Direct Activation of Nucleobases with Small Molecules for the Conditional Control of Antisense Function.

Conditionally controlled antisense oligonucleotides provide precise interrogation of gene function at different developmental stages in animal models. Only one example of small molecule-induced activation of antisense function exist. This has been restricted to cyclic caged morpholinos that, based on sequence, can have significant background activity in the absence of the trigger. Here, we provide a new approach using azido-caged nucleobases that are site-specifically introduced into antisense morpholinos. The caging group design is a simple azidomethylene (Azm) group that, despite its very small size, efficiently blocks Watson-Crick base pairing in a programmable fashion. Furthermore, it undergoes facile decaging via Staudinger reduction when exposed to a small molecule phosphine, generating the native antisense oligonucleotide under conditions compatible with biological environments. We demonstrated small molecule-induced gene knockdown in mammalian cells, zebrafish embryos, and frog embryos. We validated the general applicability of this approach by targeting three different genes.

Shear Stress and Sub-Femtomolar Levels of Ligand Synergize to Activate ALK1 Signaling in Endothelial Cells.

Endothelial cells (ECs) respond to concurrent stimulation by biochemical factors and wall shear stress (SS) exerted by blood flow. Disruptions in flow-induced responses can result in remodeling issues and cardiovascular diseases, but the detailed mechanisms linking flow-mechanical cues and biochemical signaling remain unclear. Activin receptor-like kinase 1 (ALK1) integrates SS and ALK1-ligand cues in ECs; ALK1 mutations cause hereditary hemorrhagic telangiectasia (HHT), marked by arteriovenous malformation (AVM) development. However, the mechanistic underpinnings of ALK1 signaling modulation by fluid flow and the link to AVMs remain uncertain. We recorded EC responses under varying SS magnitudes and ALK1 ligand concentrations by assaying pSMAD1/5/9 nuclear localization using a custom multi-SS microfluidic device and a custom image analysis pipeline. We extended the previously reported synergy between SS and BMP9 to include BMP10 and BMP9/10. Moreover, we demonstrated that this synergy is effective even at extremely low SS magnitudes (0.4 dyn/cm2) and ALK1 ligand range (femtogram/mL). The synergistic response to ALK1 ligands and SS requires the kinase activity of ALK1. Moreover, ALK1's basal activity and response to minimal ligand levels depend on endocytosis, distinct from cell-cell junctions, cytoskeleton-mediated mechanosensing, or cholesterol-enriched microdomains. However, an in-depth analysis of ALK1 receptor trafficking's molecular mechanisms requires further investigation.

Expanding the Genetic Code of Xenopus laevis Embryos.

The incorporation of unnatural amino acids into proteins through genetic code expansion has been successfully adapted to African claw-toed frog embryos. Six unique unnatural amino acids are incorporated site-specifically into proteins and demonstrate robust and reliable protein expression. Of these amino acids, several are caged analogues that can be used to establish conditional control over enzymatic activity. Using light or small molecule triggers, we exhibit activation and tunability of protein functions in live embryos. This approach was then applied to optical control over the activity of a RASopathy mutant of NRAS, taking advantage of generating explant cultures from Xenopus. Taken together, genetic code expansion is a robust approach in the Xenopus model to incorporate novel chemical functionalities into proteins of interest to study their function and role in a complex biological setting.

Constructing the pharyngula: Connecting the primary axial tissues of the head with the posterior axial tissues of the tail.

