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bioRxiv2026

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

bioRxiv2026

Multimodal Human Scalp Atlas Defines Cell Landscape and Lineage Architecture In Situ

Human scalp hair has an extraordinary ability to grow continuously for years while maintaining structural and functional integrity. However, the cell states and lineage organization that enable this capacity and how they are disrupted in inflammatory hair loss disorders remain poorly defined in humans. Here we establish a high-resolution, multimodal atlas of human scalp by integrating deep-coverage spatial transcriptomics with single-cell RNA-seq and multiomics data. This reference resolves spatially organized epithelial and mesenchymal states and links in situ transcriptional programs to chromatin accessibility dynamics and lineage trajectories at single-cell resolution, revealing human-specific principles of tissue organization and previously unrecognized features of hair follicle architecture and lineage progression. We validate key aspects of matrix cell organization and cell activities using live imaging, connecting molecularly defined cell states to dynamic cell behaviors and lineage progression in the matrix. Leveraging the atlas as a spatial reference, we project patient scRNA-seq profiles from alopecia areata and lichen planopilaris onto defined cell compartments, resolving disease-specific perturbations in fibroblasts, epithelial and immune populations. This comparison delineates distinct cellular programs associated with non-scarring versus scarring hair loss and highlights compartment- and state-specific pathways with diagnostic and therapeutic potential. Together, this work provides a foundational resource for human hair biology and establishes a generalizable framework for spatially resolved, multimodal interrogation of tissue organization and disease in complex human tissues.

Developmental Biology↗

bioRxiv2026

Topological Analysis of Multi-Network Threading in the Pancreas

The pancreas is a complex inner organ that develops through the concurrent formation of multiple interacting biological networks, but the geometric principles governing their spatial organization remain poorly understood. Here, we study pancreatic development by analysing loop structures in ductal, neuronal, and vascular networks using tools from topological data analysis. In particular, we employ the application of chromatic persistence, which is designed to detect topological interactions between distinct subsets of a structure; this is used to quantify how loops from different networks become spatially entangled. Our analysis reveals distinct developmental timelines for loop formation, progressive entanglement between ducts and vasculature, and spatial concentration of threading toward the organ interior, providing a geometric characterisation of coordinated network development in the pancreas.

developmental biology↗

bioRxiv2026

GPLD1 Regulates the Shedding of IZUMO1R to Block Polyspermy in Porcine Oocyte

Mammalian fertilization commences with the essential interaction between sperm IZUMO1 and its oocyte-surface receptor, JUNO. Following gamete fusion, JUNO is rapidly shed from the oocyte to establish a definitive membrane block to polyspermy, a pathological condition that remains a major hurdle in porcine in vitro fertilization (IVF). Despite its biological importance, the molecular networks driving JUNO cleavage has remained elusive. Here, by integrating proteomics, dual-color live-cell imaging, and functional perturbations, we identify the extended existence of JUNO and the GPI-specific phospholipase D1 (GPLD1) as the requisite enzyme mediating JUNO shedding in porcine oocytes. Targeted knockdown or pharmacological inhibition of GPLD1 stabilizes oocyte JUNO, prolongs the window of oocyte receptivity, and significantly exacerbates polyspermy, ultimately compromising embryonic developmental competence. Conversely, GPLD1 overexpression restricts redundant sperm adherence and enhances the efficiency of monospermic zygote formation and blastocyst development. Live-cell imaging reveals that fertilization triggers a transient, pulsed recruitment of GPLD1 in the oocyte, which precisely coincides with the biphasic kinetics of JUNO depletion. Our findings establish that the enzymatic cleavage of the GPI-anchor by GPLD1 is critical for JUNO release, defining a fundamental mechanism for the membrane-level block to polyspermy. This work provides a molecular framework for ensuring sperm-oocyte recognition and improving in vitro fertilization outcomes in mammals.

developmental biology↗

bioRxiv2025

A model of apical-out human first trimester trophoblast organoids to study regeneration after syncytial damage

The villous syncytiotrophoblast in humans is the interface between maternal blood and the placenta and its functions are essential for a successful pregnancy. The syncytium can be damaged in vivo focally by high-velocity and turbulent maternal blood flow, or more globally by oxidative stress. It then quickly regenerates, a process critical for the maintenance of placental functions including nutrient transfer and protection from infections. To investigate this process, we developed apical-out trophoblast organoids from first-trimester placentas and induced mechanical damage to the syncytium. We observed spontaneous regeneration of syncytiotrophoblast both morphologically and functionally. TNFRSF12A, the TWEAK receptor, was identified as a potential enhancer of syncytiotrophoblast regeneration. Supplementation with recombinant TWEAK in organoids increased the expression of cell proliferation and fusion markers, promoting syncytiotrophoblast formation. The source of TWEAK was found to be macrophages derived from maternal blood monocytes that adhere to sites of syncytiotrophoblast damage in vivo. This in vitro model that allows the exploration of syncytial biology has relevance for important pregnancy disorders including pre-eclampsia, where breaks occur more often, and vertical infections, where maternal monocytes could be a source of transmission.

