Biology subjects

Briscoe, J.

Publications and source records attributed to Briscoe, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube

The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme operating in progenitors throughout the vertebrate nervous systems that governs cell fate choices by regulating chromatin accessibility. Perturbation of this cis-regulatory programme affects sequential cell fate transitions in neural progenitors and the identity of their progeny. The temporal programme operates in parallel to spatial patterning, ensuring the timely availability of regulatory elements for spatial determinants to direct cell-type specific gene expression. These findings identify a chronotopic spatiotemporal integration strategy in which a global temporal chromatin programme determines the output of a spatial gene regulatory network resulting in the temporally and spatially ordered allocation of cell type identity.

developmental biology↗

bioRxiv2023

Live-imaging reveals Coordinated Cell Migration and Cardiac Fate Determination during Mammalian Gastrulation.

Heart development involves the specification of cardiac progenitors at distinct stages and locations. Using live-imaging of mouse embryos between gastrulation and heart tube formation, we tracked individual mesodermal cells and reconstructed their lineage trees for up to five cell divisions. We found independent unipotent progenitors emerging at specific times, contributing exclusively to either left ventricle/atrioventricular canal (LV/AVC) or atrial myocytes. LV/AVC progenitors differentiated early to form the cardiac crescent, while atrial progenitors later generated the heart tubes inflow tract during morphogenesis. We also identified short-lived bipotent progenitors with broad potential, illustrating early developmental plasticity. Sister cells from bipotent progenitors displayed greater dispersion and more diverse migratory trajectories within the anterior mesoderm than those from unipotent progenitors. Bipotent progenitors contributing to extraembryonic mesoderm (ExEm) exhibited the fastest and most dispersed migrations, whereas those giving rise to endocardial, LV/AVC, and pericardial cells showed a more gradual divergence, with late-stage behavioural shifts: endocardial cells increased in speed, while pericardial cells slowed relative to LV/AVC cells. Together the data reveal the regulation of individual cell directionality and cardiac fate allocation within the seemingly unorganised migratory pattern of mesoderm cells.

developmental biology↗

bioRxiv2023

Blimp-1 and c-Maf regulate common and unique gene networks to protect against distinct pathways of pathobiont-induced colitis

Intestinal immune responses to commensals and pathogens are controlled by IL-10 to avoid intestinal immune pathology. We show that the transcription factors Blimp-1 (Prdm-1) and c-Maf are co-dominant regulators of Il10 in Foxp3+ regulatory T cells, but also negatively regulate proinflammatory cytokines in effector T cells. Mice with T cell-specific deletion of Prdm-1, Maf or the combination of both transcription factors did not develop inflammatory intestinal pathologies at the steady state. Double deficient Prdm1fl/flMaffl/flCd4Cre mice infected with Helicobacter hepaticus developed severe colitis with a major increase in TH1/NK/ILC1 effector genes in lamina propria leucocytes (LPLs), while Prdm1fl/flCd4Cre and Maffl/flCd4Cre mice showed mild/moderate pathology and a less-marked Type I effector response. LPLs from infected Maffl/flCd4Cre mice showed increased Il17a expression and an accompanying increase in granulocytes and myeloid cells, which was less marked in Prdm1fl/flMaffl/flCd4Cre mice, with increased T cell-myeloid-neutrophil interactions inferred from scRNA-seq analysis and confirmed by immunofluorescent analysis of colon sections. Genes over-expressed in human IBD showed differential expression in the LPL from infected mice in the absence of Prdm1 or Maf, revealing potential pathobiologic mechanisms of human disease.

immunology↗

bioRxiv2023

Deep dynamical modelling of developmental trajectories with temporal transcriptomics

