Roadmap for the multiscale coupling of biochemical and mechanical signals during development

Real-time high-resolution microscopy reveals how single-cell lysis shapes biofilm matrix morphogenesis

During development, multiscale patterning requires that cells organize their behavior in space and time. Bacteria in biofilms must similarly dynamically pattern their behavior with a simpler toolkit. Like in eukaryotes, morphogenesis of the extracellular matrix is essential for biofilm development, but how it is patterned has remained unclear. Here, we explain how the architecture of eDNA, a key matrix component, is controlled by single cell lysis events during Pseudomonas aeruginosa biofilm development. We extend single-cell imaging methods to capture complete biofilm development, characterizing the stages of biofilm development and visualizing eDNA matrix morphogenesis. Mapping the spatiotemporal distribution of single cell lysis events reveals that cell lysis is restricted to a specific biofilm zone. Simulations indicate that this patterning couples cell lysis to growth, more uniformly distributing eDNA throughout the biofilm. Finally, we find that patterning of cell lysis is organized by nutrient gradients that act as positioning cues.

Reorganizing chromatin by cellular deformation

Biologists have the capability to edit a genome at the nanometer scale and then observe whether or not the edit affects the structure of a developing organ or organism at the centimeter scale. Our understanding of the underlying mechanisms driving this emergent phenomenon from a multiscale perspective remains incomplete. This review focuses predominantly on recent experimental developments in uncovering the mechanical interplay between the chromatin and cell scale since mechanics plays a major role in determining nuclear, cellular, and tissue structure. Here, we discuss the generation and transmission of forces through the cytoskeleton, affecting chromatin diffusivity and organization. Decoding such pieces of these multiscale connections lays the groundwork for solving the genotype-to-phenotype puzzle in biology.

Correspondence between multiple signaling and developmental cellular patterns: a computational perspective

The spatial arrangement of variant phenotypes during stem cell division plays a crucial role in the self-organization of cell tissues. The patterns observed in these cellular assemblies, where multiple phenotypes vie for space and resources, are largely influenced by a mixture of different diffusible chemical signals. This complex process is carried out within a chronological framework of interplaying intracellular and intercellular events. This includes receiving external stimulants, whether secreted by other individuals or provided by the environment, interpreting these environmental signals, and incorporating the information to designate cell fate. Here, given two distinct signaling patterns generated by Turing systems, we investigated the spatial distribution of differentiating cells that use these signals as external cues for modifying the production rates. By proposing a computational map, we show that there is a correspondence between the multiple signaling and developmental cellular patterns. In other words, the model provides an appropriate prediction for the final structure of the differentiated cells in a multi-signal, multi-cell environment. Conversely, when a final snapshot of cellular patterns is given, our algorithm can partially identify the signaling patterns that influenced the formation of the cellular structure, provided that the governing dynamic of the signaling patterns is already known.

Fly Me to the Micron: Microtechnologies for Drosophila Research

Multicellular model organisms, such as Drosophila melanogaster (fruit fly), are frequently used in a myriad of biological research studies due to their biological significance and global standardization. However, traditional tools used in these studies generally require manual handling, subjective phenotyping, and bulk treatment of the organisms, resulting in laborious experimental protocols with limited accuracy. Advancements in microtechnology over the course of the last two decades have allowed researchers to develop automated, high-throughput, and multifunctional experimental tools that enable novel experimental paradigms that would not be possible otherwise. We discuss recent advances in microtechnological systems developed for small model organisms using D. melanogaster as an example. We critically analyze the state of the field by comparing the systems produced for different applications. Additionally, we suggest design guidelines, operational tips, and new research directions based on the technical and knowledge gaps in the literature. This review aims to foster interdisciplinary work by helping engineers to familiarize themselves with model organisms while presenting the most recent advances in microengineering strategies to biologists.