The pharyngula stage of vertebrate development is characterized by stereotypical arrangement of ectoderm, mesoderm, and neural tissues from the anterior spinal cord to the posterior, yet unformed tail. While early embryologists over-emphasized the similarity between vertebrate embryos at the pharyngula stage, there is clearly a common architecture upon which subsequent developmental programs generate diverse cranial structures and epithelial appendages such as fins, limbs, gills, and tails. The pharyngula stage is preceded by two morphogenetic events: gastrulation and neurulation, which establish common shared structures despite the occurrence of cellular processes that are distinct to each of the species. Even along the body axis of a singular organism, structures with seemingly uniform phenotypic characteristics at the pharyngula stage have been established by different processes. We focus our review on the processes underlying integration of posterior axial tissue formation with the primary axial tissues that creates the structures laid out in the pharyngula. Single cell sequencing and novel gene targeting technologies have provided us with new insights into the differences between the processes that form the anterior and posterior axis, but it is still unclear how these processes are integrated to create a seamless body. We suggest that the primary and posterior axial tissues in vertebrates form through distinct mechanisms and that the transition between these mechanisms occur at different locations along the anterior-posterior axis. Filling gaps that remain in our understanding of this transition could resolve ongoing problems in organoid culture and regeneration.

Dynamic fibronectin assembly and remodeling by leader neural crest cells prevents jamming in collective cell migration.

Collective cell migration plays an essential role in vertebrate development, yet the extent to which dynamically changing microenvironments influence this phenomenon remains unclear. Observations of the distribution of the extracellular matrix (ECM) component fibronectin during the migration of loosely connected neural crest cells (NCCs) lead us to hypothesize that NCC remodeling of an initially punctate ECM creates a scaffold for trailing cells, enabling them to form robust and coherent stream patterns. We evaluate this idea in a theoretical setting by developing an individual-based computational model that incorporates reciprocal interactions between NCCs and their ECM. ECM remodeling, haptotaxis, contact guidance, and cell-cell repulsion are sufficient for cells to establish streams in silico, however, additional mechanisms, such as chemotaxis, are required to consistently guide cells along the correct target corridor. Further model investigations imply that contact guidance and differential cell-cell repulsion between leader and follower cells are key contributors to robust collective cell migration by preventing stream breakage. Global sensitivity analysis and simulated gain- and loss-of-function experiments suggest that long-distance migration without jamming is most likely to occur when leading cells specialize in creating ECM fibers, and trailing cells specialize in responding to environmental cues by upregulating mechanisms such as contact guidance.

Microsurgical Methods to Isolate and Culture the Early Gastrula Dorsal Marginal Zone.

Marginal zone explants from Xenopus embryos can be used to expose cell behaviors and tissue movements that normally operate in dorsal tissues. Dorsal explants comprise the diverse set of progenitor cells found in dorsal tissues including mesendoderm, head mesoderm, prechordal mesoderm, endoderm with bottle cells, axial mesoderm of the prospective notochord, paraxial mesoderm of the somites, lateral plate mesoderm, neural ectoderm, and ectoderm. Unlike an organoid, the dorsal marginal zone (DMZ) explant is "organotypic" in that microsurgery does not disrupt native tissue organization beyond manipulations needed to dissect the tissue from the embryo. An organotypic early gastrula DMZ explant preserves boundaries and close tissue associations in the native marginal zone. Depending on the stage, patterning and cell identities can be maintained in explants and tissue isolates. Local cell movements and behaviors may also be preserved; however, the large-scale biomechanical impact of their collective movements may be altered from those in the native marginal zone. For instance, involution is typically inhibited in the DMZ explant, precluding the two-layer association of mesoderm and prospective neural ectoderm normally achieved during gastrulation. DMZ explants may be mounted and imaged in a variety of ways, exposing interesting cell behaviors or collective movements such as mediolateral cell intercalation in the axial and paraxial mesoderm, apical constriction of bottle cells, and directional migration of mesendoderm. The flattened DMZ explant can also be used to study emergence of new tissue-defining boundaries such as the notochord-somite boundary, the ectoderm-mesoderm boundary, and the mesendoderm-mesoderm boundary.

Microsurgical Methods to Make the Keller Sandwich Explant and the Dorsal Isolate.

