Biology subjects

Strawbridge, S. E.

Publications and source records attributed to Strawbridge, S. E..

8 recordsLinked to original sources

bioRxiv2026

Mixing, competence, and commitment set the stability of cell identity

Cells maintain their identities in the face of molecular noise, yet can change them rapidly when cued. Here, we treat this tension as a problem in the control of a stochastic system. We represent a cell identity as a set of molecular configurations, or microstates, among which cells undergo stochastic transitions, and measure its stability by the effective rate of commitment to another identity, using a Markov model in which committed cells are removed. Mixing, competence, and commitment provide three channels for tuning this rate. They govern microstate transitions, how commitment is distributed among microstates, and the overall speed of commitment, respectively. Control over the effective commitment rate is shared between commitment and mixing in proportions that always sum to one. Interventions with the same effective commitment rate cannot be told apart by survival alone but, given the microstate transition rates, can be distinguished by the fraction of cells in each microstate or by how quickly cells sorted on permissive microstates commit. When competence varies in time, pulsed commitment signalling commits more cells than sustained signalling of equal dose, by an amount that grows with the depth of that variation, whereas with constant competence pulsing gains nothing in the models we studied. This suggests a possible function for pulsatile signalling, such as that of ERK, which the experiments we propose could test. Finally, reanalysing single-cell imaging of mouse embryonic stem cells leaving naive pluripotency, we estimate that cells take about as long to acquire competence as they then wait to commit, and we specify experiments to identify which channel drives this exit.

systems biology↗

bioRxiv2026

Notch signalling governs human enteric nervous system progenitor dynamics

The enteric nervous system (ENS) is the main branch of the peripheral nervous system that innervates the gastrointestinal tract controlling vital functions. It arises during embryogenesis via migration, proliferation and differentiation of neural crest-derived ENS progenitors. Perturbation of these processes, caused by mutations in key signalling pathway components and transcription factors, prevents progenitor colonisation of the distal gut causing aganglionic phenotypes and enteric neuropathies such as Hirschsprung (HSCR) disease. While animal models implicate Notch signalling in ENS specification, its role in human ENS progenitor cell fate decisions remains unclear. Here, we employ a human pluripotent stem cell-based model to show that Notch signalling is a key regulator of human ENS progenitor dynamics. Quantitative modelling of our in vitro data indicates that Notch inhibition accelerates progenitor differentiation without substantially altering neuronal versus glial lineage bias. Furthermore, we establish that Notch signalling controls human ENS progenitor migration by influencing migration velocity and directionality. Together, these findings provide mechanistic insights into how Notch signalling disruption may contribute to the pathogenesis of human intestinal aganglionosis.

developmental biology↗

bioRxiv2026

Quantification and statistical comparison of cell-state transition kinetics using a parametric failure-based model

Successful development of multicellular organisms requires cells to transition between states with precise timing. Distinct cell states are often understood as being maintained by stabilizing regulatory networks, such that a complete cell-state transition requires network rewiring through partial dismantling of the current state and concurrent reconfiguration into a new one. Empirically, these transitions are often investigated by quantifying the gain or loss of expression of a small number of state-specific markers, frequently a single proxy. A general quantitative framework for comparing the kinetics of such transitions across experimental conditions is lacking. Here, we show that the delayed Weibull distribution provides a natural description of cell-state transition kinetics when transition is viewed as the cumulative consequence of many molecular events, whose timing may vary between cells and conditions, analogous to system failure in reliability theory. This formulation yields a compact model with interpretable parameters describing the delay before transition onset, the characteristic timescale of transition, the temporal form of the transition hazard, and the fraction of cells competent to respond. Together, this framework provides a practical and interpretable approach for quantifying the kinetics of cell-state transitions and how they are altered by perturbation.

systems biology↗

bioRxiv2025

A new resource of clonal pluripotent human stem cell lines exhibiting inter- and intra-embryo consistency and variability

Human naive pluripotent stem cells can generate all somatic tissues and extra-embryonic components of the blastocyst. We derived multiple clonal naive pluripotent stem cell lines from individual embryos by physical separation of inner cell mass cells and subsequent individual expansion of each resulting dome-shaped colony, providing the foundation for a resource to investigate intra- and inter-embryo variation. Twenty lines were derived from ten embryos donated from nine couples. While differences between lines are observed, the overarching pluripotency circuitry is preserved in each. They can differentiate into extra-embryonic lineages and readily acquire post-implantation pluripotent identity when exposed to culture conditions driving in vitro capacitation, subsequently to generate derivatives of the three germ layers: ectoderm, mesoderm and endoderm. Some lines exhibit intra-chromosomal amplification and deletions and are therefore anticipated to provide a valuable, accessible system for modelling chromosomal mosaicism and its potential consequences using chimeric organoids, such as blastoids and gastruloids.

developmental biology↗

bioRxiv2024

Donor embryonic stem cells impede host epiblast specification in 8-cell stage chimeras by crowding and FGF4 signalling