Mechanics of human embryo compaction

The shaping of human embryos begins with compaction, during which cells come into close contact1,2. Assisted reproductive technology studies indicate that human embryos fail compaction primarily because of defective adhesion3,4. On the basis of our current understanding of animal morphogenesis5,6, other morphogenetic engines, such as cell contractility, could be involved in shaping human embryos. However, the molecular, cellular and physical mechanisms driving human embryo morphogenesis remain uncharacterized. Using micropipette aspiration on human embryos donated to research, we have mapped cell surface tensions during compaction. This shows a fourfold increase of tension at the cell-medium interface whereas cell-cell contacts keep a steady tension. Therefore, increased tension at the cell-medium interface drives human embryo compaction, which is qualitatively similar to compaction in mouse embryos7. Further comparison between human and mouse shows qualitatively similar but quantitively different mechanical strategies, with human embryos being mechanically least efficient. Inhibition of cell contractility and cell-cell adhesion in human embryos shows that, whereas both cellular processes are required for compaction, only contractility controls the surface tensions responsible for compaction. Cell contractility and cell-cell adhesion exhibit distinct mechanical signatures when faulty. Analysing the mechanical signature of naturally failing embryos, we find evidence that non-compacting or partially compacting embryos containing excluded cells have defective contractility. Together, our study shows that an evolutionarily conserved increase in cell contractility is required to generate the forces driving the first morphogenetic movement shaping the human body.

Elastic fibers define embryonic tissue stiffness to enable buckling morphogenesis of the small intestine

During embryonic development, tissues must possess precise material properties to ensure that cell-generated forces give rise to the stereotyped morphologies of developing organs. However, the question of how material properties are established and regulated during development remains understudied. Here, we aim to address these broader questions through the study of intestinal looping, a process by which the initially straight intestinal tube buckles into loops, permitting ordered packing within the body cavity. Looping results from elongation of the tube against the constraint of an attached tissue, the dorsal mesentery, which is elastically stretched by the elongating tube to nearly triple its length. This elastic energy storage allows the mesentery to provide stable compressive forces that ultimately buckle the tube into loops. Beginning with a transcriptomic analysis of the mesentery, we identified widespread upregulation of extracellular matrix related genes during looping, including genes related to elastic fiber deposition. Combining molecular and mechanical analyses, we conclude that elastin confers tensile stiffness to the mesentery, enabling its mechanical role in organizing the developing small intestine. These results shed light on the role of elastin as a driver of morphogenesis that extends beyond its more established role in resisting cyclic deformation in adult tissues.

Tug-of-war via ERK signaling pathway for tissue organization - ERK activation to force generation

Extracellular signal-regulated kinase (ERK) plays a crucial role in regulating collective cell behaviors observed in diverse biological phenomena. Emerging studies have shed light on the involvement of the ERK signaling pathway in the reception and generation of mechanical forces, thereby governing local mechanical interactions within multicellular tissues. Although limited in number, studies have provided insights into how ERK-mediated mechanical interactions contribute to multicellular organization. Here we explore the impact of ERK-mediated mechanical interactions on tissue morphogenesis, cell extrusion in homeostasis, and their interplay with the physical microenvironments of the extracellular matrix. We conclude that the coupling system of ERK activity with mechanical forces offers a promising avenue to unravel the emergent collective dynamics underlying tissue organization.

Morphogens enable interacting supracellular phases that generate organ architecture

During vertebrate organogenesis, increases in morphological complexity are tightly coupled to morphogen expression. In this work, we studied how morphogens influence self-organizing processes at the collective or "supra"-cellular scale in avian skin. We made physical measurements across length scales, which revealed morphogen-enabled material property differences that were amplified at supracellular scales in comparison to cellular scales. At the supracellular scale, we found that fibroblast growth factor (FGF) promoted "solidification" of tissues, whereas bone morphogenetic protein (BMP) promoted fluidity and enhanced mechanical activity. Together, these effects created basement membrane-less compartments within mesenchymal tissue that were mechanically primed to drive avian skin tissue budding. Understanding this multiscale process requires the ability to distinguish between proximal effects of morphogens that occur at the cellular scale and their functional effects, which emerge at the supracellular scale.

