Biology subjects

Streichan, S. J.

Publications and source records attributed to Streichan, S. J..

14 recordsLinked to original sources

bioRxiv2025

Stationary and germ layer-specific cellular flows shape the zebrafish gastrula

During gastrulation, a sequence of complex processes transforms the blastula into a multi-layered embryo. Fixed sample analysis has revealed much about how genetic signaling cascades determine the major body axes and organize cell fate patterns into the germ layers: ectoderm, mesoderm, and endoderm. In toto live imaging of vertebrate development highlights that embryogenesis is a dynamic process that involves on the order of ten thousand cells, but hurdles related to data handling have hampered quantitative analysis. Therefore, our understanding of the rich physical aspects of multilayered tissue reconfigurations remains incomplete. Here, we reveal that modules of stationary and germ-layer-specific tissue flows shape the zebrafish gastrula. We combine in toto live imaging with tissue-specific markers and image analysis to reveal the global shape of the enveloping layer (EVL), epiblast, and mesoderm over time. A user-friendly tissue cartography pipeline based on the Blender 3D software moves into the reference frame of individual tissue layers. We find distinct tissue flow patterns in the enveloping layer (EVL), epiblast, and mesoderm, respectively. The instantaneous tissue flow of these germ layers is organized in a temporal sequence of hours-long, constant flow patterns. This suggests that a sequence of stationary tissue flow modules transports cells to their destination during gastrulation. Mathematical decomposition suggests that epiblast flow is strongly influenced by a superposition of rotational flow in the mesoderm, and divergent flow in the EVL. Molecular and cellular complexity notwithstanding, these results hint at surprisingly, tractable physical processes that underlie vertebrate gastrulation, and set the stage for investigations of how morphogens orchestrate dynamics.

developmental biology↗

bioRxiv2025

Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data

Volumetric microscopy can image complex 3D tissues, but 3D image data remains difficult to visualize and quantify. Many biological systems are organized as thin, curved sheets (for example, epithelia). Tissue cartography extracts and cartographically projects these curved surfaces from volumetric images. This converts 3D into 2D image data, greatly facilitating visualization, analysis, and computational processing. Existing tools, however, demand advanced coding expertise and are limited to simple tissue geometries. Here, we present blender issue cartography (btc), an interactive add-on for the 3D editor Blender that makes tissue cartography user-friendly by a graphical interface, and handles complex biological shapes using powerful computer graphics algorithms. An accompanying Python library supports faithful 3D measurements in 2D cartographic projections and custom analysis pipelines. Time-lapse data can be batch-processed by algorithmically aligning all time points to a single key frame. We demonstrate btc on diverse and complex tissue shapes from Drosophila, stem-cell organoids, Arabidopsis, and zebrafish. btc enables quantitative cartographic analysis of complex 3D tissues, broadening access to methods previously restricted to specialists, while leveraging tools from computer graphics to unlock new capabilities.

bioinformatics↗

bioRxiv2024

YAP dysregulation triggers hypertrophy by CCN2 secretion and TGFβ uptake in human pluripotent stem cell-derived cardiomyocytes

Hypertrophy Cardiomyopathy (HCM) is the most prevalent hereditary cardiovascular disease - affecting >1:500 individuals. Advanced forms of HCM clinically present with hypercontractility, hypertrophy and fibrosis. Several single-point mutations in b-myosin heavy chain (MYH7) have been associated with HCM and increased contractility at the organ level. Different MYH7 mutations have resulted in increased, decreased, or unchanged force production at the molecular level. Yet, how these molecular kinetics link to cell and tissue pathogenesis remains unclear. The Hippo Pathway, specifically its effector molecule YAP, has been demonstrated to be reactivated in pathological hypertrophic growth. We hypothesized that changes in force production (intrinsically or extrinsically) directly alter the homeostatic mechano-signaling of the Hippo pathway through changes in stresses on the nucleus. Using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), we asked whether homeostatic mechanical signaling through the canonical growth regulator, YAP, is altered 1) by changes in the biomechanics of HCM mutant cardiomyocytes and 2) by alterations in the mechanical environment. We use genetically edited hiPSC-CM with point mutations in MYH7 associated with HCM, and their matched controls, combined with micropatterned traction force microscopy substrates to confirm the hypercontractile phenotype in MYH7 mutants. We next modulate contractility in healthy and disease hiPSC-CMs by treatment with positive and negative inotropic drugs and demonstrate a correlative relationship between contractility and YAP activity. We further demonstrate the activation of YAP in both HCM mutants and healthy hiPSC-CMs treated with contractility modulators is through enhanced nuclear deformation. We conclude that the overactivation of YAP, possibly initiated and driven by hypercontractility, correlates with excessive CCN2 secretion (connective tissue growth factor), enhancing cardiac fibroblast/myofibroblast transition and production of known hypertrophic signaling molecule TGF{beta}. Our study suggests YAP being an indirect player in the initiation of hypertrophic growth and fibrosis in HCM. Our results provide new insights into HCM progression and bring forth a testbed for therapeutic options in treating HCM. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/597045v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@3357aforg.highwire.dtl.DTLVardef@c1c210org.highwire.dtl.DTLVardef@abb72forg.highwire.dtl.DTLVardef@187aa80_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Learning a conserved mechanism for early neuroectoderm morphogenesis