developmental biology↗

bioRxiv2020

Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase

The recombinase RAD51, and its meiosis-specific paralog DMC1 localize at DNA double-strand break (DSB) repair sites in meiotic prophase nuclei. While both proteins are required during meiotic homologous recombination, their spatial organization during meiotic DSB repair is not fully understood. Using super-resolution microscopy on mouse spermatocyte nuclei, we aimed to define their relative position at DSB foci, and how these vary in time. We show that a large fraction of meiotic DSB repair foci (38%) contained a single RAD51 cluster and a single DMC1 cluster (D1R1 configuration) that were partially overlapping (average center-center distance around 70 nm). The majority of the rest of the foci had a similar combination of a major RAD51 and DMC1 cluster, but in combination with additional clusters (D2R1, D1R2, D2R2, or DxRy configuration) at an average distance of around 250 nm. As prophase progressed, less D1R1 and more D2R1 foci were observed, where the RAD51 cluster in the D2R1 foci elongated and gradually oriented towards the distant DMC1 cluster. This correlated with more frequently observed RAD51 bridges between the two DMC1 clusters. D1R2 foci frequency was more constant, and the single DMC1 cluster did not elongate, but was observed more frequently in between the two RAD51 clusters in early stages. D2R2 foci were rare (<10%) and nearest neighbour analyses also did not reveal pair formation between D1R1 foci. In the absence of the transverse filament of the synaptonemal complex (connecting the chromosomal axes of homologs), early configurations were more prominent, and RAD51 elongation occurred only transiently. This in-depth analysis of single cell landscapes of RAD51 and DMC1 accumulation patterns at DSB repair sites at super-resolution thus revealed the variability of foci composition, and defined functional consensus configurations that change over time. AUTHOR SUMMARYMeiosis is a specific type of cell division that is central to sperm and egg formation in sexual reproduction. It forms cells with a single copy of each chromosome, instead of the two copies that are normally present. In meiotic prophase, homologous chromosomes must connect to each other, to be correctly distributed between the daughter cells. This involves the formation and repair of double-strand breaks in the DNA. Here we used super-resolution microscopy to elucidate the localization patterns of two important DNA repair proteins: RAD51 and DMC1. We found that repair sites most often contain a single large cluster of both proteins, with or without one additional smaller cluster of either protein. RAD51 protein clusters displayed lengthening as meiotic prophase progressed. When chromosome pairing was disturbed, we observed changes in the dynamics of protein accumulation patterns, indicating that they actually correspond to certain repair intermediates changing in relative frequency of occurrence. These analyses of single meiotic DNA repair foci reveal the biological variability in protein accumulation patterns, and the localization of RAD51 and DMC1 relative to each other, thereby contributing to our understanding of the molecular basis of meiotic homologous recombination.

developmental biology↗

bioRxiv2022

Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis

Mammalian sex is determined by opposing networks of ovarian and testicular genes that are well characterized. However, its epigenetic regulation is still largely unknown, thus limiting our understanding of a fundamental process for species propagation. Here we explore the 3D chromatin landscape of sex determination in vivo, by profiling FACS-sorted embryonic mouse gonadal populations, prior and after sex determination, in both sexes. We integrate Hi-C with ChIP-seq experiments using METALoci, a novel genome spatial auto-correlation analysis that identifies 3D enhancer hubs across the genome. We uncover a prominent rewiring of chromatin interactions during sex determination, affecting the enhancer hubs of hundreds of genes that display temporal- and sex-specific expression. Moreover, the identification of the 3D enhancer hubs allows the reconstruction of regulatory networks, revealing key transcription factors involved in sex determination. By combining predictive approaches and validations in transgenic mice we identify a novel Fgf9 regulatory hub, deletion of which results in male-to-female sex reversal with the upregulation of ovarian-specific markers and the initiation of meiosis. Thus, spatial auto-correlation analysis is an effective strategy to identify regulatory networks associated to biological processes and to further characterize the functional role of the 3D genome.

developmental biology↗

bioRxiv2023

Modelling variability and heterogeneity of EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion

Epithelial-Mesenchymal Transition (EMT) is a key process in physiological and pathological settings (i.e. development, fibrosis, cancer). EMT is often presented as a linear sequence of events including (i) disassembly of cell-cell junctions, (ii) loss of epithelial polarity and (iii) reorganization of the cytoskeleton leading to basal extrusion from the epithelium. Once out, cells can adopt a migratory phenotype with a front-rear polarity and may additionally become invasive. While this stereotyped sequence can occur, many in vivo observations have challenged this notion. It is now accepted that there are multiple EMT scenarios and that cell populations implementing EMT are often heterogeneous. However, the relative importance of each EMT step towards extrusion is unclear. Similarly, the overall impact of variability and heterogeneity on the efficiency and directionality of cell extrusion has not been assessed. Here we used computational modelling of a pseudostratified epithelium to model multiple EMT-like scenarios. We confronted these in silico data to the EMT occurring during neural crest delamination. Overall, our simulated and biological data point to a key role of nuclear positioning and protrusive activity to generate timely basal extrusion of cells and suggest a non-linear model of EMT allowing multiple scenarios to co-exist.

developmental biology↗

bioRxiv2025

Clinical Interventions and Inflammatory Signaling Shape the Transcriptional and Cellular Architecture of the Early Postnatal Lung

The early postnatal period in human development is characterized by extensive remodeling of the distal lung to support gas exchange, but this critical period remains poorly understood. Here, we constructed a comprehensive cellular atlas of the early postnatal human lung (0 to 2 years) using single-nucleus RNA sequencing of histologically normal specimens from 23 individuals. Our analysis identified two previously unknown and mutually exclusive transcriptional states of alveolar type 2 (AT2) cells, one defined by upregulation of genes involved in lipid metabolism and identified by unique expression of FMO5, and the other defined by upregulation of inflammatory response genes and identified by unique expression of CFTR. Using spatial transcriptomics, we discovered that AT2 cell states reside in specific niches and interact with distinct alveolar fibroblast subtypes. Clinical data and organoid experiments further suggest that the environment dictates which state prevails as the pro-inflammatory/pro-regenerative signals TNF- and IL-1{beta} promoted the CFTR+ state in vitro, while patients treated with the anti-inflammatory drug dexamethasone (Dex) had more abundant FMO5+ AT2 cells, and Dex induced the FMO5+ state in vitro. These observations link inflammatory signaling and anti-inflammatory clinical interventions to shifts in transcriptional state of the alveolar epithelium. We benchmarked two neonatal lung diseases, bronchopulmonary dysplasia and pulmonary interstitial glycogenosis, revealing a profound disruption in the balance of AT2 states, a broad arrest of postnatal cellular development, and impaired cellular maturation. Our work uncovers a fundamental new understanding of early postnatal human lung biology, linking pro- and anti-inflammatory signaling to AT2 transcriptional phenotypes and providing a new framework for understanding lung disease.

developmental biology↗

bioRxiv2026

Development, dimorphism, and divergence of the oral dentition in threespine sticklebacks (Gasterosteus aculeatus)

How morphology forms during development and changes during evolution remain major questions in biology. In vertebrates, teeth have long served as model systems to address these questions. In threespine stickleback fish (Gasterosteus aculeatus), repeated and convergent increases in pharyngeal tooth number in derived freshwater sticklebacks occur, suggesting increased tooth number is adaptive in freshwater environments, likely due to a diet of larger prey in freshwater. Whether changes in oral tooth patterning also occur in freshwater sticklebacks was unknown. Here we describe oral tooth number and patterning in a dense developmental time course of lab-reared ancestral marine and derived freshwater fish. We address three major questions. First, is the spatial sequence of early oral tooth formation invariant as we previously described for the pharyngeal dentition? Second, is oral tooth patterning in the upper and lower jaw sexually dimorphic, and if so, when during development does this dimorphism arise? Third, have freshwater fish evolved increases in oral tooth number? We find that (1) unlike the pharyngeal dentition, the oral jaw early spatial sequence is variable, especially in the lower jaw (2) sexual dimorphism in both oral jaws arises at the late juvenile stage with males having more teeth and (3) freshwater fish have evolved more oral teeth similar to the evolved tooth gain in the pharyngeal jaw. Together our morphological descriptions advance the stickleback oral jaw as a model system to study how morphology forms during development and evolves in nature.

developmental biology↗

bioRxiv2023

Left-right asymmetry is formed in the basal bodies of the mouse node cilia in a cilia motility-dependent manner

