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Results for “developmental biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2023

Data-Driven 3D Shape Analysis Reveals Cell Shape-Fate Relationships in Zebrafish Lateral Line Neuromast

Cell shape is a powerful readout of cell state, fate, and function. With the advent of sophisticated microscopes, image segmentation algorithms, and numerical shape representations, it is becoming more feasible to study cell shape in developing tissues. However, few studies have analyzed cell shape in three dimensions in living, intact organisms. Here, we took advantage of the favorable imaging qualities of zebrafish lateral line neuromasts to generate a dataset of high resolution images with labeled cells and nuclei. Using a custom Python-based workflow, we performed semi-automated, 3D cell and nucleus segmentation. We then used spherical harmonics and principal components analysis to distill neuromast cell and nuclear shape variation into several interpretable, biologically meaningful parameters. We found that neuromast cell and nuclear shapes vary with cell location and identity. The distinction between hair cells and support cells was discrete and accounted for much of the variation in neuromast cell and nucleus shape, which allowed us to train classifiers to predict hair cell identity from cell and nucleus shape features. Using markers for support cell subpopulations, we found that support cell subtypes also had different shapes from each other; however, shape features did not distinguish as sharply between support cell subtypes, suggesting that support cells vary continuously in shape. To investigate the effects of genetic perturbation that results in loss of a cell type on neuromast cell shape, we examined atoh1a mutants that lack hair cells. We found that neuromasts from atoh1a mutants lacked the cell shape phenotype associated with hair cells, but did not exhibit a mutant-specific cell shape. Our results demonstrate the utility of using 3D cell shape features to characterize, compare, and classify cells in a living, developing organism.

developmental biology↗

bioRxiv2024

Resolving the design principles that control postnatal vascular growth and scaling

After birth, tissues grow continuously until reaching adult size, with each organ exhibiting unique cellular dynamics, growth patterns, and (stem or non-stem) cell sources. Using a suite of experimental and computational multiscale approaches, we found that aortic expansion is guided by specific biological principles and scales with the vertebral column rather than animal body weight. Expansion proceeds via two distinct waves of arterial cell proliferation along blood flow that are spatially stochastic, yet temporally coordinated. Each wave exhibits unique cell cycle kinetics and properties, with the first wave exhibiting cell cycle durations as fast as 6 hours. Single-cell RNA sequencing showed changes in fatty acid metabolism concomitant with an increase in cell size. Mathematical modeling and experiments indicated endothelial cell extrusion is essential for homeostatic aortic growth and balancing excess proliferation. In a genetic model of achondroplasia, the aorta achieves proper scaling through enhanced cell extrusion while maintaining normal proliferation dynamics. Collectively, these results provide a blueprint of the principles that orchestrate aortic growth which depends entirely on differentiated cell proliferation rather than resident stem cells.

developmental biology↗

bioRxiv2021

Morphological integration during postnatal ontogeny: implications for evolutionary biology

How covariance patterns of phenotypes change during development is fundamental for a broader understanding of evolution. There is compelling evidence that mammalian skull covariance patterns change during ontogeny. However, it is unclear to what extent variation in covariance patterns during ontogeny can impact the response to selection. To tackle this question we explored: i) the extent to which covariance patterns change during postnatal ontogeny; ii) in which ontogenetic stages covariance patterns differ the most, and iii) the extent to which the phenotypic covariance pattern at different ontogenetic stages can be explained by the same processes determining additive genetic covariance. We sampled postnatal ontogenetic series for both marsupials, and placentals. Within each ontogenetic series, we compared covariance matrices (P-matrices) at different ontogenetic stages. Furthermore, we compared these P-matrices to two target matrices [adult P-matrix and an additive genetic covariance matrix (G-matrix)]. Our results show that for all ontogenetic series, covariance patterns from weaning onward are conserved and probably shaped by the same processes determining the G-matrix. We conclude that irrespective of eventual differences in how selection operates during most of postnatal ontogeny, the net response to such pressures will probably not be affected by ontogenetic differences in the covariance pattern.

developmental biology↗

bioRxiv2023

E3 ubiquitin ligase Deltex facilitates the expansion of Wingless gradient and antagonizes Wingless signaling through a conserved mechanism of transcriptional effector Armadillo/β-catenin degradation