This protocol summarizes preparation of the dorsal marginal zone sandwich explant (a.k.a. the "Keller sandwich") and the dorsal isolate from Xenopus embryos. The Keller sandwich is assembled from two early gastrula stage dorsal marginal zone (DMZ) explants. DMZ explants isolated before involution maintain planar patterning processes and block radial signals that might be exchanged between pre- and postinvolution tissues. DMZ explants isolated later in gastrulation, but subsequently opened and flattened may have both planar and radial patterning. The epithelial margins of DMZ explants in Keller sandwiches heal and basal contacts form between the deep layers of the two DMZ explants. The dorsal isolate is dissected from mid- to late-gastrula stage embryos after involution and archenteron formation. Germ-layer contacts between dorsal endoderm, mesoderm, and ectoderm generated by gastrulation movements are maintained in the dorsal isolate. These two explants can be used to study tissue, cell, and subcellular processes relevant to convergent extension, from patterning to cell behaviors, and their collective biomechanics. Skills needed to dissect the Keller sandwich are greater than those needed to dissect animal cap ectoderm and can be mastered in a few weeks; skills needed to dissect the dorsal isolate are similar to those needed to dissect animal caps and can be learned in a week.

Microsurgical Manipulations to Isolate Collectively Migrating Mesendoderm.

Mesendoderm mantle closure completes the gastrulation movements of the Xenopus laevis embryo and provides an unparalleled opportunity to study collective cell behaviors within a mesenchymal tissue. Free-edge sheet-like collective movements of these tissues contrast with movements of epithelial tissues in that mesendodermal cells are not constrained by tight junctions or adherens junctions, yet migrate in a coherent and persistent mode over several hours. Mesendoderm cells are the largest motile cells in the Xenopus embryo and complete a 500-µm migratory path. When mesendoderm is cultured on rigid glass substrates, these cells can exceed 100 µm in length and show a highly persistent leading lamellipodia that can exceed 20 µm from tip to base. These large collectively migrating cells provide a unique imaging opportunity to visualize polarized adhesive and cytoskeletal structures with high-numerical-aperture objectives. Mesendodermal cells in the early embryo originate from around the entirety of the marginal zone and may also be distinguished by their source along the animal-vegetal axis. Here we use the term mesendoderm but note alternative terms for these cells can include head mesoderm, endomesoderm, and prechordal mesoderm. This protocol summarizes microsurgical preparation of mesendoderm tissue explants and "windowed" embryos. Skills needed to dissect fragments of the mesendoderm mantle are marginally greater than those needed to isolate animal cap ectoderm and can be mastered within 2 weeks; skills needed to isolate the mesendoderm "donut" or "ring" or to prepare windowed embryos are significantly greater and may require several additional weeks of training.

Chambers for Culturing and Immobilizing Xenopus Embryos and Organotypic Explants for Live Imaging.

Live imaging of Xenopus embryos and organotypic explants can be challenging because of their large size and slippery nature. This protocol covers the preparation of special chambers for immobilizing Xenopus embryos and embryonic explants for live-cell and tissue imaging. The opaque nature of Xenopus embryonic tissues enables simple bright-field imaging techniques for tracking surface movements across large regions. Such surface imaging of embryos or organotypic explants can directly reveal cell behaviors, obviating the need for complex postprocessing commonly required to extract this data from 3D confocal or light-sheet observations of more transparent embryos. Furthermore, Xenopus embryos may be filled with light-absorbing pigment granules and light-scattering yolk platelets, but these limitations are offset by the utilitarian nature of Xenopus organotypic explants that expose and stabilize large embryonic cells in a nearly native context for high-resolution live-cell imaging. Additionally, whole embryos can be stabilized for long-term bright-field and confocal microscopy. Simple explants can be prepared using a single cell type, and organotypic explants can be prepared in which multiple tissue types are dissected while retaining native tissue-tissue interactions. These preparations enable both in-toto imaging of tissue dynamics and super-resolution imaging of protein dynamics within individual cells. We present detailed protocols for these methods together with references to applications.

Imaging Methods in Xenopus Cells, Embryos, and Tadpoles.