Morphogenesis is the process whereby the body of an organism develops its target shape. The morphogen BMP is known to play a conserved role across bilaterian organisms in determining the dorsoventral (DV) axis. Yet, how BMP governs the spatio-temporal dynamics of cytoskeletal proteins driving morphogenetic flow remains an open question. Here, we use machine learning to mine a morphodynamic atlas of Drosophila development, and construct a mathematical model capable of predicting the coupled dynamics of myosin, E-cadherin, and morphogenetic flow. Mutant analysis shows that BMP sets the initial condition of this dynamical system according to the following signaling cascade: BMP establishes DV pair-rule-gene patterns that set-up an E-cadherin gradient which in turn creates a myosin gradient in the opposite direction through mechanochemical feedbacks. Using neural tube organoids, we argue that BMP, and the signaling cascade it triggers, prime the conserved dynamics of neuroectoderm morphogenesis from fly to humans.

developmental biology↗

bioRxiv2023

Scale-independent topological interactions drive the first fate decision in the Drosophila embryo

During embryogenesis, the earliest cell fate decision is often linked to nuclear positioning, whose control arises from the integration of the cell cycle oscillator and associated cytoskeletal dynamics. Yet, the mechanisms that ensure that the correct number of nuclei move to the appropriate place remain poorly understood. Here, using light sheet microscopy, we show that in Drosophila embryos spindle orientation controls which nuclei migrate towards the cortex and which remains inside the embryo, thereby determining nuclear fate and the number of cells undergoing development. Combining computational methods inspired by integral geometry and manipulations of cell cycle genes, we show that spindle orientation is controlled by topological spindle-spindle interactions and not by internuclear distance. Using arguments describing the behavior of space-filling systems, we develop a theory for topological dependency in microtubule structures. Our work shows how topological interplay of microtubule mechanics can ensure robust control of density and cell fate determination.

developmental biology↗

bioRxiv2022

Morphodynamic Atlas for Drosophila Development

During morphogenesis, diverse cell-scale and tissue-scale processes couple to dynamically sculpt organs. In this coupling, genetic expression patterns and biochemical signals regulate and respond to mechanical deformations to ensure reproducible and robust changes in tissue geometry. A long-standing approach to characterize these interactions has been the construction of expression atlases, and these atlases have necessarily relied on fixed snapshots of embryogenesis. Addressing how expression profiles relate to tissue dynamics, however, requires a scheme for spatiotemporal registration across different classes of data that incorporates both live samples and fixed datasets. Here, we construct a morphodynamic atlas that unifies fixed and live datasets - from gene expression profiles to cytoskeletal components - into a single, morphological consensus timeline. This resource and our computational approach to global alignment facilitate hypothesis testing using quantitative comparison of data both within and across ensembles, with resolution in both space and time to relate genes to tissue rearrangement, cell behaviors, and out-of-plane motion. Examination of embryo kinematics reveals stages in which tissue flow patterns are quasi-stationary, arranged as a sequence of morphodynamic modules. Temperature perturbations tune the duration of one such module - during body axis elongation - according to a simple, parameter-free scaling in which the total integrated tissue deformation is achieved at a temperature-dependent rate. By extending our approach to visceral organ formation during later stages of embryogenesis, we highlight how morphodynamic atlases can incorporate complex shapes deforming in 3D. In this context, morphodynamic modules are reflected in some, but not all, measures of tissue motion. Our approach and the resulting atlas opens up the ability to quantitatively test hypotheses with resolution in both space and time, relating genes to tissue rearrangement, cell behaviors, and organ motion.

developmental biology↗

bioRxiv2022

Integrated single-cell sequencing reveals principles of epigenetic regulation of human gastrulation and germ cell development in a 3D organoid model