A mechanism-based theory of cellular and tissue plasticity

Plastic deformation in cells and tissues has been found to play crucial roles in collective cell migration, cancer metastasis, and morphogenesis. However, the fundamental question of how plasticity is initiated in individual cells and then propagates within the tissue remains elusive. Here, we develop a mechanism-based theory of cellular and tissue plasticity that accounts for all key processes involved, including the activation and development of active contraction at different scales as well as the formation of endocytic vesicles on cell junctions and show that this theory achieves quantitative agreement with all existing experiments. Specifically, it reveals that, in response to optical or mechanical stimuli, the myosin contraction and thermal fluctuation-assisted formation and pinching of endocytic vesicles could lead to permanent shortening of cell junctions and that such plastic constriction can stretch neighboring cells and trigger their active contraction through mechanochemical feedbacks and eventually their plastic deformations as well. Our theory predicts that endocytic vesicles with a size around 1 to 2 µm will most likely be formed and a higher irreversible shortening of cell junctions could be achieved if a long stimulation is split into multiple short ones, all in quantitative agreement with experiments. Our analysis also shows that constriction of cells in tissue can undergo elastic/unratcheted to plastic/ratcheted transition as the magnitude and duration of active contraction increases, ultimately resulting in the propagation of plastic deformation waves within the monolayer with a constant speed which again is consistent with experimental observations.

Cell contractility in early animal evolution

Tissue deformation mediated by collective cell contractility is a signature characteristic of animals. In most animals, fast and reversible contractions of muscle cells mediate behavior, while slow and irreversible contractions of epithelial or mesenchymal cells play a key role in morphogenesis. Animal tissue contractility relies on the activity of the actin/myosin II complex (together referred to as 'actomyosin'), an ancient and versatile molecular machinery that performs a broad range of functions in development and physiology. This review synthesizes emerging insights from morphological and molecular studies into the evolutionary history of animal contractile tissue. The most ancient functions of actomyosin are cell crawling and cytokinesis, which are found in a wide variety of unicellular eukaryotes and in individual metazoan cells. Another contractile functional module, apical constriction, is universal in metazoans and shared with choanoflagellates, their closest known living relatives. The evolution of animal contractile tissue involved two key innovations: firstly, the ability to coordinate and integrate actomyosin assembly across multiple cells, notably to generate supracellular cables, which ensure tissue integrity but also allow coordinated morphogenesis and movements at the organism scale; and secondly, the evolution of dedicated contractile cell types for adult movement, belonging to two broad categories respectively defined by the expression of the fast (striated-type) and slow (smooth/non-muscle-type) myosin II paralogs. Both contractile cell types ancestrally resembled generic contractile epithelial or mesenchymal cells and might have played a versatile role in both behavior and morphogenesis. Modern animal contractile cells span a continuum between unspecialized contractile epithelia (which underlie behavior in modern placozoans), epithelia with supracellular actomyosin cables (found in modern sponges), epitheliomuscular tissues (with a concentration of actomyosin cables in basal processes, for example in sea anemones), and specialized muscle tissue that has lost most or all epithelial properties (as in ctenophores, jellyfish and bilaterians). Recent studies in a broad range of metazoans have begun to reveal the molecular basis of these transitions, powered by the elaboration of the contractile apparatus and the evolution of 'core regulatory complexes' of transcription factors specifying contractile cell identity.

How to Grow a Flat Leaf

Growing a flat lamina such as a leaf is almost impossible without some feedback to stabilize long wavelength modes that are easy to trigger since they are energetically cheap. Here we combine the physics of thin elastic plates with feedback control theory to explore how a leaf can remain flat while growing. We investigate both in-plane (metric) and out-of-plane (curvature) growth variation and account for both local and nonlocal feedback laws. We show that a linearized feedback theory that accounts for both spatially nonlocal and temporally delayed effects suffices to suppress long wavelength fluctuations effectively and explains recently observed statistical features of growth in tobacco leaves. Our work provides a framework for understanding the regulation of the shape of leaves and other leaflike laminar objects.

