Biology subjects

Briscoe, J.

Publications and source records attributed to Briscoe, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Minimal essential requirements for neural tube self-organisation

The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from pluripotent stem cells (PSCs) provide powerful systems for identifying principles governing tissue self-organisation. Neural tube organoids (NTOs), initiated from single PSCs with a pulse of retinoic acid (RA), self-organise into structures containing floorplate cells that secrete SHH morphogen to pattern adjacent neural tissue. Yet, how the initial cellular diversity arises and how appropriate cell-type proportions are allocated has remained unclear. Here, using time-resolved single-cell transcriptomics, quantitative immunofluorescence, and dynamical systems modelling we show that RA triggers a transient co-expression state of the transcription factors PAX6 and FOXA2 from which cells asynchronously resolve into two opposing fates: PAX6 neural precursors and FOXA2 floorplate precursors. PAX6 and FOXA2 are both necessary and sufficient to reconstitute self-organisation, establishing these transcription factors as key determinants of emergent tissue pattern. Rather than operating as a simple feed-forward system in which cells are guided solely by RA, feedback between the alternative cell fates, mediated by BMP signalling from floorplate precursors, determines cell type proportions and ensures reproducible cell-type diversity in each NTO. This dual expression state was also identified in mouse embryos, demonstrating how in vitro models inform in vivo biology. These findings establish a general design strategy - symmetry breaking through opposing fate determinants coupled to proportioning via signal feedback control - that may operate broadly across developmental contexts to generate tissues with predictable cellular compositions.

developmental biology↗

bioRxiv2026

Minimal social context decouples affective response modalities

Emotions often occur within social interactions where affective cues are partly accessible or inferable by others. This raises questions regarding how and to which degree social context modulates subjective, physiological and behavioural affective responses, as well as their coherence, questions which remain points of tension in emotion research. To investigate this, we measured subjective affective ratings, autonomic sympathetic and parasympathetic activity, and facial behaviour while participants completed an emotion-induction task. In the social-context condition (but not control), participants believed that their video feed was accessible to a potential future interaction partner. Results show that even such "minimal social context" selectively and differentially modulated affective response modalities, characterised by both intensification of autonomic responses and dampening of overt facial and subjective affect. Multivariate dimensionality analysis further identified a cross-modal affective dimension. Notably, social context reduced participants coupling with this shared affective response structure, indicating weaker cross-modal coherence. These findings suggest that emotional responding relies on a flexible, rather than rigid, configuration of affective features, likely recruited to meet the socioemotional demands of a given context. This has important implications for understanding the structure and function of emotion, as well as typical and atypical socioemotional responding.

neuroscience↗

bioRxiv2026

Co-option of a mouse-specific retrotransposon rewires Ash2l isoform usage to prime developmental promoters

How pluripotent stem cells pre-configure the chromatin landscape to enable timely activation of developmental gene programs remains a central question in developmental biology. Here we demonstrate that the core chromatin regulator ASH2L undergoes a developmentally regulated transcription start site (TSS) switch that generates two protein isoforms with distinct developmental functions: a full-length ASH2L containing an N-terminal intrinsically disordered region (IDR), and a conserved, truncated protein isoform lacking this region. In mouse pluripotent stem cells, a lineage-specific ERV-K retrotransposon drives the upstream TSS, which suppresses the downstream TSS through transcription-coupled SETD2-mediated histone H3 lysine 36 methylation. The resulting stem cell-specific truncated ASH2L assembles into COMPASS complexes and enhances histone H3 lysine 4 trimethylation at promoters governing early development. Despite being restricted to pluripotent stem cells, truncated ASH2L is required for proper axial patterning in gastruloids and for the transition of neural progenitors to motor neurons. This temporal decoupling, wherein a chromatin state established during pluripotency executes its function only after the establishing isoform disappears, defines an epigenetic priming mechanism for developmental timing. Thus, lineage-specific retrotransposon co-option reveals how a dedicated protein isoform configures the pluripotent epigenome for developmental transitions after its own expression has ceased.

molecular biology↗

bioRxiv2026

ESFS: A Noise-Resilient Framework for Feature Selection and Marker Gene Discovery in Single-Cell Transcriptomics