Xenopus is an excellent vertebrate model system ideally suited for a wide range of imaging methods designed to investigate cell and developmental biology processes. The individual cells of Xenopus are much larger than those in many other vertebrate model systems, such that both cell behavior and subcellular processes can more easily be observed and resolved. Gene function in Xenopus can be manipulated and visualized using a variety of approaches, and the embryonic fate map is stereotypical, such that microinjections can target specific tissues and cell types during development. Tissues, organotypic explants, and individual cells can also be mounted in stable chambers and cultured easily in simple salt solutions without cumbersome environmental controls. Furthermore, Xenopus embryonic tissues can be microsurgically isolated and shaped to expose cell behaviors and protein dynamics in any regions of the embryo to high-resolution live-cell imaging. The combination of these attributes makes Xenopus a powerful system for understanding cell and developmental processes as well as disease mechanisms, through quantitative analysis of protein dynamics, cell movements, tissue morphogenesis, and regeneration. Here, we introduce various methods, of both fixed and living tissues, for visualizing Xenopus cells, embryos, and tadpoles. Specifically, we highlight protocol updates for whole-mount in situ hybridization and immunofluorescence, as well as robust live imaging approaches including methods for optimizing the time-lapse imaging of whole embryos and explants.

Furry is required for cell movements during gastrulation and functionally interacts with NDR1.

Gastrulation is a key event in animal embryogenesis during which germ layer precursors are rearranged and the embryonic axes are established. Cell polarization is essential during gastrulation, driving asymmetric cell division, cell movements, and cell shape changes. The furry (fry) gene encodes an evolutionarily conserved protein with a wide variety of cellular functions, including cell polarization and morphogenesis in invertebrates. However, little is known about its function in vertebrate development. Here, we show that in Xenopus, Fry plays a role in morphogenetic processes during gastrulation, in addition to its previously described function in the regulation of dorsal mesoderm gene expression. Using morpholino knock-down, we demonstrate a distinct role for Fry in blastopore closure and dorsal axis elongation. Loss of Fry function drastically affects the movement and morphological polarization of cells during gastrulation and disrupts dorsal mesoderm convergent extension, responsible for head-to-tail elongation. Finally, we evaluate a functional interaction between Fry and NDR1 kinase, providing evidence of an evolutionarily conserved complex required for morphogenesis.

Xenopus Deep Cell Aggregates: A 3D Tissue Model for Mesenchymal-to-Epithelial Transition.

Mesenchymal-to-epithelial transition (MET) describes the ability of loosely associated migratory cells to form a more adherent sheet-like assembly of cells. MET is a conserved motif occurring throughout organogenesis and plays a key role in regeneration and cancer metastasis, and is the first step in producing induced pluripotent stem cells (iPSCs). To resolve fundamental biological questions about MET, its relation to epithelial-to-mesenchymal transition, and to explore MET's role in tissue assembly and remodeling requires live models for MET that are amenable to experimentation. Many cases of clinically important MET are inferred since they occur deep with the body of the embryo or adult. We have developed a tractable model for MET, where cellular transitions can be directly observed under conditions where molecular, mechanical, and cellular contexts can be controlled experimentally. In this chapter, we introduce a 3-dimensional (3D) tissue model to study MET using Xenopus laevis embryonic mesenchymal cell aggregates.

Endothelial cell polarization and orientation to flow in a novel microfluidic multimodal shear stress generator.

Endothelial cells (EC) respond to shear stress to maintain vascular homeostasis, and a disrupted response is associated with cardiovascular diseases. To understand how different shear stress modalities affect EC morphology and behavior, we developed a microfluidic device that concurrently generates three different levels of uniform wall shear stress (WSS) and six different WSS gradients (WSSG). In this device, human umbilical vein endothelial cells (HUVECs) exhibited a rapid and robust response to WSS, with the relative positioning of the Golgi and nucleus transitioning from a non-polarized to polarized state in a WSS magnitude- and gradient-dependent manner. By contrast, polarized HUVECs oriented their Golgi and nucleus polarity to the flow vector in a WSS magnitude-dependent manner, with positive WSSG inhibiting and negative WSSG promoting upstream orientation. Having validated this device, this chip can now be used to dissect the mechanisms underlying EC responses to different WSS modalities, including shear stress gradients, and to investigate the influence of flow on a diverse range of cells during development, homeostasis and disease.

