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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2026

Serotonergic Control of Spine Morphology During Growth in Zebrafish

Scoliosis is a three-dimensional deformity of the vertebral column that commonly emerges during growth, yet the biological mechanisms that initiate and drive curve progression remain poorly understood. Serotonin (5-hydroxytryptamine [5-HT]) has long been linked to scoliosis through its relationship with pineal melatonin signaling and through genetic associations with human disease, but its role in spinal morphogenesis has remained unclear. Here, using zebrafish, we show that serotonergic signaling is required for normal spine morphology. Transient exposure to 5-HT during development induces later spinal abnormalities, while loss of Tph2, the principal enzyme required for neuronal 5-HT synthesis, causes progressive three-dimensional spinal curvature during juvenile growth, mimicking aspects of adolescent idiopathic scoliosis (AIS). tph2 mutants undergo initially normal vertebral patterning while targeted ablation of the pineal gland does not induce scoliosis, arguing against a pineal or early skeletal origin for the 5-HT-associated spinal curves. The Reissner fiber, which has been linked to spinal curvature in zebrafish, also formed normally in tph2 mutants. Instead, mutants showed a marked reduction in Fev-expressing intraspinal serotonergic neurons together with increased locomotor activity. Mutants exhibited longer swim bouts and shorter periods of inactivity between bouts. Importantly, these motor defects were evident shortly before the onset of overt spinal curvature. Together, these findings identify neuronal serotonin as a critical regulator of spinal stability and support a model in which altered serotonergic control of motor function changes the mechanical environment experienced by the growing spine, increasing its susceptibility to progressive curvature.

developmental biology↗
bioRxiv2023

Cold Storage and Cryopreservation Methods for Spermatozoa of the Sea Urchin, Lytechinus pictus .

Sea urchins have contributed greatly to knowledge of fertilization, embryogenesis and cell biology. However, until now, they have not been a genetic model organism because of the long generation times of commonly used species, and lack of tools for husbandry and genetic manipulation. We recently established Lytechinus pictus, as a multigenerational sea urchin model, because of its relatively short generation time of 4-6 months and ease of laboratory culture. To take full advantage of this new multigenerational species, methods are needed to biobank and share mutant L. pictus sperm. Here, we describe a new extender based on sperm ion physiology before spawning of sperm into seawater. This extender maintains sperm capable of fertilization for at least 5-10 weeks when stored at 0 {degrees}C. We use the extender, and the cryoprotectant dimethyl sulfoxide (DMSO), to cryopreserve sperm of both L. pictus, and the widely used sea urchin, Strongylocentrotus purpuratus. The simple methods we describe work well for both species, achieving > 90% development and producing larvae that successfully undergo metamorphosis to juvenile sea urchins. Sperm of these two species can be frozen and thawed at least twice and still give rise to larvae that undergo metamorphosis. Main PointsO_LISperm can maintain fertilizing capacity ex vivo for 5-10 weeks when stored at 0{degrees}C. C_LIO_LIWhen freezing in liquid nitrogen no stepwise addition of cryoprotectant, or stepwise drop in temperature are required. C_LIO_LIA standard fertilization assay is presented to score cleavage stage sea urchin embryos produced by cryopreserved sperm. C_LIO_LISperm frozen and thawed more than once can produce larvae. C_LI