Single-cell RNA sequencing (scRNA-seq) has transformed our ability to resolve cellular heterogeneity, but extracting meaningful signals remains challenging due to technical noise and batch effects. Most methods for denoising scRNA-seq data have focused on using latent representations such as principal component analysis and deep learning to prioritise biological signals. By contrast, despite its influence on downstream analyses, feature selection has received relatively limited attention, leading to widespread reliance on the comparatively simplistic strategy of highly variable gene selection. Here we present Entropy Sorting Feature Selection (ESFS), a modular, user-friendly framework that substantially improves the interpretability of scRNA-seq data. Notably, ESFS reveals complex expression dynamics that are obscured in latent representations. We demonstrate the utility of ESFS in diverse data: identifying coherent developmental programs across eight independent human embryo datasets without batch integration; resolving spatial gene expression in mouse colon missed by conventional analyses; disambiguating shared and tumour-specific microenvironments in glioblastoma; and disentangling spatial, temporal, and neurogenic programs in the developing mouse neural tube. Beyond delivering a powerful and user-friendly software that deepens insight into complex biological systems, our work establishes Entropy Sorting as a novel information theoretic for advanced data analysis methods.

bioinformatics↗

bioRxiv2025

Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding

The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into molecularly defined domains, but how lineage relationships shape neuronal diversity and function has remained unclear. Here, we combine genomic barcoding with single- cell RNA sequencing in chick and human embryos to generate cell-type-resolved clonal maps. We find that spinal neurogenesis follows a hierarchical organisation in which the neural tube first partitions into five broad subdivisions that resolve into the eleven progenitor domains generating the cardinal neuronal classes. This bifurcating architecture implies a patterning mechanism of sequential binary decisions. The most prominent lineage restriction occurs at the embryonic alar-basal boundary, separating sensory-processing from motor-control circuits. Individual progenitors generate neurons across multiple temporal waves while remaining constrained within their lineage subdivision, demonstrating persistence of spatial identity despite temporal competence changes. Among sensory populations, we identify two developmental routes, via unifated or bifated progenitors, to pain- and itch-processing interneurons. These principles are conserved between chick and human, with clonal analysis in human embryos revealing that most fate choices are resolved by six weeks post-conception. Together, these findings provide a framework for spinal cord development and reveal lineage compartmentalisation as a fundamental principle in neural circuit assembly and evolution.

developmental biology↗

bioRxiv2025

Reconstructing Waddington's Landscape from Data

The development of a zygote into a functional organism requires that this single progenitor cell gives rise to numerous distinct cell types. Attempts to exhaustively tabulate the interactions within developmental signaling networks that coordinate these hierarchical cell fate transitions are difficult to interpret or fit to data. An alternative approach models the cellular decision-making process as a flow in an abstract landscape whose signal-dependent topography defines the possible developmental outcomes and the transitions between them. Prior applications of this formalism have built landscapes in low-dimensional spaces without explicit reference to gene expression. Here, we present a computational geometry framework for fitting dynamical landscapes directly to high-dimensional single-cell data. Our method models the time evolution of probability distributions in gene expression space, enabling landscape construction with minimal free parameters and precise characterization of dynamical features, including fixed points, unstable manifolds, and basins of attraction. We demonstrate the applicability of this framework to multicolor flow-cytometry and RNA-seq data. Applied to a stem cell system that models ventral neural tube patterning, we recover a family of morphogen-dependent landscapes whose valleys align with canonical neural progenitor types. Remarkably, simple linear interpolation between landscapes captures signaling dependence, and chaining landscapes together reveals irreversible behavior following transient morphogen exposure. Our method combines the interpretability of landscape models with a direct connection to data, providing a general framework for understanding and controlling developmental dynamics.

developmental biology↗

bioRxiv2025

Boundary constraints can determine pattern emergence

The robust patterning of cell fates during embryonic development requires precise coordination of signalling gradients within defined spatial constraints. Using a geometrically confined in vitro system derived from human embryonic stem cells, we demonstrate that patterning of neuromesodermal progenitors (NMPs) during axial elongation is driven by boundary-dependent mechanisms. Despite extensive work on radial fate patterning in confined 2D systems, the quantitative role of boundary conditions in shaping spatiotemporal dynamics remains unclear. Here, we show that a minimal reaction-diffusion model coupled with a simplified gene regulatory network accurately predicts spatial patterns across diverse geometries. Guided by its predictions, we identify Wnt signalling as a key component of the activator signal. Inhibition of Wnt secretion preserved initiation of patterning but disrupted subsequent morphogenesis, indicating distinct mechanisms govern pattern establishment versus maintenance. Our findings reveal how geometry encodes positional information that directs molecular patterning, providing insight into how spatial constraints and signalling dynamics guide robust tissue self-organisation during development.