During mouse embryo compaction, outer cells become trophectoderm, while inner cells form the inner cell mass (ICM), later differentiating into primitive endoderm and epiblast - source of embryonic stem cells (ESCs) - during blastocyst formation. Trophectoderm specification is driven by position-governed polarisation, while primitive endoderm specification is positively regulated by FGF4 signalling from the ICM and epiblast. When injected into an 8-cell stage morula, ESCs can exclude host cells from the epiblast, leading to mice derived entirely from these cells. While evidence suggests roles for ESC-produced FGF4 and physical crowding in host cell displacement from the ICM, the interplay between these possible mechanisms has yet to be dissected, in part due to the lack of studies using Fgf4-/- ESCs. Here, we combine chimaera titration assays with mathematical modelling to study these mechanisms of host cell displacement. Both Fgf4+/+ and Fgf4-/- ESCs displaced host cells from the epiblast, while only Fgf4-/- injected embryos reduced primitive endoderm and increased trophectoderm, indicating sequential exclusion by displacement crowding followed by FGF4 signalling. SUMMARY STATEMENTIn mouse blastocyst chimeras, donor cells displace host cells from the epiblast by a combination of crowding and FGF4 signalling.

developmental biology↗

bioRxiv2021

insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology

A crucial aspect of embryology is relating the position of individual cells to the broader geometry of the embryo. A classic example of this is the first cell-fate decision of the mouse embryo, where interior cells become inner cell mass and exterior cells become trophectoderm. Fluorescent labelling, imaging, and quantification of tissue-specific proteins have advanced our understanding of this dynamic process. However instances arise where these markers are either not available, or not reliable, and we are left only with the cells spatial locations. Therefore, a simple, robust method for classifying interior and exterior cells of an embryo using spatial information is required. Here, we describe a simple mathematical framework and an unsupervised machine learning approach, termed insideOutside, for classifying interior and exterior points of a three-dimensional point-cloud, a common output from imaged cells within the early mouse embryo. We benchmark our method against other published methods to demonstrate that it yields greater accuracy in classification of nuclei from the pre-implantation mouse embryos and greater accuracy when challenged with local surface concavities. We have made MATLAB and Python implementations of the method freely available. This method should prove useful for embryology, with broader applications to similar data arising in the life sciences.

developmental biology↗

bioRxiv2020

Embryonic stem cells commit to differentiation by symmetric divisions following a variable lag period

Mouse embryonic stem (ES) cells are derived from the epiblast of the preimplantation embryo and retain the capacity to give rise to all embryo lineages. ES cells can be released into differentiation from a near-homogeneous maintenance condition. Exit from the ES cell state can be accurately monitored using the Rex1-GFPd2 transgenic reporter, providing a powerful system for examining a mammalian cell fate transition. Here, we performed live-cell imaging and tracking of ES cells during entry into differentiation for 48 hours in defined conditions. We observed a greater cell surface area and a modest shortening of the cell cycle prior to exit and subsequently a reduction in cell size and increase in motility. We did not see any instance of cells regaining ES cell identity, consistent with unidirectional developmental progression. Transition occurred asynchronously across the population but genealogical tracking revealed a high correlation in cell-cycle length and Rex1-GFPd2 expression between daughter cells. A population dynamics model was consistent with symmetric divisions during exit from naive pluripotency. Collapse of ES cell identity occurred acutely in individual cells but after a variable delay. The variation in lag period can extend up to three generations, creating marked population asynchrony.

developmental biology↗

bioRxiv2020

Oct4 regulates embryonic pluripotency via metabolic mechanisms and Stat3 signalling.

OCT4 is a fundamental component of the molecular circuitry governing pluripotency in vivo and in vitro. To determine how OCT4 protects the pluripotent lineage from differentiation into trophoblast, we used single cell transcriptomics and quantitative immunofluorescence on blastocysts and established differentially expressed genes and pathways between control and OCT4 null cells. Activation of most pluripotency-associated transcription factors in the early mouse inner cell mass appears independent of OCT4, whereas JAK/STAT signalling requires OCT4, via activation of IL6ST. Single cell deconvolution, diffusion component and trajectory inference dissected the process of differentiation of OCT4 null cells by activating specific gene-network and transcription factors. Downregulation of glycolytic and oxidative metabolism was observed. CHIPseq analysis suggests OCT4 directly targets rate-limiting glycolytic enzymes. Concomitant with significant disruption of the STAT3 pathway, oxidative respiration is significantly diminished in OCT4 null cells. Upregulation of the lysosomal pathway detected in OCT4 null embryos is likely attributable to aberrant metabolism. Highlights and noveltyO_LIMajor pluripotency-associated transcription factors are activated in OCT4-deficient early mouse ICM cells, coincident with ectopic expression of trophectoderm markers C_LIO_LIJAK/STAT signalling is defective in OCT4 null embryos C_LIO_LIOCT4 promotes expression of KATS enzymes by means of glycolytic production of Acetyl CoA to secure chromatin accessibility for acquisition of epiblast identity C_LIO_LIOCT4 regulates the metabolic and biophysical processes required for establishment of embryonic pluripotency C_LI

developmental biology↗