Laterality of the shapes and arrangements of the visceral organs in mice is determined in the node, a small cavity found at the ventral side of 7.5 dpc (days post coitum) embryos. On the node cells, motile cilia which are tilted toward the posterior side of the embryos show clockwise movement and thus produce fluid flow in the node toward the left side of the embryos. This left-ward flow regulates left/right (L/R) asymmetric gene expressions and L/R asymmetric morphogenesis in later stages. Structurally, node cilia have the characteristics of primary cilia and their basal body (mother centriole) is accompanied by a daughter centriole. Here, to obtain insights into the process of symmetry breaking by node cilia, we investigated whether the structure of the cilia themselves have L/R asymmetry, and found that positions of the daughter centrioles become biased to the right side of the mother centrioles in a stage-dependent manner. We found that this L/R asymmetry of the basal bodies is absent in iv mutant mice, in which node cilia are immotile, suggesting that formation of this L/R asymmetry in the basal bodies requires cilia motility. It has been reported that culturing embryos in a flow chamber with artificial counter-flow, which is toward the opposite direction to the endogenous leftward flow in the node, results in reversed laterality of the visceral organs in later stages. However, we found that applying such artificial counter-flow did not reverse the L/R asymmetry of the basal bodies, and the daughter centrioles were still biased to the right side of the mother centrioles, suggesting that the L/R asymmetry of the basal bodies is formed independently from the direction of the fluid flow in the node and that it is independent from the laterality of the visceral organs. Although the biological significance of this phenomenon is unknown so far, these results suggest that node cilia have a previously unknown mechanism to produce L/R asymmetry in the basal bodies inside the cells in early development, independently from the canonical fluid flow-dependent L/R determining pathway.

developmental biology↗

bioRxiv2025

Electrical Stimulation Rejuvenates Tunicates: Altered Stem Cell and Immune Activity

Applicable methods of rejuvenating organisms and improving resistance to environmental stimuli are needed. During attempts to synchronize heart rates in unhealthy colonial chordates, we observed morphological rejuvenation. While the importance of endogenously generated bioelectric currents in development is well-established1,2, and exogenously applied current has shown promise in regenerative medicine3,4,5,6,7,8,9, a model that robustly increases longevity and fertility while providing detailed mechanistic insights has not been reported. Here, we report the establishment of such a model using pulsatile electrical current (PEC) in Botryllus schlosseri, an established colonial chordate model10,11,12,13,14,15. PEC treatment significantly improved survival, morphological integrity, stem cell mediated regeneration, and gonad production in Botryllus. Transcriptomic analysis revealed pathway changes associated with cellular metabolism, cell cycle, stem cell activity, DNA repair, and immune modulation. Notably, PEC-induced expression patterns resemble the exercise-induced macrophage-associated transcriptional response previously observed across several mammalian species16,17. This transcriptomic signature correlated with an increase in immune-cell-containing populations. These findings demonstrate that PEC can improve longevity, vitality, and reproduction in an established model renowned for defining broadly applicable biological principles. These studies offer insights into novel strategies for promoting healthy aging and organismal survival.

developmental biology↗

bioRxiv2024

Ultrack: pushing the limits of cell tracking across biological scales

Tracking live cells across 2D, 3D, and multi-channel time-lapse recordings is crucial for understanding tissue-scale biological processes. Despite advancements in imaging technology, achieving accurate cell tracking remains challenging, particularly in complex and crowded tissues where cell segmentation is often ambiguous. We present Ultrack, a versatile and scalable cell-tracking method that tackles this challenge by considering candidate segmentations derived from multiple algorithms and parameter sets. Ultrack employs temporal consistency to select optimal segments, ensuring robust performance even under segmentation uncertainty. We validate our method on diverse datasets, including terabyte-scale developmental time-lapses of zebrafish, fruit fly, and nematode embryos, as well as multi-color and label-free cellular imaging. We show that Ultrack achieves state-of-the-art performance on the Cell Tracking Challenge and demonstrates superior accuracy in tracking densely packed embryonic cells over extended periods. Moreover, we propose an approach to tracking validation via dual-channel sparse labeling that enables high-fidelity ground truth generation, pushing the boundaries of long-term cell tracking assessment. Our method is freely available as a Python package with Fiji and napari plugins and can be deployed in a high-performance computing environment, facilitating widespread adoption by the research community.