systems biology↗

bioRxiv2025

Multimodal profiling unveils a reversible basal-like breast cancer cell state resistant to AKT inhibition

The PI3K/AKT/mTOR pathway is central to cell metabolism and growth. However, pharmacological inhibition of the pathway is not uniformly effective across cancer types, or even within a single cancer model. In this study, we leverage oblique plane microscopy of triple negative breast cancer organoids, as well as lineage tracing to uncover a source of heterogeneity. Non-genetic resistance to AKT inhibition is associated with basal cell features of normal breast epithelium and the master transcription factor of basal cell state, {Delta}Np63, is sufficient to confer resistance. Cells can transition between states within four weeks and therefore, AKT inhibition only delays tumour growth, with tumours rich in KRT14+ cells resulting. Thus, under selection, triple negative breast cancer exploits a repertoire of cell states inherent to the breast.

cancer biology↗

bioRxiv2025

Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data

Building a mechanistic understanding of cell fate decisions remains a fundamental goal of developmental biology, with implications for stem cell therapies, regenerative medicine and understanding disease mechanisms. Single-cell transcriptomics provides a detailed picture of the cellular states observed during these decisions, but building dynamic and predictive models from these data remains a challenge. Here, we present dynamic landscape analysis (DLA), a framework that applies dynamical systems theory to identify stable cell states, map transition pathways, and generate a predictive cell fate decision landscape from single-cell data. Applying this framework to vertebrate neural tube development, revealed that progenitor specification by Sonic Hedgehog (Shh) can be captured in a landscape with an unexpected topology in which initially divergent lineages converge to the same fate through multiple distinct routes. The model accurately predicted cellular responses and cell fate allocation for unseen dynamic signalling regimes. Cross-species validation using human embryonic organoid data demonstrated conservation of this decision-making architecture. By modelling the dynamic responses that drive cell fate decisions, the DLA framework provides a quantitative and generative framework for extracting mechanistic insights from high-dimensional single-cell data.

developmental biology↗

bioRxiv2025

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. We identify that glioblastoma heterogeneity is driven by spatially-patterned transitions of cancer cells from developmental-like states towards those defined by a glial injury response and hypoxia. This cellular trajectory regionalises tumours into distinct tissue niches and manifests in a molecularly conserved manner across tumours as well as genetically distinct tumour subclones. Moreover, using a new deep learning framework to map cancer cell states jointly with clones in situ, we show that tumour subclones are finely spatially intermixed through glioblastoma tissue niches. Finally, we show that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments. Our findings define a stereotyped trajectory of cancer cells in glioblastoma and unify glioblastoma tumour heterogeneity into a tractable cellular and tissue framework.

cancer biology↗

bioRxiv2025

A single cell ATAC-seq atlas uncovers dynamic changes in chromatin accessibility during cell fate specification at the neural plate border

During development, dynamic changes in gene expression and chromatin architecture drive the transition from progenitors to specialised cell types. Here we use single cell ATAC sequencing (scATAC-seq) to investigate changes in chromatin accessibility as neural plate border cells segregate into neural, neural crest and placode cells. We developed a Nextflow pipeline, single cell Advanced Chromatin Exploration (scACE), which integrates scATAC-seq and scRNA-seq data to identify cell state specific accessibility profiles and groups of chromatin regions with coordinated dynamic behaviour, termed accessibility modules (AMs). We find that progenitors are characterised by broadly open chromatin, reflecting their broad potential to generate any ectodermal derivative. As development proceeds, cell-type-specific chromatin signatures are established. Inferring an enhancer-centric gene regulatory network, we predict Foxk2 as new regulator for placode specification and verify this prediction experimentally. Foxk2 target enhancers are open in placodal, but not any other ectodermal cells. This finding suggests that on a regulatory level, cells can use different strategies to control fate choice: differential accessibility of enhancers and broad accessibility controlled by differentially expressed transcription factors.