The emergence of different cell types and the role of the epigenome in regulating transcription is a key yet understudied event during human gastrulation. Investigating these questions remain infeasible due to the lack of availability of embryos at these stages of development. Further, human gastrulation is marked by dynamic changes in cell states that are difficult to isolate at high purity, thereby making it challenging to map how epigenetic reprogramming impacts gene expression and cellular phenotypes. To overcome these limitations, we describe scMAT-seq, a high-throughput one-pot single-cell multiomics technology to simultaneously quantify DNA methylation, DNA accessibility and the transcriptome from the same cell. Applying scMAT-seq to 3D human gastruloids, we characterized the epigenetic landscape of major cell types corresponding to the germ layers and primordial germ cell-like cells (hPGCLC). As the identity of the progenitors that give rise to human PGCLCs remain unclear, we used this system to discover that the progenitors emerge from epiblast cells and show transient characteristics of both amniotic- and mesoderm-like cells, before getting specified towards hPGCLCs. Finally, as cells differentiate along different lineages during gastrulation, we surprisingly find that while changes in DNA accessibility are tightly correlated to both upregulated and downregulated genes, reorganization of gene body DNA methylation is strongly related to only genes that get downregulated, with genes that turn on displaying a lineage trajectory-dependent correlation with DNA methylation. Collectively, these results demonstrate that scMAT-seq is a high-throughput and sensitive approach to elucidate epigenetic regulation of gene expression in complex systems such as human gastrulation that are marked by rapidly transitioning cell states.

genomics↗

bioRxiv2022

Geometric control of Myosin-II orientation during axis elongation

The actomyosin cytoskeleton is a crucial driver of morphogenesis. Yet how the behavior of large-scale cytoskeletal patterns in deforming tissues emerges from the interplay of geometry, genetics, and mechanics remains incompletely understood. Convergent extension flow in D. melanogaster embryos provides the opportunity to establish a quantitative understanding of the dynamics of anisotropic non-muscle myosin II. Cell-scale analysis of protein localization in fixed embryos suggests that there are complex rules governing how the control of myosin anisotropy is regulated by gene expression patterns. However, technical limitations have impeded quantitative and dynamic studies of this process at the whole embryo level, leaving the role of geometry open. Here we combine in toto live imaging with quantitative analysis of molecular dynamics to characterize the distribution of myosin anisotropy and corresponding genetic patterning. We found pair rule gene expression continuously deformed, flowing with the tissue frame. In contrast, myosin anisotropy orientation remained nearly static, aligned with the stationary dorsal-ventral axis of the embryo. We propose myosin recruitment by a geometrically defined static source, potentially related to the embryo-scale epithelial tension, and account for transient deflections by the interplay of cytoskeletal turnover with junction reorientation by flow. With only one parameter, this model quantitatively accounts for the time course of myosin anisotropy orientation in wild-type, twist, and even-skipped embryos as well as embryos with perturbed egg geometry. Geometric patterning of the cytoskeleton suggests a simple physical strategy to ensure a robust flow and formation of shape.

developmental biology↗

bioRxiv2021

Patterned mechanical feedback establishes a global myosin gradient

Morphogenesis, the coordinated execution of developmental programs that shape embryos, raises many fundamental questions at the interface between physics and biology. In particular, how the dynamics of active cytoskeletal processes are coordinated across the surface of entire embryos to generate global cell flows is poorly understood. Two distinct regulatory principles have been identified: genetic programs and dynamic response to mechanical stimuli. Despite progress, disentangling these two contributions remains challenging. Here, we combine in toto light sheet microscopy with genetic and optogenetic perturbations of tissue mechanics to examine theoretically predicted dynamic recruitment of non-muscle myosin II to cell junctions during Drosophila embryogenesis. We find dynamic recruitment has a long-range impact on global myosin configuration, and the rate of junction deformation sets the rate of myosin recruitment. Mathematical modeling and high frequency analysis reveal myosin fluctuations on junctions around a mean value set by mechanical feedback. Our model accounts for the early establishment of the global myosin pattern at 80% fidelity. Taken together our results indicate spatially modulated mechanical feedback as a key regulatory input in the establishment of long-range gradients of cytoskeletal configurations and global tissue flow patterns.

developmental biology↗

bioRxiv2021

Visceral organ morphogenesis via calcium-patterned muscle contractions

How organs achieve their final shape is a problem at the interface between physics and developmental biology. Organs often involve multiple interacting tissue layers that must be coordinated to orchestrate the complex shape changes of development. Intense study uncovered genetic, and physical ingredients driving the form of mono layer tissue. Yet, tracing dynamics across tissue layers, and scales - from cell to tissue, to entire organs - remains an outstanding challenge. Here, we study the midgut of Drosophila embryos as a model visceral organ, to reconstruct in toto the dynamics of multi-layer organ formation in vivo. Using light-sheet microscopy, genetics, computer vision, and tissue cartography, we extract individual tissue layers to map the time course of shape across scales from cells to organ. We identify the kinematic mechanism driving the shape change due to tissue layer interactions by linking out-of-plane motion to active contraction patterns, revealing a convergent extension process in which cells deform as they flow into deepening folds. Acute perturbations of contractility in the muscle layer using non-neuronal optogenetics reveals that these contraction patterns are due to muscle activity, which induces cell shape changes in the adjacent endoderm layer. This induction cascade relies on high frequency calcium pulses in the muscle layer, under the control of hox genes. Inhibition of targets of calcium involved in myosin phosphorylation abolishes constrictions. Our study of multi-layer organogenesis reveals how genetic patterning in one layer triggers a dynamic molecular mechanism to control a physical process in the adjacent layer, to orchestrate whole-organ shape change.