Developmental cell fate decisions are dynamic processes driven by the complex behaviour of gene regulatory networks. A challenge in studying these processes using single-cell genomics is that the data provides only a static snapshot with no detail of dynamics. Metabolic labelling and splicing can provide time-resolved information, but current methods have limitations. Here, we present experimental and computational methods that overcome these limitations to allow dynamical modelling of gene expression from single-cell data. We developed sci-FATE2, an optimised metabolic labelling method that substantially increases data quality, and profiled approximately 45,000 embryonic stem cells differentiating into multiple neural tube identities. To recover dynamics, we developed velvet, a deep learning framework that extends beyond instantaneous velocity estimation by modelling gene expression dynamics through a neural stochastic differential equation system within a variational autoencoder. Velvet outperforms current velocity tools across quantitative benchmarks, and predicts trajectory distributions that accurately recapitulate underlying dataset distributions while conserving known biology. Velvet trajectory distributions capture dynamical aspects such as decision boundaries between alternative fates and correlative gene regulatory structure. Using velvet to provide a dynamical description of in vitro neural patterning, we highlight a process of sequential decision making and fate-specific patterns of developmental signalling. Together, these experimental and computational methods recast single-cell analyses from descriptions of observed data distributions to models of the dynamics that generated them, providing a new framework for investigating developmental gene regulation and cell fate decisions.

bioinformatics↗

bioRxiv2023

Clonal neural tube organoids self-organise floorplate through BMP-mediated cluster competition

The neural tube (NT) has been a hallmark example of embryonic induction and patterning whereby the notochord induces an organiser, the floorplate, that secretes Sonic Hedgehog (SHH) to pattern the surrounding field of neural progenitors. On the other hand, NT organoids (NTOs) formed from embryonic stem cells (ESCs) undergo spontaneous floorplate formation and patterning in the absence of their normal embryonic inducers. Understanding how stem cells undergo regulative organiser formation is a central challenge in biology. Here, we investigated the self-organisation of a SHH-expressing floorplate organiser using clonal NTOs. Expression of FOXA2, a floorplate transcription factor, was initially spatially scattered before resolving into multiple clusters. These FOXA2+ clusters underwent competition and physical sorting, resulting in a stable "winning" floorplate. We identified BMP signalling as a key governor of long-range cluster competition. FOXA2+ clusters expressed BMP4 ligand suppressing FOXA2 in receiving cells, while simultaneously expressing the BMP-inhibitor NOGGIN to secure FOXA2+ cluster survival. Genetic mutation of Noggin perturbed the floorplate not only in NTOs but also in vivo at the mid-hindbrain region of the mouse NT. These results demonstrate how the floorplate can form autonomously without its well-known inducer, the notochord, suggesting redundant mechanisms ensuring robustness. Defining molecular pathways that govern organiser self-organisation is critical in harnessing the developmental plasticity of stem cells toward directed tissue engineering.

developmental biology↗

bioRxiv2023

Notochord and axial progenitor generation by timely BMP and NODAL inhibition during vertebrate trunk formation

The formation of the vertebrate body involves the coordinated and progressive production of trunk tissues from progenitors located in the posterior of the embryo. In vitro models based on pluripotent stem cells (PSCs) replicate aspects of this process, but they lack some tissue components normally present in the trunk. Most strikingly, the notochord, a hallmark of chordates and the source of midline signals that pattern surrounding tissues, is absent from current models of human trunk formation. To investigate how trunk tissue is formed, we performed single-cell transcriptomic analysis of chick embryos. This delineated molecularly discrete progenitor populations, which we spatially locate in the embryo, compare across species, and relate to signalling activity. Guided by this map, we determined how differentiating human PSCs develop a stereotypical spatial organization of tissue types. We found that LATS1/2 repression of YAP activity, in conjunction with FGF-mediated MAPK activation, induced the transcription factor Bra/TBXT and facilitated WNT signaling. In addition, inhibiting a WNT-induced NODAL and BMP signaling cascade at the appropriate time regulated the proportions of different tissue types produced, including notochordal cells. We used this information to create an integrated 3D model of human gastrulation undergoing morphogenetic movements to produce elongated structures with a notochord and spatially patterned neural tissue formation. Together the data provide insight into the mechanisms responsible for the formation of the tissues that comprise the vertebrate trunk and pave the way for future studies of patterning in a tissue-like environment.

developmental biology↗

bioRxiv2022

Optimal control of gene regulatory networks for morphogen-driven tissue patterning

