral, which is essential for their functions. Chirality also occurs at the whole-cell level, which was first studied mostly in ciliates, single-celled protozoans. Ciliates show chirality in their cortical structures, which is not determined by genetics, but by 'cortical inheritance'. These studies suggested that molecular chirality directs whole-cell chirality. Intriguingly, chirality in cellular structures and functions is also found in metazoans. In Drosophila, intrinsic cell chirality is observed in various left-right (LR) asymmetric tissues, and appears to be responsible for their LR asymmetric morphogenesis. In other invertebrates, such as snails and Caenorhabditis elegans, blastomere chirality is responsible for subsequent LR asymmetric development. Various cultured cells of vertebrates also show intrinsic chirality in their cellular behaviours and intracellular structural dynamics. Thus, cell chirality may be a general property of eukaryotic cells. In Drosophila, cell chirality drives the LR asymmetric development of individual organs, without establishing the LR axis of the whole embryo. Considering that organ-intrinsic LR asymmetry is also reported in vertebrates, this mechanism may contribute to LR asymmetric development across phyla.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

Establishment of lateral organ asymmetries in the invertebrate chordate, Ciona intestinalis

BACKGROUND

The evolutionary emergence and diversification of the chordates appear to involve dramatic changes in organ morphogenesis along the left/right axis. However, the ancestral chordate mechanism for establishing lateral asymmetry remains ambiguous. Additionally, links between the initial establishment of lateral asymmetry and subsequent asymmetries in organ morphogenesis are poorly characterized.

RESULTS

To explore asymmetric organ morphogenesis during chordate evolution, we have begun to characterize left/right patterning of the heart and endodermal organs in an invertebrate chordate, Ciona intestinalis. Here, we show that Ciona has a laterally asymmetric, right-sided heart. Our data indicate that cardiac lateral asymmetry requires H+/K+ ion flux, but is independent of Nodal signaling. Our pharmacological inhibitor studies show that ion flux is required for polarization of epidermal cilia and neurula rotation and suggest that ion flux functions synergistically with chorion contact to drive cardiac laterality. Live imaging analysis revealed that larval heart progenitor cells undergo a lateral shift without displaying any migratory behaviors. Furthermore, we find that this passive shift corresponds with the emergence of lateral asymmetry in the endoderm, which is also ion flux dependent.

CONCLUSIONS

Our data suggest that ion flux promotes laterally asymmetric morphogenesis of the larval endoderm rudiment leading to a passive, Nodal-independent shift in the position of associated heart progenitor cells. These findings help to refine hypotheses regarding ancestral chordate left/right patterning mechanisms and how they have diverged within invertebrate and vertebrate chordate lineages.

Biologically constrained optimization based cell membrane segmentation in C. elegans embryos

BACKGROUND

Recent advances in bioimaging and automated analysis methods have enabled the large-scale systematic analysis of cellular dynamics during the embryonic development of Caenorhabditis elegans. Most of these analyses have focused on cell lineage tracing rather than cell shape dynamics. Cell shape analysis requires cell membrane segmentation, which is challenging because of insufficient resolution and image quality. This problem is currently solved by complicated segmentation methods requiring laborious and time consuming parameter adjustments.

RESULTS

Our new framework BCOMS (Biologically Constrained Optimization based cell Membrane Segmentation) automates the extraction of the cell shape of C. elegans embryos. Both the segmentation and evaluation processes are automated. To automate the evaluation, we solve an optimization problem under biological constraints. The performance of BCOMS was validated against a manually created ground truth of the 24-cell stage embryo. The average deviation of 25 cell shape features was 5.6%. The deviation was mainly caused by membranes parallel to the focal planes, which either contact the surfaces of adjacent cells or make no contact with other cells. Because segmentation of these membranes was difficult even by manual inspection, the automated segmentation was sufficiently accurate for cell shape analysis. As the number of manually created ground truths is necessarily limited, we compared the segmentation results between two adjacent time points. Across all cells and all cell cycles, the average deviation of the 25 cell shape features was 4.3%, smaller than that between the automated segmentation result and ground truth.

CONCLUSIONS

BCOMS automated the accurate extraction of cell shapes in developing C. elegans embryos. By replacing image processing parameters with easily adjustable biological constraints, BCOMS provides a user-friendly framework. The framework is also applicable to other model organisms. Creating the biological constraints is a critical step requiring collaboration between an experimentalist and a software developer.

In vivo Live Imaging of Calcium Waves and Other Cellular Processes during Fertilization in Caenorhabditis elegans

Fertilization calcium waves are a conserved trigger for animal development; however, genetic analysis of these waves has been limited due to the difficulty of imaging in vivo fertilization. Here we describe a protocol to image calcium dynamics during in vivo fertilization in the genetic animal model Caenorhabditis elegans. This protocol consists of germline microinjection of a chemical calcium indicator, worm immobilization, live imaging, and image processing that quantifies the calcium fluorescence in the oocyte region moving in the field-of-view during ovulation. This imaging protocol can also be used to image other cellular processes during in vivo fertilization in C. elegans, such as membrane fusion and cytoskeletal dynamics.