ELASTIC FIBERS DEFINE EMBRYONIC TISSUE STIFFNESS TO ENABLE BUCKLING MORPHOGENESIS OF THE SMALL INTESTINE

During embryonic development, tissues must possess precise material properties to ensure that cell-generated forces give rise to the stereotyped morphologies of developing organs. However, the question of how material properties are established and regulated during development remains understudied. Here, we aim to address these broader questions through the study of intestinal looping, a process by which the initially straight intestinal tube buckles into loops, permitting ordered packing within the body cavity. Looping results from elongation of the tube against the constraint of an attached tissue, the dorsal mesentery, which is elastically stretched by the elongating tube to nearly triple its length. This elastic energy storage allows the mesentery to provide stable compressive forces that ultimately buckle the tube into loops. Beginning with a transcriptomic analysis of the mesentery, we identified widespread upregulation of extracellular matrix related genes during looping, including genes related to elastic fiber deposition. Combining molecular and mechanical analyses, we conclude that elastin confers tensile stiffness to the mesentery, enabling its mechanical role in organizing the developing small intestine. These results shed light on the role of elastin as a driver of morphogenesis that extends beyond its more established role in resisting cyclic deformation in adult tissues.

Mathematical modeling for developmental processes

We review several mathematical models and concepts in developmental biology that have been established over the last decade. (1) Feedback vertex set: Ascidian embryos contain cells of seven types, and cell fate is controlled by ~100 interacting genes. The "feedback vertex set" of the directed graph of the gene regulatory network consists of a small number of genes. By experimentally manipulating them, we can differentiate cells into any cell type. (2) Tissue deformation: Describing morphological changes in tissues and relating them to gene expression and other cellular processes is key in understanding morphogenesis. Expansion and anisotropy of the tissue are described by a "deformation tensor" at each location. A study on chick limb bud formation revealed that both the volume growth rate and anisotropy in deformation differed significantly between locations and stages. (3) Mechanobiology: Forces operating on each cell may alter cell shape and gene expression, which may subsequently exert forces on their surroundings. Measurements of force, tissue shape, and gene expression help us understand autonomous tissue deformation. (4) Adaptive design of development: An optimal growth schedule in fluctuating environments explains the growth response to starvation in Drosophila larvae. Adaptive placement of morphogen sources makes development robust to noises.

A chemo-mechanical model of endoderm movements driving elongation of the amniote hindgut

While mechanical and biochemical descriptions of development are each essential, integration of upstream morphogenic cues with downstream tissue mechanics remains understudied in many contexts during vertebrate morphogenesis. A posterior gradient of Fibroblast Growth Factor (FGF) ligands generates a contractile force gradient in the definitive endoderm, driving collective cell movements to form the hindgut. Here, we developed a two-dimensional chemo-mechanical model to investigate how mechanical properties of the endoderm and transport properties of FGF coordinately regulate this process. We began by formulating a 2-D reaction-diffusion-advection model that describes the formation of an FGF protein gradient due to posterior displacement of cells transcribing unstable Fgf8 mRNA during axis elongation, coupled with translation, diffusion, and degradation of FGF protein. This was used together with experimental measurements of FGF activity in the chick endoderm to inform a continuum model of definitive endoderm as an active viscous fluid that generates contractile stresses in proportion to FGF concentration. The model replicated key aspects of hindgut morphogenesis, confirms that heterogeneous - but isotropic - contraction is sufficient to generate large anisotropic cell movements, and provides new insight into how chemo-mechanical coupling across the mesoderm and endoderm coordinates hindgut elongation with outgrowth of the tailbud.