The organised generation of functionally distinct cell types in developing tissues depends on establishing spatial patterns of gene expression. In many cases, this is directed by spatially graded chemical signals - known as morphogens. In the influential "French Flag Model", morphogen concentration is proposed to instruct cells to acquire their specific fate. However, this mechanism has been questioned. It is unclear how it produces timely and organised cell-fate decisions, despite the presence of changing morphogen levels, molecular noise and individual variability. Moreover, feedback is present at various levels in developing tissues introducing dynamics to the process that break the link between morphogen concentration, signaling activity and position. Here we develop an alternative approach using optimal control theory to tackle the problem of morphogen-driven patterning. In this framework, intracellular signalling is derived as the control strategy that guides cells to the correct fate while minimizing a combination of signalling levels and the time taken. Applying this approach demonstrates its utility and recovers key properties of the patterning strategies that are found in experimental data. Together, the analysis offers insight into the design principles that produce timely, precise and reproducible morphogen patterning and it provides an alternative framework to the French Flag paradigm for investigating and explaining the control of tissue patterning.

developmental biology↗

bioRxiv2022

Developmental cell fate choice employs two distinct cis regulatory strategies

In many developing tissues the patterns of gene expression that assign cell fate are organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. In the neural tube, a gradient of the morphogen Sonic hedgehog allocates neural progenitor identity. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. In the majority of ventral neural progenitors a common set of CREs are used to control gene activity. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for FOXA2-mediated regulatory strategy across tissues.

developmental biology↗

bioRxiv2022

A gradient border model for cell fate decisions at the neural plate border

The vertebrate neural plate border is a transient territory located at the edge of the neural plate containing precursors for all ectodermal derivatives: the neural plate; neural crest; placodes; and epidermis. Elegant functional experiments in a range of vertebrate models have provided an in-depth understanding of gene regulatory interactions within the ectoderm. However, these experiments conducted at tissue level raise seemingly contradictory models for fate allocation of individual cells. Here, we carry out single cell RNA sequencing of chick ectoderm from primitive streak to neurulation stage, to explore cell state diversity and heterogeneity. We characterise the dynamics of gene modules containing key factors known to regulate ectodermal cell fates, allowing us to model the order in which these fates are specified. Furthermore, we find that genes previously classified as neural plate border specifiers typically exhibit dynamic expression patterns and are biased towards either placodal or neural crest fates, revealing that the neural plate border should be seen as an anatomical region of the ectoderm and not a discrete transcriptional state. Through co-expression of placodal and neural crest markers, we identify a population of border located unstable progenitors (BLUPs) which gradually reduces in size as fate segregation occurs. Considering our findings, we propose a gradient border model for cell fate choice at the neural plate border, with the probability of cell fate allocation closely tied to the spatiotemporal positioning of cells.

developmental biology↗

bioRxiv2021

Single cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human specific features

The spinal cord receives input from peripheral sensory neurons and controls motor output by regulating muscle innervating motor neurons. These functions are carried out by neural circuits comprising molecularly and physiologically distinct neuronal subtypes that are generated in a characteristic spatial-temporal arrangement from progenitors in the embryonic neural tube. The systematic mapping of gene expression in mouse embryos has provided insight into the diversity and complexity of cells in the neural tube. For human embryos, however, less information has been available. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions in four human embryos of Carnegie Stages (CS) CS12, CS14, CS17 and CS19 from Gestational Weeks (W) 4-7. In total we recovered the transcriptomes of 71,219 cells. Analysis of progenitor and neuronal populations from the neural tube, as well as cells of the peripheral nervous system, in dorsal root ganglia adjacent to the neural tube, identified dozens of distinct cell types and facilitated the reconstruction of the differentiation pathways of specific neuronal subtypes. Comparison with existing mouse datasets revealed the overall similarity of mouse and human neural tube development while highlighting specific features that differed between species. These data provide a catalogue of gene expression and cell type identity in the developing neural tube that will support future studies of sensory and motor control systems and can be explored at https://shiny.crick.ac.uk/scviewer/neuraltube/.

developmental biology↗

bioRxiv2021

A quantitative landscape of cell fate transitions identifies principles of cellular decision-making