developmental biology↗
bioRxiv2025

Circulating hemocytes continue to proliferate throughout lifespan in Daphnia

Daphnia is a classic model organism for the study of circulation and hemocyte biology. Despite the ease of observation and separation of hemocytes, it is not known whether the circulating hemocytes continue to be produced throughout Daphnia lifespan, and if yes, whether they are generated in any specific hemopoietic tissue or represent a reproducing population as known in some arthropods. We detected de novo DNA synthesis by means of EdU staining in a significant portion of circulating hemocytes in adult D. magna. This portion did not significantly vary among phases of molting/ovary cycle and showed only a slight decrease with age. We did not detect any matching newly synthesized DNA anywhere in any other tissues of adult daphnids, eliminating the hypothesis of the existence of a population of hemopoietic stem cells. Rather, it appears that circulating hemocytes are a reproducing population with mitoses continuing throughout life. Hemocytes showed average ploidy of 4, with a considerable variation around that value indicating that either some endomitoses were also present or a significant portion of hemocytes were sampled in G2. However, while there was no difference in total DNA content measured by Hoechst fluorescence between hemocytes that showed and did not show recent DNA synthesis, among EdU-positive hemocytes there was a positive correlation between Hoechst and EdU fluorescence, indicating that many cells were sampled during S-phase. It is not known whether the total number of hemocytes increases with age or the observed proliferation compensates for losses of hemocytes, as well as whether the EdU-positive hemocytes represent a separate mitotically active stem subpopulation of circulating hemocytes.

developmental biology↗
bioRxiv2026

SOPSim: A cell vertex-based application for simulating sensory bristle patterning with dynamic filopodia

Repeating patterns, such as the bristles on the thorax of fruit flies developed from sensory organ precursor (SOP) cells, play important roles in the lives of flies as they are connected to the central nervous system and help detect environmental cues and threats. Notch signaling is known to regulate the formation of these patterns. Primarily, Notch signaling involves local communication between neighboring cells in direct contact (apical or junctional interaction). However, this short-range interaction alone cannot fully explain the complex biological patterns observed. Further studies have revealed long-range communication between cells through actin-based protrusions known as filopodia. The precise understanding of how the dynamics of filopodia, such as protrusion and retraction, lead to Notch-Delta activation remains unclear, which limits our ability to fully comprehend the mechanisms underlying cell fate decisions and the emergence of spatially organized patterns during tissue development and regeneration. In this study, we extend the modeling framework for Notch signaling by incorporating a filopodia dynamics model driven by myosin-mediated contraction. We address existing gaps by defining criteria under which any given pair of filopodia will physically intersect. We also introduce the local sensory area (LSA), a metric for quantifying local SOP spacing, and use experimental data to calibrate a Notch threshold that distinguishes SOP from epithelial cells. Through numerical simulations, we confirm that long-range communication via filopodia is essential for reproducing the refined patterns observed in vivo. Additionally, we explore how filopodia length, lifetime, and orientation influence the spatial organization of SOP cells. To this end, a Python library has been developed which allows users to perform simulations of Notch Delta signaling via a (1) Graphical User Interface/website, local to the user's computer, (2) via commands in the command line interface, or (3) by calling the simulation using a function via a Python API. This library allows users without computational expertise to easily specify a small number of input parameters and generate simulations of the model.

developmental biology↗
bioRxiv2021

Growth and development of trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata) reflects locomotor behavior, life-history, and neuromuscular development.

We aim to broaden the analysis of bone structure by suggesting a new way to incorporate the interactions between behavior, neuromuscular development, and life-history. We examine the associations between these variables and age-related variation in trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata). If skeletal markers linking these variables can be established, our inferences of the biology and behavior of fossil species would be significantly improved. We {micro}CT scanned the calcaneus in a cross-sectional sample of 36 juveniles aged between 0 and 7 years old and 5 adults at the Primate Research Institute, Japan. We calculated whole bone averages of standard trabecular properties and generated whole-bone morphometric maps of bone volume fraction and Youngs modulus. Trabecular structure is increasingly heterogeneous in older individuals. BV/TV decreases during the first month of life and increases afterwards, coinciding with the onset of independent locomotion. At birth, primary Youngs modulus is oriented orthogonal to the ossification center, but after locomotor onset bone structure becomes stiffest in the direction of joint surfaces and muscle attachments. Age-related variation in bone volume fraction is best predicted by an interaction between neuromaturation, body mass, and locomotor independence. Results support the common assumption that trabecular structure dynamically adapts to novel joint loading conditions during ontogeny. The timing of independent locomotion, body size, and neuromuscular development, are all correlated to age-related variation in the trabecular structure of the macaque calcaneus. The causal mechanisms behind the observed patterns cannot be directly inferred from our cross-sectional study. If the model presented in this paper holds up under longitudinal experimental conditions, trabecular structure can be used both to infer behavior from fossil morphology and to serve as a valuable proxy for neuromuscular maturation and life history events like locomotor onset and the achievement of an adult-like gait.