Precise alternating cellular pattern in the inner ear by coordinated hopping intercalations and delaminations

The mammalian hearing organ, the organ of Corti, is one of the most organized tissues in mammals. It contains a precisely positioned array of alternating sensory hair cells (HCs) and nonsensory supporting cells. How such precise alternating patterns emerge during embryonic development is not well understood. Here, we combine live imaging of mouse inner ear explants with hybrid mechano-regulatory models to identify the processes that underlie the formation of a single row of inner hair cells (IHCs). First, we identify a previously unobserved morphological transition, termed "hopping intercalation," that allows cells differentiating toward IHC fate to "hop" under the apical plane into their final position. Second, we show that out-of-row cells with low levels of the HC marker Atoh1 delaminate. Last, we show that differential adhesion between cell types contributes to straightening of the IHC row. Our results support a mechanism for precise patterning based on coordination between signaling and mechanical forces that is likely relevant for many developmental processes.

Orchestration of tissue shape changes and gene expression patterns in development

In development, tissue shape changes and gene expression patterns give rise to morphogenesis. Understanding tissue shape changes requires the analysis of mechanical properties of the tissue such as tissue rigidity, cell influx from neighboring tissues, cell shape changes and cell proliferation. Local and global gene expression patterns can be influenced by neighbor exchange and tissue shape changes. Here we review recent studies on the mechanisms for tissue elongation and its influences on dynamic gene expression patterns by focusing on vertebrate somitogenesis. We first introduce mechanical and biochemical properties of the segmenting tissue that drive tissue elongation. Then, we discuss patterning in the presence of cell mixing, scaling of signaling gradients, and dynamic phase waves of rhythmic gene expression under tissue shape changes. We also highlight the importance of theoretical approaches to address the relation between tissue shape changes and patterning.

Reconstruction of distinct vertebrate gastrulation modes via modulation of key cell behaviors in the chick embryo

The morphology of gastrulation driving the internalization of the mesoderm and endoderm differs markedly among vertebrate species. It ranges from involution of epithelial sheets of cells through a circular blastopore in amphibians to ingression of mesenchymal cells through a primitive streak in amniotes. By targeting signaling pathways controlling critical cell behaviors in the chick embryo, we generated crescent- and ring-shaped mesendoderm territories in which cells can or cannot ingress. These alterations subvert the formation of the chick primitive streak into the gastrulation modes seen in amphibians, reptiles, and teleost fish. Our experimental manipulations are supported by a theoretical framework linking cellular behaviors to self-organized multicellular flows outlined in detail in the accompanying paper. Together, this suggests that the evolution of gastrulation movements is largely determined by changes in a few critical cell behaviors in the mesendoderm territory across different species and controlled by a relatively small number of signaling pathways.

Modeling Biochemical Gradients In Vitro to Control Cell Compartmentalization in a Microengineered 3D Model of the Intestinal Epithelium

Gradients of signaling pathways within the intestinal stem cell (ISC) niche are instrumental for cellular compartmentalization and tissue function, yet how are they sensed by the epithelium is still not fully understood. Here a new in vitro model of the small intestine based on primary epithelial cells (i), apically accessible (ii), with native tissue mechanical properties and controlled mesh size (iii), 3D villus-like architecture (iv), and precisely controlled biomolecular gradients of the ISC niche (v) is presented. Biochemical gradients are formed through hydrogel-based scaffolds by free diffusion from a source to a sink chamber. To confirm the establishment of spatiotemporally controlled gradients, light-sheet fluorescence microscopy and in-silico modeling are employed. The ISC niche biochemical gradients coming from the stroma and applied along the villus axis lead to the in vivo-like compartmentalization of the proliferative and differentiated cells, while changing the composition and concentration of the biochemical factors affects the cellular organization along the villus axis. This novel 3D in vitro intestinal model derived from organoids recapitulates both the villus-like architecture and the gradients of ISC biochemical factors, thus opening the possibility to study in vitro the nature of such gradients and the resulting cellular response.