Fate decisions in developing tissues involve cells transitioning between a set of discrete cell states, each defined by a distinct gene expression profile. Geometric models, often referred to as Waddington landscapes, in which developmental paths are given by the gradient and cell states by the minima of the model, are an appealing way to describe differentiation dynamics and developmental decisions. To construct and validate accurate dynamical landscapes, quantitative methods based on experimental data are necessary. To this end we took advantage of the differentiation of neural and mesodermal cells from pluripotent mouse embryonic stem cells exposed to different combinations and durations of signalling factors. We developed a principled statistical approach using flow cytometry data to quantify differentiating cell states. Then, using a framework based on Catastrophe Theory and approximate Bayesian computation, we constructed the corresponding dynamical landscape. The result was a quantitative model that accurately predicted the proportions of neural and mesodermal cells differentiating in response to specific signalling regimes. Analysis of the geometry of the landscape revealed two distinct ways in which cells make a binary choice between one of two fates. We discuss the biological relevance of these mechanisms and suggest that they represent general archetypal designs for developmental decisions. Taken together, the approach we describe is broadly applicable for the quantitative analysis of differentiation dynamics and for determining the logic of developmental cell fate decisions.

developmental biology↗

bioRxiv2020

Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation

WNT signalling has multiple roles. It maintains pluripotency of embryonic stem cells, assigns posterior identity in the epiblast and induces mesodermal tissue. We provide evidence that these distinct functions are conducted by the transcription factor SOX2, which adopts different modes of chromatin interaction and regulatory element selection depending on its level of expression. At high levels, SOX2 acts as a pioneer factor, displacing nucleosomes from regulatory elements with high affinity SOX2 binding sites and recruiting the WNT effector, TCF/{beta}-catenin, to maintain pluripotent gene expression. Reducing SOX2 levels destabilises pluripotency and reconfigures SOX2/TCF/{beta}-catenin occupancy to caudal epiblast expressed genes. These contain low-affinity SOX2 sites and are co-occupied by T/Bra and CDX. The loss of SOX2 allows WNT induced mesodermal differentiation. These findings define a role for Sox2 levels in dictating the chromatin occupancy of TCF/{beta}-catenin and reveal how context specific responses to a signal are configured by the level of a transcription factor.

developmental biology↗

bioRxiv2020

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

Transcriptional and epigenetic profiling of single-cells has advanced our knowledge of the molecular bases of gastrulation and early organogenesis. However, current approaches rely on dissociating cells from tissues, thereby losing the crucial spatial context that is necessary for understanding cell and tissue interactions during development. Here, we apply an image-based single-cell transcriptomics method, seqFISH, to simultaneously and precisely detect mRNA molecules for 387 selected target genes in 8-12 somite stage mouse embryo tissue sections. By integrating spatial context and highly multiplexed transcriptional measurements with two single-cell transcriptome atlases we accurately characterize cell types across the embryo and demonstrate how spatially-resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary and the developing gut tube. Our spatial atlas uncovers axes of resolution that are not apparent from single-cell RNA sequencing data - for example, in the gut tube we observe early dorsal-ventral separation of esophageal and tracheal progenitor populations. In sum, by computationally integrating high-resolution spatially-resolved gene expression maps with single-cell genomics data, we provide a powerful new approach for studying how and when cell fate decisions are made during early mammalian development.

developmental biology↗

bioRxiv2020

Temporal patterning of the central nervous system by a shared transcription factor code

The molecular mechanisms that ensure the reproducible generation of neuronal diversity in the vertebrate nervous system are incompletely understood. Here we provide evidence of a temporal patterning program consisting of cohorts of transcription factors expressed in neurons generated at successive developmental timepoints. This program acts in parallel to spatial patterning, diversifying neurons throughout the nervous system and in neurons differentiated in-vitro from stem cells. We demonstrate the TGF{beta} signalling pathway controls the pace of the temporal program. Furthermore, targeted perturbation of components of the temporal program, Nfia and Nfib, reveals their requirement for the generation of late-born neuronal subtypes. Together, our results provide evidence for the existence of a previously unappreciated global temporal program of neuronal subtype identity and suggest that the integration of spatial and temporal patterning programs diversifies and organises neuronal subtypes in the vertebrate nervous system.