developmental biology↗
bioRxiv2025

Inverted Assembly of the Lens Within Ocular Organoids Reveals Alternate Paths to Ocular Morphogenesis

The eye is a complex organ composed of two main structures - the retina and the lens. It forms by the invagination of the lens forming head surface ectoderm embedding into the forming optic cup. This "outside-in" mode of morphogenesis ensures that the light focusing lens is positioned centrally inside of the eye in the highly constrained environment of the developing embryo. Advances in stem cell biology in the last decade introduced organoids as model to study organogenesis under normal and diseased conditions. However, even though strikingly similar at some points, it remained elusive to which extend the generation of individual structural features in organoids recapitulates in vivo organogenesis. Here we describe the generation of fish ocular organoids composed of both, lens and retina, using pluripotent embryonic cells from medaka (Oryzias latipes). Formation of the organoid lens followed the key molecular features of the process in vivo, including the establishment of lens progenitor cells and their subsequent differentiation into lens fiber cells. In a process dependent on the coordinated activity of BMP and FGF signaling, lens formation in ocular organoids was marked by the expression of key genes implicated in organismal lens development. Despite adhering to the basic molecular machinery of lens formation in vivo, the morphogenesis into a spherical lens followed an "inside-out" mode. Lens progenitor cells were initially established and differentiated into a spherical lens directly inside of the retina. Subsequent displacement of the lens from the center of the organoid towards its surface ultimately led to the formation of a cup-like shaped retina with a centrally positioned lens. Our study highlights that the self-organization of the organoid can favor routes that were not selected for in the developing embryo. Those routes can lead to an alternative, though highly similar outcome with the respect to achieving specific structural features in an unconstrained, embryo-free environment.

developmental biology↗
bioRxiv2026

Trans-regenerational RNAi Memory in Planarians

How cells and organisms preserve molecular memory is a central question in biology. Chromatin states can maintain cellular memory in animals, yet DNA and histone modifications are typically reset in the germ line and early embryo. In Caenorhabditis elegans, RNA-dependent RNA polymerases (RdRPs) amplify small RNAs and enable transgenerational gene regulation. However, many organisms, including mammals, lack canonical RdRPs. Here we find that planarians, highly regenerative flatworms that lack canonical RdRPs and critical nuclear RNAi machinery, mount long-term heritable gene regulatory responses. We show that ingestion of double-stranded RNA induces potent, sequence-specific silencing that persists for months, withstands repeated cycles of whole-body regeneration, and can be transferred between animals. This long-term silencing, heritable during asexual reproduction, follows two phases: an early, transient response to exogenous RNA, and a stable, cell-autonomous memory phase that maintains repression long after the RNA trigger is gone. The memory phase is maintained post-transcriptionally, as transcription and chromatin accessibility remain unchanged while mature mRNA is depleted. This phase coincides with the emergence of A-tailed 21-23-nt antisense small RNAs and with silencing responses that act in trans and spread across the length of the target transcript. These results reveal a two-step, canonical RdRP-independent mechanism for persistent RNAi memory in a regenerating animal and establish planarians as a model for RNA-based inheritance, illuminating a novel mode by which RNA can encode durable gene-silencing states in metazoans.