A physical model for dynamic assembly of human salivary stem/progenitor microstructures

The in vitro reconstructions of human salivary glands in service of their eventual medical use represent a challenge for tissue engineering. Here, we present a theoretical approach to the dynamical formation of acinar structures from human salivary cells, focusing on observed stick-slip radial expansion as well as possible growth instabilities. Our findings demonstrate the critical importance of basement membrane remodeling in controlling the growth process.

Image-based parameter inference for epithelial mechanics

Measuring mechanical parameters in tissues, such as the elastic modulus of cell-cell junctions, is essential to decipher the mechanical control of morphogenesis. However, their in vivo measurement is technically challenging. Here, we formulated an image-based statistical approach to estimate the mechanical parameters of epithelial cells. Candidate mechanical models are constructed based on force-cell shape correlations obtained from image data. Substitution of the model functions into force-balance equations at the cell vertex leads to an equation with respect to the parameters of the model, by which one can estimate the parameter values using a least-squares method. A test using synthetic data confirmed the accuracy of parameter estimation and model selection. By applying this method to Drosophila epithelial tissues, we found that the magnitude and orientation of feedback between the junction tension and shrinkage, which are determined by the spring constant of the junction, were correlated with the elevation of tension and myosin-II on shrinking junctions during cell rearrangement. Further, this method clarified how alterations in tissue polarity and stretching affect the anisotropy in tension parameters. Thus, our method provides a novel approach to uncovering the mechanisms governing epithelial morphogenesis.

Learning developmental mode dynamics from single-cell trajectories

Embryogenesis is a multiscale process during which developmental symmetry breaking transitions give rise to complex multicellular organisms. Recent advances in high-resolution live-cell microscopy provide unprecedented insights into the collective cell dynamics at various stages of embryonic development. This rapid experimental progress poses the theoretical challenge of translating high-dimensional imaging data into predictive low-dimensional models that capture the essential ordering principles governing developmental cell migration in complex geometries. Here, we combine mode decomposition ideas that have proved successful in condensed matter physics and turbulence theory with recent advances in sparse dynamical systems inference to realize a computational framework for learning quantitative continuum models from single-cell imaging data. Considering pan-embryo cell migration during early gastrulation in zebrafish as a widely studied example, we show how cell trajectory data on a curved surface can be coarse-grained and compressed with suitable harmonic basis functions. The resulting low-dimensional representation of the collective cell dynamics enables a compact characterization of developmental symmetry breaking and the direct inference of an interpretable hydrodynamic model, which reveals similarities between pan-embryo cell migration and active Brownian particle dynamics on curved surfaces. Due to its generic conceptual foundation, we expect that mode-based model learning can help advance the quantitative biophysical understanding of a wide range of developmental structure formation processes.

Sculpting with stem cells: how models of embryo development take shape

During embryogenesis, organisms acquire their shape given boundary conditions that impose geometrical, mechanical and biochemical constraints. A detailed integrative understanding how these morphogenetic information modules pattern and shape the mammalian embryo is still lacking, mostly owing to the inaccessibility of the embryo in vivo for direct observation and manipulation. These impediments are circumvented by the developmental engineering of embryo-like structures (stembryos) from pluripotent stem cells that are easy to access, track, manipulate and scale. Here, we explain how unlocking distinct levels of embryo-like architecture through controlled modulations of the cellular environment enables the identification of minimal sets of mechanical and biochemical inputs necessary to pattern and shape the mammalian embryo. We detail how this can be complemented with precise measurements and manipulations of tissue biochemistry, mechanics and geometry across spatial and temporal scales to provide insights into the mechanochemical feedback loops governing embryo morphogenesis. Finally, we discuss how, even in the absence of active manipulations, stembryos display intrinsic phenotypic variability that can be leveraged to define the constraints that ensure reproducible morphogenesis in vivo.

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.