developmental biology↗

bioRxiv2020

Local retinoic acid directs emergence of the extraocular muscle functional unit

Coordinated development of muscles, tendons, and their attachment sites ensures emergence of functional musculoskeletal units that are adapted to diverse anatomical demands among different species. How these different tissues are patterned and functionally assembled during embryogenesis is poorly understood. Here, we investigated the morphogenesis of extraocular muscles (EOMs), an evolutionary conserved cranial muscle group that is crucial for the coordinated movement of the eyeballs and for visual acuity. By means of lineage analysis, we redefined the cellular origins of periocular connective tissues interacting with the EOMs, which do not arise exclusively from neural crest mesenchyme as previously thought. Using 3D imaging approaches, we established an integrative blueprint for the EOM functional unit. By doing so, we identified a developmental time window where individual EOMs emerge from a unique muscle anlage and establish insertions in the sclera, which sets these muscles apart from classical muscle-to-bone type of insertions. Further, we demonstrate that the eyeballs are a source of diffusible retinoic acid that allow their targeting by the EOMs in a temporal and dose dependent manner. Using genetically modified mice and inhibitor treatments, we find that endogenous local variations in the concentration of retinoids contribute to the establishment of tendon condensations and attachment sites that precede the initiation of muscle patterning. Collectively, our results highlight how global and site-specific programs are deployed for the assembly of muscle functional units with precise definition of muscle shapes and topographical wiring of their tendon attachments.

developmental biology↗

bioRxiv2019

Species-specific developmental timing is associated with global differences in protein stability in mouse and human

What determines the pace of embryonic development? Although many molecular mechanisms controlling developmental processes are evolutionarily conserved, the speed at which these operate can vary substantially between species. For example, the same genetic programme, comprising sequential changes in transcriptional states, governs the differentiation of motor neurons in mouse and human, but the tempo at which it operates differs between species. Using in vitro directed differentiation of embryonic stem cells to motor neurons, we show that the programme runs twice as fast in mouse as in human. We provide evidence that this is neither due to differences in signalling, nor the genomic sequence of genes or their regulatory elements. Instead, we find an approximately two-fold increase in protein stability and cell cycle duration in human cells compared to mouse. This can account for the slower pace of human development, indicating that global differences in key kinetic parameters play a major role in interspecies differences in developmental tempo.

developmental biology↗

bioRxiv2019

A switch in cilia-mediated Hedgehog signaling controls muscle stem cell quiescence and cell cycle progression

Tissue homeostasis requires a tight control of stem cells to maintain quiescence in normal conditions, and ensure a balance between progenitor cell production and the need to preserve a stem cell pool in repair conditions. Using ex-vivo and in-vivo genetic approaches, we provide evidence that primary cilium-mediated repressive Hedgehog (Hh) signalling is required to maintain skeletal muscle stem cells (MuSCs) in a quiescent state. De-repression and further activation of Hh signalling initiates MuSC entry and progression through the cell cycle, and controls self-renewal to ensure efficient repair of injured muscles. We propose a model whereby disassembly of primary cilia upon MuSC activation induces a switch in Hh signalling from a repressive to active state that controls exit from quiescence. Positive Hh response in bi-potential muscle progenitor cells regulates also cell cycle progression and drives MuSC self-renewal. These findings identify Hh signalling as a major regulator of MuSC activity. HighlightsO_LICilia-containing quiescent MuSCs are Hh signalling suppressed C_LIO_LIMuSC activation coincides with a switch to active Hh signalling C_LIO_LISmo mutation delays cell cycle entry and progression, and causes impaired self-renewal C_LIO_LIPtch1 mutation promotes exit from quiescence, rapid cell cycle and increased self-renewal C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/884601v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1cbaa81org.highwire.dtl.DTLVardef@273898org.highwire.dtl.DTLVardef@f4b26corg.highwire.dtl.DTLVardef@edda2c_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2019

Precision of Tissue Patterning is Controlled by Dynamical Properties of Gene Regulatory Networks

During development, gene regulatory networks allocate cell fates by partitioning tissues into spatially organised domains of gene expression. How the sharp boundaries that delineate these gene expression patterns arise, despite the stochasticity associated with gene regulation, is poorly understood. We show, in the vertebrate neural tube, using perturbations of coding and regulatory regions, that the structure of the regulatory network contributes to boundary precision. This is achieved, not by reducing noise in individual genes, but by the configuration of the network modulating the ability of stochastic fluctuations to initiate gene expression changes. We use a computational screen to identify network properties that influence boundary precision, revealing two dynamical mechanisms by which small gene circuits attenuate the effect of noise in order to increase patterning precision. These results highlight design principles of gene regulatory networks that produce precise patterns of gene expression.

developmental biology↗