Non-junctional role of Cadherin3 in cell migration and contact inhibition of locomotion via domain-dependent, opposing regulation of Rac1.

Classical cadherins are well-known adhesion molecules responsible for physically connecting neighboring cells and signaling this cell-cell contact. Recent studies have suggested novel signaling roles for "non-junctional" cadherins (NJCads); however, the function of cadherin signaling independent of cell-cell contacts remains unknown. In this study, mesendodermal cells and tissues from gastrula stage Xenopus laevis embryos demonstrate that deletion of extracellular domains of Cadherin3 (Cdh3; formerly C-cadherin in Xenopus) disrupts contact inhibition of locomotion. In both bulk Rac1 activity assays and spatio-temporal FRET image analysis, the extracellular and cytoplasmic Cdh3 domains disrupt NJCad signaling and regulate Rac1 activity in opposing directions. Stabilization of the cytoskeleton counteracted this regulation in single cell migration assays. Our study provides novel insights into adhesion-independent signaling by Cadherin3 and its role in regulating single and collective cell migration.

From biomechanics to mechanobiology: Xenopus provides direct access to the physical principles that shape the embryo.

Features of amphibian embryos that have served so well to elucidate the genetics of vertebrate development also enable detailed analysis of the physics that shape morphogenesis and regulate development. Biophysical tools are revealing how genes control mechanical properties of the embryo. The same tools that describe and control mechanical properties are being turned to reveal how dynamic mechanical information and feedback regulate biological programs of development. In this review we outline efforts to explore the various roles of mechanical cues in guiding cilia biology, axonal pathfinding, goblet cell regeneration, epithelial-to-mesenchymal transitions in neural crest, and mesenchymal-to-epithelial transitions in heart progenitors. These case studies reveal the power of Xenopus experimental embryology to expose pathways integrating mechanical cues with programs of development, organogenesis, and regeneration.

Chemotactic Responses of Jurkat Cells in Microfluidic Flow-Free Gradient Chambers.

Gradients of soluble molecules coordinate cellular communication in a diverse range of multicellular systems. Chemokine-driven chemotaxis is a key orchestrator of cell movement during organ development, immune response and cancer progression. Chemotaxis assays capable of examining cell responses to different chemokines in the context of various extracellular matrices will be crucial to characterize directed cell motion in conditions which mimic whole tissue conditions. Here, a microfluidic device which can generate different chemokine patterns in flow-free gradient chambers while controlling surface extracellular matrix (ECM) to study chemotaxis either at the population level or at the single cell level with high resolution imaging is presented. The device is produced by combining additive manufacturing (AM) and soft lithography. Generation of concentration gradients in the device were simulated and experimentally validated. Then, stable gradients were applied to modulate chemotaxis and chemokinetic response of Jurkat cells as a model for T lymphocyte motility. Live imaging of the gradient chambers allowed to track and quantify Jurkat cell migration patterns. Using this system, it has been found that the strength of the chemotactic response of Jurkat cells to CXCL12 gradient was reduced by increasing surface fibronectin in a dose-dependent manner. The chemotaxis of the Jurkat cells was also found to be governed not only by the CXCL12 gradient but also by the average CXCL12 concentration. Distinct migratory behaviors in response to chemokine gradients in different contexts may be physiologically relevant for shaping the host immune response and may serve to optimize the targeting and accumulation of immune cells to the inflammation site. Our approach demonstrates the feasibility of using a flow-free gradient chamber for evaluating cross-regulation of cell motility by multiple factors in different biologic processes.

Evolutionary expansion of apical extracellular matrix is required for the elongation of cells in a novel structure.

One of the fundamental gaps in our knowledge of how novel anatomical structures evolve is understanding the origins of the morphogenetic processes that form these features. Here, we traced the cellular development of a recently evolved morphological novelty, the posterior lobe of D. melanogaster. We found that this genital outgrowth forms through extreme increases in epithelial cell height. By examining the apical extracellular matrix (aECM), we also uncovered a vast matrix associated with the developing genitalia of lobed and non-lobed species. Expression of the aECM protein Dumpy is spatially expanded in lobe-forming species, connecting the posterior lobe to the ancestrally derived aECM network. Further analysis demonstrated that Dumpy attachments are necessary for cell height increases during posterior lobe development. We propose that the aECM presents a rich reservoir for generating morphological novelty and highlights a yet unseen role for aECM in regulating extreme cell height.