developmental biology↗

bioRxiv2025

Predictable Engineering of Signal-DependentCis-Regulatory Elements

Cis-regulatory elements (CREs) control how genes respond to external signals, but the principles governing their structure and function remain poorly understood. While differential transcription factor binding is known to regulate gene expression, how CREs integrate the amount and combination of inputs to secure precise spatiotemporal profiles of gene expression remains unclear. Here, we developed a high-throughput combinatorial screening strategy, that we term NeMECiS, to investigate signal- dependent synthetic CREs (synCREs) in differentiating mammalian stem cells. By concatenating fragments of functional CREs from genes that respond to Sonic Hedgehog in the developing vertebrate neural tube, we found that CRE activity follows hierarchical design rules. While individual 200-base-pair fragments showed minimal activity, their combinations generated thousands of functional signal-responsive synCREs, many exceeding the activity of natural sequences. Statistical modelling revealed CRE function can be decomposed into specific quantitative contributions in which sequence fragments combine through a multiplicative rule, tuned by their relative positioning and spacing. These findings provide a predictive framework for CRE redesign, which we used to engineer synthetic CREs that alter the pattern of motor neuron differentiation in neural tissue. These findings establish quantitative principles for engineering synthetic regulatory elements with programmable signal responses to rewire genetic circuits and control stem cell differentiation, providing a basis for understanding developmental gene regulation and designing therapeutic gene expression systems.

developmental biology↗

bioRxiv2024

From naïve pluripotency to human neural organoids through a three-dimensional morphogenetic continuum

Human central nervous system (CNS) development involves complex transitions from pluripotency to regionalised neural tissues. The early phases of this process are inaccessible in humans but can potentially be modelled in vitro using brain organoids, including to study neurodevelopmental disorders. However, current methods are based on post-implantation-like human pluripotent stem cells (hPSCs), which exhibit a hypermethylated state and show epigenetic memory retention. Here we developed a 3D model of human CNS development, starting from naive human induced PSCs (hiPSCs), which exhibit a hypomethylated pre-implantation-like state of pluripotency and develop into 3D neuroepithelial cysts in a timely morphogenetic continuum. Upon treatment with appropriate signalling cues, naive-derived neuroepithelial cysts can be specified toward different axial identities. Extended culture of anterior-specified organoids results in forebrain-like structures containing both dorsal and ventral neural precursors as well as mature neurons, exhibiting appropriate cellular diversity and functional properties. We applied this system to model Fragile X Syndrome (FXS), an epigenetically regulated neurodevelopmental disorder. We found that FXS patient-derived naive hiPSCs, initially demethylated at the Fmr1 locus, gradually underwent remethylation during organoid development. In addition, Fmr1 silencing started much earlier than can be detected by pre-natal analysis, and is concomitant with the development of mosaicisms. Our approach provides a new platform for studying human CNS development, including early epigenetic events and regional patterning, demonstrating the potential of naive hiPSC-derived organoids for modelling neurodevelopmental disorders with complex epigenetic regulation. Highlights- single naive hiPSCs differentiate into 3D neuroepithelial cysts in a timely morphogenetic continuum - signalling cues at appropriate developmental transitions can direct naive hiPSC- derived organoids to different regional identities of the human CNS - naive hiPSC-derived forebrain organoids display cellular complexity representing both dorsal and ventral identities - forebrain organoids from Fragile X Syndrome patients recapitulate the genetic instability and epigenetic dysregulation of Fmr1 locus.

cell biology↗

bioRxiv2024

Protein degradation shapes developmental tempo in mouse and human neural progenitors

The pace of embryonic development differs markedly across mammalian species, yet the molecular mechanisms underlying these tempo differences remain largely unknown. Here, we systematically compared protein dynamics in mouse and human neural progenitors (NPs) and examined how protein stability influences developmental timing. We find that mouse NPs exhibit faster protein production and degradation than human NPs. Human NPs display broadly increased protein half-lives, independent of cellular compartment or protein function, and this difference persists in post-mitotic neurons. Consistent with this, proteasomal activity is lower in human embryonic spinal cord and stem cell-derived neural progenitors than mouse, correlating with reduced expression of proteasome-associated proteins. Functionally, accelerating the degradation of the key transcriptional repressor IRX3 in mouse NPs speeds the activation of its target gene, providing causal evidence that protein turnover modulates developmental tempo. These results reveal that species-specific regulation of protein degradation shapes the timing of neural development and suggest that evolutionary tuning of proteasomal activity contributes to differences in embryonic developmental pace.