The Wnt/Wg pathway controls myriads of biological phenomena throughout the development and adult life of all organisms across the phyla. Thus, an aberrant Wnt signaling is associated with a wide range of pathologies in humans. Tight regulation of Wnt/Wg signaling is required to maintain proper cellular homeostasis. Here we report a novel role of E3 ubiquitin ligase Deltex in Wg signaling regulation. Drosophila dx genetically interacts with wg and its pathway components. Further, Dx LOF results in a reduced spreading of Wg while its over-expression expands the diffusion gradient of the morphogen. We attribute this change in Wg gradient to the endocytosis of Wg through Dx which directly affects the short and long-range Wg targets. We also demonstrate the role of Dx in regulating Wg effector Armadillo where Dx down-regulates Arm through proteasomal degradation. We also showed the conservation of Dx function in the mammalian system where DTX1 is shown to bind with {beta}-catenin and facilitates its proteolytic degradation, spotlighting a novel step that potentially modulates Wnt/Wg signaling cascade.

developmental biology↗

bioRxiv2019

Application of Optogenetic Amyloid-β Distinguishes Between Metabolic and Physical Damage in Neurodegeneration

The brains of Alzheimers Disease patients show a decrease in brain mass and a preponderance of extracellular Amyloid-{beta} plaques. These plaques are formed by aggregation of polypeptides that are derived from Amyloid Precursor Protein (APP). Amyloid-{beta} plaques are thought to play either a direct or an indirect role in disease progression, however the exact role of aggregation and plaque formation in the ethology of Alzheimers Disease is subject to debate, not least because the biological effects of soluble and aggregated Amyloid-{beta} peptides are difficult to separate in vivo. To investigate the consequences of formation of Amyloid-{beta} oligomers in living tissues, we developed a fluorescently tagged, optogenetic Amyloid-{beta} peptide that oligomerizes rapidly in the presence of blue light. We applied this system to the crucial question of how intracellular Amyloid-{beta} oligomers underlie the pathologies of Alzheimers Disease. We show that, although both expression and induced oligomerization of Amyloid-{beta} were detrimental to lifespan and healthspan, we were able to separate the metabolic and physical damage caused by light-induced Amyloid-{beta} oligomerization from Amyloid-{beta} expression alone. The physical damage caused by Amyloid-{beta} oligomers also recapitulated the catastrophic tissue loss that is a hallmark of late AD. We show that the lifespan deficit induced by Amyloid-{beta} oligomers was reduced with Li+ treatment. Our results present the first model to separate different aspects of disease progression.

developmental biology↗

bioRxiv2021

Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye

Pattern formation of biological structures involves the arrangement of different types of cells in an ordered spatial configuration. In this study, we investigate the mechanism of patterning the Drosophila eye into a precise triangular grid of photoreceptor clusters called ommatidia. Previous studies had led to a long-standing biochemical model whereby a reaction-diffusion process is templated by recently formed ommatidia to propagate a molecular prepattern across the eye epithelium. Here, we find that the templating mechanism is instead, mechanical in origin; newly born columns of ommatidia serve as a template to spatially pattern cell flows that move the cells in the epithelium into position to form each new column of ommatidia. Cell flow is generated by a pressure gradient that is caused by a narrow zone of cell dilation precisely positioned behind the growing wavefront of ommatidia. The newly formed lattice grid of ommatidia cells are immobile, deflecting and focusing the flow of other cells. Thus, the self-organization of a regular pattern of cell fates in an epithelium is mechanically driven.

developmental biology↗

bioRxiv2022

KLF5-regulated extracellular matrix remodeling secures biliary epithelial tissue integrity against cholestatic liver injury

Abstract / Introductory paragraphTubular epithelial tissues in the body play fundamental roles as infrastructure constituting conduits to transport various types of biological fluids, for which contiguous and integrated epithelial tissue structures should be maintained continuously and even under stressed conditions. Compared to tissue morphological processes that take place during ontogeny, the mechanisms whereby tubular epithelial tissues maintain their structural integrity in adulthood remains largely unclear. Here, we show that the transcription factor Klf5 is crucial for maintaining the biliary epithelial integrity in tissue remodeling processes induced under cholestatic injury conditions in the adult liver. Loss of Klf5 in the biliary epithelia led to tissue collapse in vivo in injured mouse livers, as well as in vitro in bile ductular organoids in a tissue-autonomous manner and independent of cell proliferation. Klf5 regulated cell junction organization and cell adhesion, along with extracellular matrix remodeling around the expanding biliary epithelia through deposition of Lamb3-containing laminin complexes. Targeting the Lamb3 expression in biliary epithelia in mice recapitulated the tissue collapse phenotype. Together, our results highlight a novel mechanism whereby the epithelial tissue maintains its integrity while undergoing unstable structural transformation.