developmental biology↗

bioRxiv2021

A rat model of male pregnancy

Male pregnancy is a unique phenomenon in syngnathidae which refers to embryo or fetus incubation by males. However, whether male mammalian animals have the potential to conceive and maintain pregnancy remains unclear. Here, we constructed a rat model of pregnancy in the male parabiont using a four-step strategy. First, a heterosexual parabiotic pair was produced by surgically joining a castrated male rat and a female rat. After 8 weeks, uterus transplantation was performed on the male parabiont. After recovery, blastocyst-stage embryos were transplanted to the grafted uterus of the male parabiont and the native uterus of the female parabiont. Caesarean section was performed at embryonic day 21.5. The success rate of the model was 3.68%, and pups were only delivered from the male parabiont under pregnant blood exposure. Our results reveal the potential for rat embryonic development in male parabionts, which may have a profound impact on reproductive biology. One-sentence summaryA rat model of pregnancy was constructed in the male parabiont using a four-step strategy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/447686v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1f0694eorg.highwire.dtl.DTLVardef@91997forg.highwire.dtl.DTLVardef@f47086org.highwire.dtl.DTLVardef@7a33f_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2024

Mast cells are not essential for pubertal mammary gland branching.

Mast cells are long-lived, tissue-resident immune cells of the myeloid lineage with cardinal functions in allergy and atopic disease. They are now increasingly recognized also for protective roles e.g. against infections and venoms. Other functions originally assigned to mast cells in development and physiology, however, have been refuted, and for yet others, their true contribution remains uncertain. Mast cells have been implicated in promoting ductal branching in the pubertal mammary gland, the organ that produces and secretes milk in mammals, but these findings are based on mouse models that are not mast cell-specific. In this study, we therefore re-addressed the impact of mast cells on mammary gland branching using several complementary genetic models, including a new transgenic line. We report that neither constitutive deficiency of mast cells, nor their conditional ablation induced at puberty affected mammary gland branching. Our results thus dispute that mast cells promote this process in mice, at least in a unique and non-redundant manner. This study adds to a growing body of work clarifying the biological roles of mast cells, and further expands the toolbox available to the field of mast cell research.

developmental biology↗

bioRxiv2024

The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA

Like all canonical PUF proteins, C. elegans FBF-2 binds to specific RNAs via tripartite recognition motifs (TRMs). Here we report that an FBF-2 mutant protein that cannot bind to RNA, is nonetheless biologically active and maintains stem cells. This unexpected result challenges the conventional wisdom that RBPs must bind to RNAs to achieve biological activity. Also unexpectedly, FBF-2 interactions with partner proteins can compensate for loss of RNA-binding. FBF-2 only loses biological activity when its RNA-binding and partner interactions are both defective. These findings highlight the complementary contributions of RNA-binding and protein partner interactions to activity of an RNA-binding protein.

developmental biology↗

bioRxiv2017

Cardiac directed differentiation using small molecule Wnt modulation at single-cell resolution

Differentiation into diverse cell lineages requires the orchestration of gene regulatory networks guiding diverse cell fate choices. Utilizing human pluripotent stem cells, we measured expression dynamics of 17,718 genes from 43,168 cells across five time points over a thirty day time-course of in vitro cardiac-directed differentiation. Unsupervised clustering and lineage prediction algorithms were used to map fate choices and transcriptional networks underlying cardiac differentiation. We leveraged this resource to identify strategies for controlling in vitro differentiation as it occurs in vivo. HOPX, a non-DNA binding homeodomain protein essential for heart development in vivo was identified as dys-regulated in in vitro derived cardiomyocytes. Utilizing genetic gain and loss of function approaches, we dissect the transcriptional complexity of the HOPX locus and identify the requirement of hypertrophic signaling for HOPX transcription in hPSC-derived cardiomyocytes. This work provides a single cell dissection of the transcriptional landscape of cardiac differentiation for broad applications of stem cells in cardiovascular biology.

developmental biology↗

bioRxiv2018

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

Cell lineages provide the framework for understanding how multicellular organisms are built and how cell fates are decided during development. Describing cell lineages in most organisms is challenging, given the number of cells involved; even a fruit fly larva has ~50,000 cells and a small mammal has more than 1 billion cells. Recently, the idea of using CRISPR to induce mutations during development as heritable markers for lineage reconstruction has been proposed and trialled by several groups. While an attractive idea, its practical value depends on the accuracy of the cell lineages that can be generated by this method. Here, we use computer simulations to estimate the performance of this approach under different conditions. Our simulations incorporate empirical data on CRISPR-induced mutation frequencies in Drosophila. We show significant impacts from multiple biological and technical parameters - variable cell division rates, skewed mutational outcomes, target dropouts and different mutation sequencing strategies. Our approach reveals the limitations of recently published CRISPR recorders, and indicates how future implementations can be optimised to produce accurate cell lineages.

developmental biology↗