developmental biology↗

bioRxiv2024

Multiscale mechanics drive functional maturation of the vertebrate heart

How simple tissue primordia sculpt complex functional organs, robustly and reproducibly, remains elusive. As the zebrafish embryo grows into a larva, to improve its heart function, the embryonic myocardial wall transforms into an intricate 3D architecture, composed of an outer compact layer enveloping an inner layer of multicellular trabecular ridges. How these tissue layers acquire their characteristic form suited for their function remains an open question. Here, we find that multiscale mechanochemical coupling and an emergent tissue-scale morphological transition steer functional maturation of the developing zebrafish heart. Single-celled trabecular seeds recruit outer compact layer cells to mature into clonally heterogenous multicellular ridges, thereby amplifying cardiac contractile forces. In response, remaining compact layer cells are stretched, which impedes their further recruitment, thereby constraining trabecular ridge density. Concomitantly, Notch-dependent actomyosin dampening triggers a sharp transition in myocardial tissue area, activating rapid organ growth that expands blood filling capacity. Thus, multiscale self-organizing interactions optimize heart size and contractile efficiency to support embryonic life.

developmental biology↗

bioRxiv2024

Dynamics of positional information in the vertebrate neural tube

In developing embryos, cells acquire distinct identities depending on their position in a tissue. Secreted signaling molecules, known as morphogens, act as long-range cues to provide the spatial information that controls these cell fate decisions. In several tissues, both the level and the duration of morphogen signaling appear to be important for determining cell fates. This is the case in the forming vertebrate nervous system where antiparallel morphogen gradients pattern the dorsal-ventral axis by partitioning the tissue into sharply delineated domains of molecularly distinct neural progenitors. How information in the gradients is decoded to generate precisely positioned boundaries of gene expression remains an open question. Here, we adopt tools from information theory to quantify the positional information in the neural tube and investigate how temporal changes in signaling could influence positional precision. The results reveal that the use of signaling dynamics, as well as the signaling level, substantially increases the precision possible for the estimation of position from morphogen gradients. This analysis links the dynamics of opposing morphogen gradients with precise pattern formation and provides an explanation for why time is used to impart positional information.

developmental biology↗

bioRxiv2024

Illuminating morphogen and patterning dynamics with optogenetic control of morphogen production

Cells use dynamic spatial and temporal cues to instruct cell fate decisions during development. Morphogens are key examples, where the concentration and duration of morphogen exposure produce distinct cell fates that drive tissue patterning. Studying the dynamics of these processes has been challenging. Here, we establish an optogenetic system for morphogen production that enables the investigation of developmental patterning in vitro. Using a tunable light-inducible gene expression system, we generate long-range Shh gradients that pattern neural progenitors into spatially distinct progenitor domains mimicking the spatial arrangement of neural progenitors found in vivo during vertebrate neural tube development. With this system, we investigate how biochemical features of Shh and the presence of morphogen-interacting proteins affect the patterning length scale. We measure tissue clearance rates, revealing that Shh has an extracellular half-life of about 1h, and we probe how the level and duration of morphogen exposure govern the acquisition and maintenance of cell fates. The rate of Shh turnover is substantially faster than the downstream gene expression dynamics, indicating that the gradient is continually renewed during patterning. Together the optogenetic approach establishes a simple experimental system for the quantitative interrogation of morphogen patterning. Controlling morphogen dynamics in a reproducible manner provides a framework to dissect the interplay between biochemical cues, the biophysics of gradient formation, and the transcriptional programmes underlying developmental patterning.

developmental biology↗

bioRxiv2024

An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast

Tissue development relies on the coordinated differentiation of stem cells in dynamically changing environments. The formation of the vertebrate neural tube from stem cells in the caudal lateral epiblast (CLE) is a well characterized example. Despite an understanding of the signalling pathways involved, the gene regulatory mechanisms remain poorly defined. To address this, we developed a multiplexed in vivo CRISPR screening approach in chick embryos targeting genes expressed in the caudal epiblast and neural tube. This revealed a role for MLLT3, a component of the super elongation complex, in the specification of neural fate. Perturbation of MLLT3 disrupted neural tube morphology and reduced neural fate acquisition. Mutant forms of Retinoic Acid Receptor A lacking the MLLT3 binding domain similarly reduced neural fate acquisition. Together, these findings validate an in vivo CRISPR screen strategy in chick embryos and identify a previously unreported role for MLLT3 in caudal neural tissue specification.

developmental biology↗