developmental biology↗

bioRxiv2024

Theca cell mechanics and tissue pressure regulate mammalian ovarian folliculogenesis

The maturation of functional eggs within the ovaries is essential for successful reproduction and organismal functions in mammals. Yet, despite its biological and clinical importance, the underlying mechanisms regulating folliculogenesis remain enigmatic. Here, we report a novel role of the surface-anchoring theca cells (TCs) in regulating follicle growth through mechanical signalling. Direct mechanical measurements reveal that these TCs are highly contractile and exert compressive stress to the follicular interior, potentially through active assembly of fibronectin scaffold around the follicles. Abolishing TC contractility disrupts fibronectin assembly, increases follicle size, and decreases intrafollicular pressure and viscosity. We further reveal that the granulosa cells (GCs) within the follicles exhibit spatial patterns of YAP signalling and proliferation, which appear to be decoupled. Transient manipulation of tissue pressure through bulk follicle compression, laser ablation or pharmacological perturbation of TC contractility leads to changes in GC YAP signalling, proliferation, and oocyte-GC communications, while long term abrogation of TC contractility leads to impaired follicle growth. Altogether, our study unveils the unique role of TC-mediated tissue pressure in ensuring robust mammalian ovarian folliculogenesis.

developmental biology↗

bioRxiv2020

Single-cell Protein Atlas of Transcription Factors Reveals the Combinatorial Code for Spatiotemporal Patterning the C. elegans Embryo

A high-resolution protein atlas is essential for understanding the molecular basis of biological processes. Using protein-fusion reporters and imaging-based single-cell analyses, we present a protein expression atlas of C. elegans embryogenesis encompassing 266 transcription factors (TFs) in nearly all (90%) lineage-resolved cells. Single-cell analysis reveals a combinatorial code and cascade that elucidate the regulatory hierarchy between a large number of lineage-, tissue-, and time-specific TFs in spatiotemporal fate patterning. Guided by expression, we identify essential functions of CEH-43/DLX, a lineage-specific TF, and ELT-1/GATA3, a well-known skin fate specifier, in neuronal specification; and M03D4.4 as a pan-muscle TF in converging muscle differentiation in the body wall and pharynx. Finally, systems-level analysis of TF regulatory state uncovers lineage- and time-specific kinetics of fate progression and widespread detours of the trajectories of cell differentiation. Collectively, our work reveals a single-cell molecular atlas and general principles underlying the spatiotemporal patterning of a metazoan embryo.

developmental biology↗

bioRxiv2025

Cell size control emerges from the vein-dependent coordinated divisions of distinct cell groups in Drosophila wing

During morphogenesis, cell divisions are precisely regulated in space and time. The biological objectives achieved by such regulation are not fully understood. Here, by applying a newly developed lineage-reconstruction pipeline to Drosophila pupal wing, we reveal that the wing is composed of distinct cell groups that differ in division number, timing, and spatial positioning relative to wing veins. We show that the frequencies of these lineages, together with their initial cell sizes and growth profiles, converge to achieve a highly conserved average cell size. Our data further suggest that distance from veins provides spatial information that biases where distinct lineages arise, and that loss of veins caused by perturbation of EGFR signaling suppresses a specific lineage and disrupts cell-size control. Finally, our results point to a multiscale organization of division patterns, in which vein-associated spatial information is integrated with local neighbor effects in a manner that would mitigate mechanical instability within the tissue. Together, these findings delineate a cell-size control mechanism based on coordinated divisions of distinct cell groups that supports robust morphogenesis and functional tissue design.

developmental biology↗

bioRxiv2022

A promoter-proximal silencer modifies the activity of a shared enhancer to mediate divergent expression of nub and pdm2 paralogs in wing development