developmental biology↗
bioRxiv2025

Genetics of growth rate in induced pluripotent stem cells

Human induced pluripotent stem cells (iPSCs) have transformed biomedical research by enabling the generation of diverse cell types from accessible somatic tissues. However, certain fundamental biological properties, such as the genetic and epigenetic determinants of iPSC proliferation, remain poorly characterized. We measured the growth of iPSC lines derived from 602 unique donors using high-throughput time-lapse imaging, quantified proliferation through a growth Area-Under-the-Curve (gAUC) phenotype, and correlated gAUC with the gene expression and genotype of the cell lines. We identified 3,091 genes associated with gAUC, many of which are well established regulators of cell proliferation. We also found that rare deleterious variants in WDR54 were associated with reduced iPSC growth and that WDR54 was differentially expressed with respect to gAUC. Although no common variants showed a genome-wide association with gAUC, iPSC lines from monozygotic twins were highly correlated, and common genetic variation explained approximately 71-75% of the variance in iPSC growth rates. These results indicate a complex genetic architecture of iPSC growth rates, where rare, large-effect variants in important growth regulators, including WDR54, are layered onto a highly polygenic background. These findings have important implications for the design of pooled iPSC-based studies and disease models, which may be confounded by intrinsic growth differences.

developmental biology↗
bioRxiv2018

A human cell model of cardiac pathophysiological valvulogenesis

Genetically modified mice have advanced our understanding of valve development and related pathologies. Yet, little is known regarding human valvulogenesis in health and diseases. Genuine human in vitro models that reproduce valvular (patho)biology are thus needed. We here developed a human pluripotent stem cell-derived model fit to decode the early steps of human valvulogenesis and to recapitulate valve disease traits in a dish.\n\nUsing cellular based, single cell omics-informed and in vivo-validated approaches, we derived a population of pre-valvular endocardial cells from a pluripotent stem cell source. These human prevalvular cells (HPVCs) expressed gene patterns conforming to the atrio-ventricular canal (AVC) endocardium signature originally established in E9.0 mouse embryos. In fact, HPVC treated with BMP2, cultured onto mouse AVC cushions, or transplanted into the AVC of embryonic mouse hearts, underwent endothelial-to-mesenchymal transition and expressed markers of valve interstitial cells of different valvular layers demonstrating tissue functionality. HPVCs also differentiated into tendinous/chondrogenic cells in line with the valvular repertoire. Extending this valvulogenic model to patient specific iPS cells, we recapitulated features of mitral valve prolapse and uncovered that dysregulation of the SHH pathway is likely to be at the origin of the disease thus providing a putative therapeutic target.\n\nHuman pluripotent stem cells recapitulate early valvulogenesis and provide a powerful model to systematically decipher the origin and lineage contribution of different valvular cell types in humans as well as to study valve diseases in a dish.

developmental biology↗
bioRxiv2019

Organogenesis and Distribution of the Ocular Lymphatic Vessels in the Anterior Eye: Implication to Glaucoma Surgery Site Selection

Glaucoma surgeries, such as trabeculectomy, are performed to lower the intraocular pressure to reduce the risk of vision loss. The surgeries create a new passage in the eye that reroutes the aqueous humor outflow to the subconjunctival space, where the fluid is presumably absorbed by the conjunctival lymphatics. However, the current knowledge of these ocular surface lymphatics remains limited. Here, we characterized the biology and function of the ocular lymphatics using transgenic lymphatic reporter mice and rats. We found that the limbal and conjunctival lymphatic networks are progressively formed by a primary lymphatic vessel that grows out from the nasal-side medial canthus region at the time of birth. This primary lymphatic vessel immediately branches out and invades the limbus and conjunctiva, and then simultaneously encircles the cornea in a bidirectional manner. As a result, the distribution of the ocular lymphatic is significantly polarized toward the nasal side, and the limbal lymphatics are directly connected to the conjunctival lymphatics. New lymphatic spouts are mainly produced from the nasal-side limbal lymphatics, posing the nasal side of the eye more responsive to fluid drainage and inflammatory stimuli. Consistently, when a fluorescent tracer was injected, fluid clearance was much more efficient in the nasal side than the temporal side of the eyes. In comparison, blood vessels are evenly distributed on the front surface of the eyes. We found that these distinct vascular distribution patterns were also conserved in human eyes. Together, our study demonstrated that the ocular surface lymphatics are more densely present in the nasal side and uncovered the potential clinical benefits in selecting the nasal side as a surgical site for glaucoma surgeries to improve the fluid drainage.