The Midbody and its Remnant in Cell Polarization and Asymmetric Cell Division

The midbody is a protein-dense assembly that forms during cytokinesis when the actomyosin ring constricts around bundling central spindle microtubules. After its initial description by Walther Flemming in the late nineteenth century and its rediscovery through electron microscopy in the 1960s and 1970s, its ultrastructural organization and the sequential recruitment of its molecular constituents has only been elucidated in the past decade. Recently, it has become clear that the midbody can serve as a polarity cue during asymmetric cell division, cell polarization, and spindle orientation by coordinating cytoskeletal organization, vesicular transport, and localized cortical cues. In this chapter, these newly emerging functions will be discussed as well as asymmetries during midbody formation and their consequences for cellular organization in tissues.

Heterotaxy in Caenorhabditis: widespread natural variation in left-right arrangement of the major organs

Although the arrangement of internal organs in most metazoans is profoundly left-right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness, we found that L/R asymmetry of the major organs, the gut and gonad, varies among natural isolates of the species in both males and hermaphrodites. In hermaphrodites, heterotaxy can involve one or both bilaterally asymmetric gonad arms. Male heterotaxy is probably not attributable to relaxed selection in this hermaphroditic species, as it is also seen in gonochoristic Caenorhabditis species. Heterotaxy increases in many isolates at elevated temperature, with one showing a pregastrulation temperature-sensitive period, suggesting a very early embryonic or germline effect on this much later developmental outcome. A genome-wide association study of 100 isolates showed that male heterotaxy is associated with three genomic regions. Analysis of recombinant inbred lines suggests that a small number of loci are responsible for the observed variation. These findings reveal that heterotaxy is a widely varying quantitative trait in an animal with an otherwise highly stereotyped anatomy, demonstrating unexpected plasticity in an L/R arrangement of the major organs even in a simple animal.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

Nanowire Magnetoscope Reveals a Cellular Torque with Left-Right Bias

Cellular force regulates many types of cell mechanics and the associated physiological behaviors. Recent evidence suggested that cell motion with left-right (LR) bias may be the origin of LR asymmetry in tissue architecture. As actomyosin activity was found essential in the process, it predicts a type of cellular force that coordinates the development of LR asymmetry in tissue formation. However, due to the lack of appropriate platform, cellular force with LR bias has not yet been found. Here we report a nanowire magnetoscope that reveals a rotating force-torque-exerted by cells. Ferromagnetic nanowires were deposited and internalized by micropatterned cells. Within a uniform, horizontal magnetic field, the nanowires that initially aligned with the magnetic field were subsequently rotated due to the cellular torque. We found that the torque is LR-biased depending on cell types. While NIH 3T3 fibroblasts and human vascular endothelial cells exhibited counterclockwise torque, C2C12 myoblasts showed torque with slight clockwise bias. Moreover, an actin ring composed of transverse arcs and radial fibers was identified as a major factor determining the LR bias of cellular torque, since the disruption of actin ring by biochemical inhibitors or elongated cell shape abrogated the counterclockwise bias of NIH 3T3 fibroblasts. Our finding reveals a LR-biased torque of single cells and a fundamental origin of cytoskeletal chirality. More broadly, we anticipate that our method will provide a different perspective on mechanics-related cell physiology and force transmission necessary for LR propagation in tissue formation.

Substrate Stiffness Regulates the Development of Left-Right Asymmetry in Cell Orientation

Left-right (LR) asymmetry of tissue/organ structure is a morphological feature essential for many tissue functions. The ability to incorporate the LR formation in constructing tissue/organ replacement is important for recapturing the inherent tissue structure and functions. However, how LR asymmetry is formed remains largely underdetermined, which creates significant hurdles to reproduce and regulate the formation of LR asymmetry in an engineering context. Here, we report substrate rigidity functioning as an effective switch that turns on the development of LR asymmetry. Using micropatterned cell-adherent stripes on rigid substrates, we found that cells collectively oriented at a LR-biased angle relative to the stripe boundary. This LR asymmetry was initiated by a LR-biased migration of cells at stripe boundary, which later generated a velocity gradient propagating from stripe boundary to the center. After a series of cell translocations and rotations, ultimately, an LR-biased cell orientation within the micropatterned stripe was formed. Importantly, this initiation and propagation of LR asymmetry was observed only on rigid but not on soft substrates, suggesting that the LR asymmetry was regulated by rigid substrate probably through the organization of actin cytoskeleton. Together, we demonstrated substrate rigidity as a determinant factor that mediates the self-organizing LR asymmetry being unfolded from single cells to multicellular organization. More broadly, we anticipate that our findings would pave the way for rebuilding artificial tissue constructs with inherent LR asymmetry in the future.