Tissue mechanics drives regeneration of a mucociliated epidermis on the surface of Xenopus embryonic aggregates.

Injury, surgery, and disease often disrupt tissues and it is the process of regeneration that aids the restoration of architecture and function. Regeneration can occur through multiple strategies including stem cell expansion, transdifferentiation, or proliferation of differentiated cells. We have identified a case of regeneration in Xenopus embryonic aggregates that restores a mucociliated epithelium from mesenchymal cells. Following disruption of embryonic tissue architecture and assembly of a compact mesenchymal aggregate, regeneration first restores an epithelium, transitioning from mesenchymal cells at the surface of the aggregate. Cells establish apico-basal polarity within 5 hours and a mucociliated epithelium within 24 hours. Regeneration coincides with nuclear translocation of the putative mechanotransducer YAP1 and a sharp increase in aggregate stiffness, and regeneration can be controlled by altering stiffness. We propose that regeneration of a mucociliated epithelium occurs in response to biophysical cues sensed by newly exposed cells on the surface of a disrupted mesenchymal tissue.

Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: An approximate Bayesian computation approach.

Advanced imaging techniques generate large datasets capable of describing the structure and kinematics of tissue spreading in embryonic development, wound healing, and the progression of many diseases. These datasets can be integrated with mathematical models to infer biomechanical properties of the system, typically identifying an optimal set of parameters for an individual experiment. However, these methods offer little information on the robustness of the fit and are generally ill-suited for statistical tests of multiple experiments. To overcome this limitation and enable efficient use of large datasets in a rigorous experimental design, we use the approximate Bayesian computation rejection algorithm to construct probability density distributions that estimate model parameters for a defined theoretical model and set of experimental data. Here, we demonstrate this method with a 2D Eulerian continuum mechanical model of spreading embryonic tissue. The model is tightly integrated with quantitative image analysis of different sized embryonic tissue explants spreading on extracellular matrix (ECM) and is regulated by a small set of parameters including forces on the free edge, tissue stiffness, strength of cell-ECM adhesions, and active cell shape changes. We find statistically significant trends in key parameters that vary with initial size of the explant, e.g., for larger explants cell-ECM adhesion forces are weaker and free edge forces are stronger. Furthermore, we demonstrate that estimated parameters for one explant can be used to predict the behavior of other similarly sized explants. These predictive methods can be used to guide further experiments to better understand how collective cell migration is regulated during development.

Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf.

Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles and predict the collective cell behavior that follows from a set of interaction rules. In particular, vertex-based models are a popular tool for studying the mechanics of confluent, epithelial cell layers. They represent the junctions between three (or sometimes more) cells in confluent tissues as point particles, connected using structural elements that represent the cell boundaries. A disadvantage of these models is that cell-cell interfaces are represented as straight lines. This is a suitable simplification for epithelial tissues, where the interfaces are typically under tension, but this simplification may not be appropriate for mesenchymal tissues or tissues that are under compression, such that the cell-cell boundaries can buckle. In this paper, we introduce a variant of VMs in which this and two other limitations of VMs have been resolved. The new model can also be seen as on off-the-lattice generalization of the Cellular Potts Model. It is an extension of the open-source package VirtualLeaf, which was initially developed to simulate plant tissue morphogenesis where cells do not move relative to one another. The present extension of VirtualLeaf introduces a new rule for cell-cell shear or sliding, from which cell rearrangement (T1) and cell extrusion (T2) transitions emerge naturally, allowing the application of VirtualLeaf to problems of animal development. We show that the updated VirtualLeaf yields different results than the traditional vertex-based models for differential adhesion-driven cell sorting and for the neighborhood topology of soft cellular networks.