developmental biology↗
bioRxiv2016

Zika Fetal Neuropathogenesis: Etiology of a Viral Syndrome

The ongoing Zika Virus epidemic in the Americas, and the observed association with both fetal abnormalities (primary microcephaly) and adult autoimmune pathology (Guillain-Barre syndrome) has brought attention to this neglected pathogen. While initial case studies generated significant interest in the Zika virus outbreak, larger prospective epidemiology and basic virology studies examining the mechanisms of Zika viral infection and associated pathophysiology are only now starting to be published. In this review, we analyze Zika fetal neuropathogenesis from a comparative pathology perspective, using the historic metaphor of \"TORCH\" viral pathogenesis to provide context. By drawing parallels to other viral infections of the fetus, we identify common themes and mechanisms that may illuminate the observed pathology. The existing data on the susceptibility of various cells to both Zika and other flavivirus infections are summarized. Finally, we highlight relevant aspects of the known molecular mechanisms of flavivirus replication.\n\nKey Learning PointsO_LIViral TORCH pathogens reveal common patterns of fetal pathophysiology and vertical transmission which are relevant to Zika Virus fetal neuropathogenesis.\nC_LIO_LIThe teratogenic effects of Zika Virus infection during the first trimester may involve infection of the trophoblast, viral translocation across the placenta, migration of infected cells resulting in embryonic infection, or indirect effects associated with high levels of inflammatory cytokines produced by infected placenta.\nC_LIO_LIPre-existing maternal non-neutralizing antibody to Zika virus may enhance the probability of infection or more severe disease in the fetus.\nC_LIO_LIAXL has been identified as a major receptor for Zika Virus.\nC_LIO_LIZika virus activation of Toll Like Receptor 3 (TLR-3) pathways in central nervous system cells may trigger apoptosis and attenuate neurogenesis, directly contributing to fetal neuropathology.\nC_LIO_LIFlaviviruses subvert host autophagy and noncoding RNA regulatory pathways.\nC_LIO_LIRecognition of viral sequences by regulatory RNA binding proteins such as Musashi may have a role in Zika pathogenesis and host tissue tropism.\nC_LIO_LIEvidence from other TORCH viral pathogen studies indicate multiple plausible hypotheses for transplacental infection by Zika virus during the second or third trimester, including transcytosis of non-neutralizing antibody-coated Zika virus complexes.\nC_LI\n\nKey ReferencesAdibi JJ, Marques ET Jr, Cartus A, Beigi RH. Teratogenic effects of the Zika virus and the role of the placenta. Lancet 2016; 387: 1587-90 (Hypothesis)\nAdams Waldorf KM, McAdams RM. Influence of infection during pregnancy on fetal development. Reproduction. 2013 Oct 1;146(5) (Review)\nHamel R, Dejarnac O, Wichit S, Ekchariyawat P, Neyret A, Luplertlop N, et al. Biology of Zika Virus Infection in Human Skin Cells. J Virol. 2015;89(17):8880-96.\nMlakar J, Korva M, Tul N, Popovi[c] M, Polj[s]ak-Prijatelj M, Mraz J, et al. Zika Virus Associated with Microcephaly. N Engl J Med. 2016 Feb 10.\nPaul LM, Carlin ER, Jenkins MM, Tan AL, Barcellona CM, Nicholson CO, Trautmann L, Michael SF, Isern S. Dengue Virus Antibodies Enhance Zika Virus Infection. bioRxiv doi: http://dx.doi.org/10.1101/050112\nCrow YJ, Manel N. Aicardi-Goutieres syndrome and the type I interferonopathies. Nat Rev Immunol. 2015;15(7):429-40.\nTonduti D, Orcesi S, Jenkinson EM, Dorboz I, Renaldo F, Panteghini C, et al. Clinical, radiological and possible pathological overlap of cystic leukoencephalopathy without megalencephaly and Aicardi-Goutieres syndrome. Eur J Paediatr Neurol. 2016.\nCipolat Mis MS, Brajkovic S, Frattini E, Di Fonzo A, Corti S. Autophagy in motor neuron disease: Key pathogenetic mechanisms and therapeutic targets. Molecular and Cellular Neurosciences. 2016;72:84-90.\nDang J, Tiwari SK, Lichinchi G, Qin Y, Patil VS, Eroshkin AM, Rana TM. Zika Virus Depletes Neural Progenitors in Human Cerebral Organoids through Activation of the Innate Immune Receptor TLR3. Cell Stem Cell. 2016: 19: 1-8.\nVianna FS, Schuler-Faccini L, Leite JC, de Sousa SH, da Costa LM, Dias MF, et al. Recognition of the phenotype of thalidomide embryopathy in countries endemic for leprosy: new cases and review of the main dysmorphological findings. Clin Dysmorphol. 2013;22(2):59-63.