Duplication of genes and their associated cis-regulatory elements, or enhancers, is a key contributor to genome evolution and biological complexity. Moreover, many paralogs, particularly tandem duplicates, are fixed for long periods of time under the control of shared enhancers. However, in most cases the mechanism by which gene expression and function diverge following duplication is not known. Here we dissect the regulation and function of the paralogous nubbin/pdm2 genes during wing development in Drosophila melanogaster. We show that these paralogs play a redundant role in the wing and that their expression relies on a single shared wing enhancer. However, the two genes differ in their ability to respond to this enhancer, with nub responding in all wing progenitor cells and pdm2 only in a small subset. This divergence is a result of a pdm2-specific silencer element at the pdm2 promoter that receives repressive input from the transcription factor Rotund. Repression through this silencer also depends on nub, allowing pdm2 to fully respond to the wing enhancer when nub expression is perturbed and functional compensation to occur. Thus, expression divergence downstream of a shared enhancer arises as a consequence of silencing the promoter of one paralog.

developmental biology↗

bioRxiv2024

WNT signaling coordinately controls mouse limb bud outgrowth and establishment of the digit-interdigit pattern

Self-organization, such as the emergence of a pattern from a homogenous state, is a fascinating property of biological systems. Early limb bud outgrowth and patterning in mice are controlled by a robust and self-regulatory signaling system, and initiation of the periodic digit-interdigit pattern appears under control of a self-regulatory Turing system. Previous studies established the requirement of WNT and BMP signaling for both early limb bud and digit-interdigit morphogenesis, but the molecular changes underlying the transition from early limb bud signaling to the digit-interdigit patterning system remained unknown. Here, we use small molecule inhibitors to rapidly but transiently block WNT signaling to identify the early transcriptional targets that are altered during disruption and recovery of limb bud and digit development. Together, this study highlights the overarching role of WNT signaling in controlling early limb bud outgrowth and patterning, and establishment of the periodic digit-interdigit pattern. Finally, the transient WNT signaling disruption approach reveals the plasticity and robustness of these self-organizing limb bud and digit patterning systems.

developmental biology↗

bioRxiv2025

A blastocyst-derived in vitro model of the human chorion

The placenta supports the foetus by mediating nutrient and gas exchange, hormone production, and immune protection. Yet, human placental biology remains poorly understood due to limited in vitro models. The foetal part of the placenta, the chorion, consists of a trophoblast-derived layer and a mesenchymal zone containing extraembryonic mesoderm cells. Here, we show that human blastocysts can give rise to both trophoblast organoids and extraembryonic mesoderm cells under the same culture conditions. Trophoblast organoids originate from both outer trophoblast cells and inner cells of the blastocyst, while extraembryonic mesoderm cells derive exclusively from inner cells. These organoids recapitulate the cellular composition, morphology, and function of the in vivo trophoblast. Moreover, given the high rate of aneuploidy at the blastocyst stage, aneuploid trophoblast organoids can be readily generated. These models reflect the trophoblasts unique ability to tolerate aneuploidy and offer a valuable platform to study human placental development and pathophysiology.

developmental biology↗

bioRxiv2021

Heterozygous loss of ZBTB38 leads to early embryonic lethality in mice via suppressing Nanog and Sox2

Mammalian DNA methylation is an epigenetic modification which is involved in various biological processes, including gene expression regulation. In mice, methyltransferases are responsible for DNA methylation, which are critical for early embryogenesis. However, the significance of methyl-CpG binding proteins (MBPs) that bind methylated CpG remains largely unknown. We previously demonstrated that ZBTB38/CIBZ-a zinc finger type of MBP-is required for ES cell proliferation by positively regulating Nanog expression. However, the physiological function of ZBTB38 remains unclear. In this study, we generated conditional ZBTB38 knockout mice using Cre-loxP technology. Unexpectedly, our results showed that germline loss of the ZBTB38 single allele resulted in decreased epiblast cell proliferation and increased apoptosis shortly after implantation, leading to early embryonic lethality. We found that heterozygous loss of ZBTB38 reduced the expression of Nanog, Sox2, and the genes responsible for epiblast proliferation, differentiation, and cell viability. Despite this lethal phenotype, ZBTB38 is dispensable for ES cell establishment and identity. Together, these findings indicate that ZBTB38 is essential for early embryonic development, providing new insights into the roles of MBP in implantation.

developmental biology↗

bioRxiv2021

Ergodic patterns of cell state transitions underlie the reproducibility of embryonic development