developmental biology↗

bioRxiv2021

Deconstructing Gastrulation at the Single Cell Level

Gastrulation movements in all animal embryos start with regulated deformations of patterned epithelial sheets. Current studies of gastrulation use a wide range of model organisms and emphasize either large-scale tissue processes or dynamics of individual cells and cell groups 1,2,11-13,3-10. Here we take a step towards bridging these complementary strategies and deconstruct early stages of gastrulation in the entire Drosophila embryo, where transcriptional patterns in the blastoderm give rise to region-specific cell behaviors. Our approach relies on an integrated computational framework for cell segmentation and tracking and on efficient algorithms for event detection. Our results reveal how thousands of cell shape changes, divisions, and intercalations drive large-scale deformations of the patterned blastoderm, setting the stage for systems-level dissection of a pivotal step in animal development.

developmental biology↗

bioRxiv2021

Active Cell Divisions Generate Exotic Fourfold Orientationally Ordered Phase in Living Tissue

AO_SCPLOWBSTRACTC_SCPLOWMorphogenesis, the process through which genes generate form, establishes tissue scale order as a template for constructing the complex shapes of the body plan. The extensive growth required to build these ordered substrates is fuelled by cell proliferation, which, naively, should destroy order. The active mechanisms that couple cellular and physical processes to generate and maintain global order, thereby reconciling this seeming contradiction, remain elusive. Using live imaging and tissue cartography, we quantitatively analyze the dynamics of fourfold tissue ordering in the crustacean Parhyale hawaiensis. We show that cell divisions are the main drivers of tissue flow leading to a fourfold orientationally ordered phase. Waves of anisotropic cell proliferation propagate across the embryo with precise choreography, such that defects introduced into the nascent lattice by cell divisions are healed by subsequent divisions through active defect climb. Orchestrating cell proliferation rates and orientations enables cell divisions to organize, rather than fluidize, the tissue. The result is a robust, active mechanism for generating global orientational order in a non-equilibrium system that sets the stage for the subsequent development of shape and form.

developmental biology↗

bioRxiv2021

Self-organized morphogenesis of a human neural tube in vitro by geometric constraints

Understanding how human embryos develop their shape is a fundamental question in physics of life with strong medical implications. However, it is challenging to study the dynamics of organ formation in humans. Animals differ from humans in key aspects, and in particular in the development of the nervous system. Conventional organoids are quantitatively unreproducible and exhibit highly variable morphology. Here we present a morphologically reproducible and scalable approach for studying human organogenesis in a dish, which is compatible with live imaging. We achieve this by precisely controlling cell fate pattern formation in 2D stem cell sheets, while allowing for self-organization of tissue shape in 3D. Upon triggering neural pattern formation, the initially flat stem cell sheet undergoes folding morphogenesis and self-organizes into a millimeter long anatomically accurate model of the neural tube, covered by epidermis. We find that neural and epidermal human tissues are necessary and sufficient for folding morphogenesis in the absence of mesoderm activity. Furthermore, we find that molecular inhibition of tissue contractility leads to defects similar to neural tube closure defects, consistent with in vivo studies. Finally, we discover that neural tube shape, including the number and location of hinge points, depends on neural tissue size. This suggests that neural tube morphology along the anterior posterior axis depends on neural plate geometry in addition to molecular gradients. Our approach provides a new path to study human organ morphogenesis in health and disease.

developmental biology↗

bioRxiv2018

3D Tissue elongation via ECM stiffness-cued junctional remodeling

Organs are sculpted by extracellular as well as cell-intrinsic forces, but how collective cell dynamics are orchestrated in response to microenvironmental cues is poorly understood. Here we apply advanced image analysis to reveal ECM-responsive cell behaviors that drive elongation of the Drosophila follicle, a model 3D system in which basement membrane stiffness instructs tissue morphogenesis. Through in toto morphometric analyses of WT and round egg mutants, we find that neither changes in average cell shape nor oriented cell division are required for appropriate organ shape. Instead, a major element is a reorientation of elongated cells at the follicle anterior. Polarized reorientation is regulated by mechanical cues from the basement membrane, which are transduced by the Src tyrosine kinase to alter junctional E-cadherin trafficking. This mechanosensitive cellular behavior represents a conserved mechanism that can elongate edgeless tubular epithelia in a process distinct from those that elongate bounded, planar epithelia.

developmental biology↗