Developmental Biology↗
bioRxiv2024

Contraction-induced endocardial id2b plays a dual role in regulating myocardial contractility and valve formation

Biomechanical cues play an essential role in sculpting organ formation. Comprehending how cardiac cells perceive and respond to biomechanical forces is a biological process with significant medical implications that remains poorly understood. Here we show that biomechanical forces activate endocardial id2b (inhibitor of DNA binding 2b) expression, thereby promoting cardiac contractility and valve formation. Taking advantage of the unique strengths of zebrafish, particularly the viability of embryos lacking heartbeats, we systematically compared the transcriptomes of hearts with impaired contractility to those of control hearts. This comparison identified id2b as a gene sensitive to blood flow. By generating a knockin reporter line, our results unveiled the presence of id2b in the endocardium, and its expression is sensitive to both pharmacological and genetic perturbations of contraction. Furthermore, id2b loss-of-function resulted in progressive heart malformation and early lethality. Combining RNA-seq analysis, electrophysiology, calcium imaging, and echocardiography, we discovered profound impairment in atrioventricular (AV) valve formation and defective excitation-contraction coupling in id2b mutants. Mechanistically, deletion of id2b reduced AV endocardial cell proliferation and led to a progressive increase in retrograde blood flow. In the myocardium, id2b directly interacted with the bHLH component tcf3b (transcription factor 3b) to restrict its activity. Inactivating id2b unleashed its inhibition on tcf3b, resulted in enhanced repressor activity of tcf3b, which subsequently suppressed the expression of nrg1 (neuregulin 1), an essential mitogen for heart development. Overall, our findings identify id2b as an endocardial cell-specific, biomechanical signaling-sensitive gene, which mediates intercellular communications between endocardium and myocardium to sculpt heart morphogenesis and function.

developmental biology↗
bioRxiv2023

Reversal of Biological Age in Multiple Rat Organs by Young Porcine Plasma Fraction

Young blood plasma is known to confer beneficial effects on various organs in mice and rats. However, it was not known whether plasma from young pigs rejuvenates old rat tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n=613 tissue samples. As indicated by their respective names, the rat pan-tissue clock can be applied to DNA methylation profiles from all rat tissues, while the rat brain-, liver-, and blood clocks apply to the corresponding tissue types. We also developed two epigenetic clocks that apply to both human and rat tissues by adding n=1366 human tissue samples to the training data. We employed these six rat clocks to investigate the rejuvenation effects of a porcine plasma fraction treatment in different rat tissues. The treatment more than halved the epigenetic ages of blood, heart, and liver tissue. A less pronounced, but statistically significant, rejuvenation effect could be observed in the hypothalamus. The treatment was accompanied by progressive improvement in the function of these organs as ascertained through numerous biochemical/physiological biomarkers and behavioral responses to assess cognitive functions. An immunoglobulin G (IgG) N-glycosylation pattern shift from pro-to anti-inflammatory also indicated reversal of glycan aging. Overall, this study demonstrates that a young porcine plasma-derived treatment markedly reverses aging in rats according to epigenetic clocks, IgG glycans, and other biomarkers of aging.