The reproducibility of embryonic development is a remarkable feat of biological organization, but the underlying mechanisms are poorly understood. Clearly, gene regulatory networks are central to the orderly progression of development, but noisy molecular and cellular processes should reduce reproducibility. Here, we identify ergodicity, a type of dynamical stability, as underlying the reproducibility of development. In ergodic systems, a single timepoint measurement equals a time average. Focusing on the zebrafish tailbud, we define gene expression and cell motion states using a parallel statistical analyses of single cell RNA sequencing data and in vivo timelapse cell tracking data and a change point detection algorithm. Strikingly, the cell motion state transitions in each embryo exhibit the same patterns for both a single timepoint and a 2-3 hour time average. Both the cell motion and gene expression cell states exhibit balanced influx and outflux rates reflecting a spatiotemporal stability. Stated simply, these data indicate the pattern of changes in the tailbud doesnt change. This ergodic pattern of cell state transitions may represent an emergent meta-state that links gene networks to the reproducible progression of embryogenesis.

developmental biology↗

bioRxiv2022

Homeotic compartment curvature and tension control spatiotemporal folding dynamics.

Shape is a conspicuous and fundamental property of biological systems entailing the function of organs and tissues. While much emphasis has been put on how tissue tension and mechanical properties drive shape changes, whether and how a given tissue geometry influences subsequent morphogenesis remains poorly characterized. Here, we explored how curvature, a key descriptor of tissue geometry, impinges on the dynamics of epithelial tissue invagination. We found that the morphogenesis of the fold separating the adult Drosophila head and thorax segments is driven by the invagination of the Deformed (Dfd) homeotic compartment. Dfd controls invagination by modulating actomyosin organization and in-plane epithelial tension via the Tollo and Dystroglycan receptors. By experimentally introducing curvature heterogeneity within the homeotic compartment, we established that a curved tissue geometry converts the Dfd-dependent in-plane tension into an inward force driving folding. Accordingly, the interplay between in-plane tension and tissue curvature quantitatively explains the spatiotemporal folding dynamics. Collectively, our work highlights how genetic patterning and tissue geometry provide a simple design principle driving folding morphogenesis during development.

developmental biology↗

bioRxiv2024

The chromatin remodeler DEK promotes proliferation of mammary epithelium and is associated with H3K27me3 epigenetic modifications

The DEK chromatin remodeling protein was previously shown to confer oncogenic phenotypes to human and mouse mammary epithelial cells using in vitro and knockout mouse models. However, its functional role in normal mammary gland epithelium remained unexplored. We developed two novel mouse models to study the role of Dek in normal mammary gland biology in vivo. Mammary gland-specific Dek over-expression in mice resulted in hyperproliferation of cells that visually resembled alveolar cells, and a transcriptional profile that indicated increased expression of cell cycle, mammary stem/progenitor, and lactation-associated genes. Conversely, Dek knockout mice exhibited an alveologenesis or lactation defect, resulting in dramatically reduced pup survival. Analysis of previously published single-cell RNA-sequencing of mouse mammary glands revealed that Dek is most highly expressed in mammary stem cells and alveolar progenitor cells, and to a lesser extent in basal epithelial cells, supporting the observed phenotypes. Mechanistically, we discovered that Dek is a modifier of Ezh2 methyltransferase activity, upregulating the levels of histone H3 trimethylation on lysine 27 (H3K27me3) to control gene transcription. Combined, this work indicates that Dek promotes proliferation of mammary epithelial cells via cell cycle deregulation. Furthermore, we report a novel function for Dek in alveologenesis and histone H3 K27 trimethylation.

developmental biology↗

bioRxiv2026

Male Age and Sexual Maturity: Lipopolysaccharide-induced tumor necrosis factor influences sperm quality and reproduction in Anopheles culicifacies

Elucidating the biological and molecular mechanisms that govern male fertility and mating behavior in mosquitoes is critical for optimizing genetic and sterile insect technique-based vector control strategies. Here, we examined age-related changes in male reproductive capacity in Anopheles culicifacies, using female egg output as an indirect indicator of male fertility. Our results demonstrated that male reproductive age follows a non-linear pattern of fertility. Morphometric analysis from emergence to day 13 post-eclosion revealed a strong correlation between seminal vesicle capacity and female fecundity, suggesting that age-dependent gonadal development directly influences reproductive potential. At the molecular level, we identified AcLITAF6 as a key regulator of male reproductive homeostasis. RNAi-mediated knockdown of AcLITAF6 impaired apoptosis-associated and phagocytic clearance, reduced sperm viability, and decreased female productive outcomes. Conclusively, we reveal a previously unrecognized role of LITAF in sperm quality control and male reproductive fitness, highlighting AcLITAF6 as a potential target for mosquito population suppression strategies.

developmental biology↗