developmental biology↗
bioRxiv2023

Temporal recording of mammalian development and precancer

Key to understanding many biological phenomena is knowing the temporal ordering of cellular events, which often require continuous direct observations [1, 2]. An alternative solution involves the utilization of irreversible genetic changes, such as naturally occurring mutations, to create indelible markers that enables retrospective temporal ordering [3-8]. Using NSC-seq, a newly designed and validated multi-purpose single-cell CRISPR platform, we developed a molecular clock approach to record the timing of cellular events and clonality in vivo, while incorporating assigned cell state and lineage information. Using this approach, we uncovered precise timing of tissue-specific cell expansion during murine embryonic development and identified new intestinal epithelial progenitor states by their unique genetic histories. NSC-seq analysis of murine adenomas and single-cell multi-omic profiling of human precancers as part of the Human Tumor Atlas Network (HTAN), including 116 scRNA-seq datasets and clonal analysis of 418 human polyps, demonstrated the occurrence of polyancestral initiation in 15-30% of colonic precancers, revealing their origins from multiple normal founders. Thus, our multimodal framework augments existing single-cell analyses and lays the foundation for in vivo multimodal recording, enabling the tracking of lineage and temporal events during development and tumorigenesis.

developmental biology↗
bioRxiv2021

Evolutionarily divergent mTOR remodels the translatome to drive rapid wound closure and regeneration

An outstanding mystery in biology is why some species, such as the axolotl, can scarlessly heal and regenerate tissues while most mammals cannot. Here, we demonstrate that rapid activation of protein synthesis is a unique, and previously uncharacterized, feature of the injury response critical for limb regeneration in the axolotl (A. mexicanum). By applying polysome sequencing, we identify hundreds of transcripts, including antioxidants and ribosome components, which do not change in their overall mRNA abundance but are selectively activated at the level of translation from pre-existing mRNAs in response to injury. In contrast, we show that protein synthesis is not activated in response to digit amputation in the non-regenerative mouse. We further identify the mTORC1 pathway as a key upstream signal that mediates this regenerative translation response in the axolotl. Inhibition of this pathway is sufficient to suppress translation and axolotl regeneration. Surprisingly, although mTOR is highly evolutionarily conserved, we discover unappreciated expansions in mTOR protein sequence among urodele amphibians. By engineering an axolotl mTOR in human cells, we demonstrate that this change creates a hypersensitive kinase that may allow axolotls to maintain this pathway in a highly labile state primed for rapid activation. This may underlie metabolic differences and nutrient sensing between regenerative and non-regenerative species that are key to regeneration. Together, these findings highlight the unanticipated impact of the translatome on orchestrating the early steps of wound healing in highly regenerative species and provide a missing link in our understanding of vertebrate regenerative potential.

developmental biology↗
bioRxiv2022

Intracellular fraction of zona pellucida protein 3 is required for the oocyte to embryo transition in mice

In oocyte biology the zona pellucida has long been known to operate three extracellular functions, namely, encasing the oocytes in ovarian follicles, mediating sperm-oocyte interaction and preventing premature embryo contact with maternal epithelia. The present study uncovers a fourth function that is fundamentally distinct from the other three, being critical for embryonic cell survival. Intriguingly, the three proteins of the mouse zona pellucida (ZP1, ZP2, ZP3) were found abundantly present also inside the embryo four days after fertilization, as shown by mass spectrometry, immunoblotting and immunofluorescence. Trim-away-mediated knockdown of ZPs in fertilized oocytes resulted in various grades of embryopathy: knockdown of ZP1 impeded blastocyst expansion, knockdown of ZP2 hampered the 2nd zygotic cleavage, while knockdown of ZP3 hampered the 1st zygotic cleavage - unlike the overexpression. Transcriptome analysis of ZP3-knockdown embryos pointed at defects of cytoplasmic translation in the context of embryonic genome activation. This conclusion was supported by reduced protein synthesis in the ZP3-knockdown and by the lack of cleavage arrest when knockdown was postponed from the 1-cell to the late 2-cell stage. These data place constraints on the long-standing notion that the zona pellucida proteins only operate in the extracellular space. We postulate that such noncanonical localization of ZP3 reflect novel roles in the embryos interior during the oocyte-to-embryo transition in mice. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/521410v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@18c0ca2org.highwire.dtl.DTLVardef@19168aeorg.highwire.dtl.DTLVardef@16f784forg.highwire.dtl.DTLVardef@143c4b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗
bioRxiv2018

Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish

A fundamental question in biology is how anatomically and functionally distinct tissues coordinate to direct growth and shape in complex organs. We address this question using as a model the eye of teleost fish, which grow while maintaining the precise shape needed for vision throughout the animals life.\n\nCombining clonal analysis in the eye of the teleost medaka (Oryzias latipes) with a computational agent based model, we find that the neural retina (NR) and retinal pigmented epithelium (RPE) differentially modulate cell divisions to coordinate their growth rates. Cell divisions in the NR are less stochastic, consistent with an upstream role as an inducer of growth in nearby tissues. Cells in the RPE display much higher stochasticity, consistent with a downstream role responding to inductive signals.\n\nOur simulation predicts that the segregation of stem- and progenitor cell domains in the retinal ciliary marginal zone niche is an emergent property, as the topology of the niche preconditions the system to undergo a spatially biased stochastic neutral drift. Clone properties in the NR support this prediction, and further suggest that NR cells control the direction of division axes to regulate organ shape and retinal cell topology.\n\nThis work highlights an as yet unappreciated mechanism for growth coordination in a complex organ, where one tissue integrates external and internal cues as a hub to synchronize growth rates in nearby tissues. In the eye of fish, proliferation parameters of neuroretinal stem cells are a minimal target node for evolution to exploit to adapt whole-organ morphogenesis in a complex vertebrate organ.

developmental biology↗
bioRxiv2024

Transient Notch Activation Converts Pluripotent Stem Cell-Derived Cardiomyocytes towards a Purkinje Fiber Fate

Cardiac Purkinje fibers form the most distal part of the ventricular conduction system. They coordinate contraction and play a key role in ventricular arrhythmias. While many cardiac cell types can be generated from human pluripotent stem cells, methods to generate Purkinje fiber cells remain limited, hampering our understanding of Purkinje fiber biology and conduction system defects. To identify signaling pathways involved in Purkinje fiber formation, we analyzed single cell data from murine embryonic hearts and compared Purkinje fiber cells to trabecular cardiomyocytes. This identified several genes, processes, and signaling pathways putatively involved in cardiac conduction, including Notch signaling. We next tested whether Notch activation could convert human pluripotent stem cell-derived cardiomyocytes to Purkinje fiber cells. Following Notch activation, cardiomyocytes adopted an elongated morphology and displayed altered electrophysiological properties including increases in conduction velocity, spike slope, and action potential duration, all characteristic features of Purkinje fiber cells. RNA-sequencing demonstrated that Notch-activated cardiomyocytes undergo a sequential transcriptome shift, which included upregulation of key Purkinje fiber marker genes involved in fast conduction such as SCN5A, HCN4 and ID2, and downregulation of genes involved in contractile maturation. Correspondingly, we demonstrate that Notch-induced cardiomyocytes have decreased contractile force in bioengineered tissues compared to control cardiomyocytes. We next modified existing in silico models of human pluripotent stem cell-derived cardiomyocytes using our transcriptomic data and modeled the effect of several anti-arrhythmogenic drugs on action potential and calcium transient waveforms. Our models predicted that Purkinje fiber cells respond more strongly to dofetilide and amiodarone, while cardiomyocytes are more sensitive to treatment with nifedipine. We validated these findings in vitro, demonstrating that our new cell-specific in vitro model can be utilized to better understand human Purkinje fiber physiology and its relevance to disease.

developmental biology↗