Biology subjects

Turner, D. A.

Publications and source records attributed to Turner, D. A..

4 recordsLinked to original sources

bioRxiv2025

N2B27 media formulations influence gastruloid development

Gastruloids are 3D aggregates of pluripotent stem cells grown in suspension culture that mimic many aspects of gastrulation and early axial elongation. The N2B27 basal medium in which mouse gastruloids are cultured can either be home-made (HM-N2B27) with materials of known origin, or commercially sourced (NDiff227), where the exact formulation is unknown. In this study we examined whether these formulations resulted in significant differences in gastruloid development. Our results reveal that while both media enable the standard gastruloid elongation, HM-N2B27 results in gastruloids that start the elongation process earlier, have higher number of cells and an increased anterior domain. RNAseq analysis showed significant differences in cell fate specification, with HM-N2B27 gastruloids exhibiting higher expression of spinal cord-related genes, while NDiff227 favours mesodermal differentiation. Furthermore, differential gene enrichment analysis suggests that changes in key signalling pathways underline the differences between HM-N2B27 and NDiff227 gastruloids. These findings highlight the importance of basal media composition for gastruloid development, underscoring the need for careful media selection during in vitro engineering of stem cell-based embryo models. Summary statementIn this work we explored the cellular and molecular sensitiveness of the mouse gastruloid model system to variations in N2B27 media formulations.

developmental biology↗

bioRxiv2024

Domain Specific AI Segmentation of IMPDH2 Rod/Ring Structures in Mouse Embryonic Stem Cells

BackgroundInosine monophosphate dehydrogenase 2 (IMPDH2) is an enzyme that catalyses the rate limiting step of guanine nucleotides. In mouse embryonic stem cells (ESCs) IMPDH2 is held as large multi-protein complexes known as rod-ring (RR) structures that dissociate when ESCs differentiate. Manual analysis of RR structures from confocal microscopy images, although possible, is not feasible on a large scale due to the quantity of RR structures present in each field of view. To address this analysis bottleneck, we have created a fully automatic RR image classification pipeline to segment, characterise and measure feature distributions of these structures in ESCs. ResultsWe find that this model can automatically segment images with a Dice score of over 80% for both rods and rings for in-domain images compared to expert annotation, with a slight drop to 70% for datasets out of domain. Important feature measurements derived from these segmentations show high agreement with the measurements derived from expert annotation, achieving an R2 score of over 90% for counting the number of rings and rods over the dataset. ConclusionsWe have established for the first time a quantitative baseline for RR distribution in pluripotent ESCs and have made a pipeline available for training to be applied to other models in which RR remain an open topic of study.

bioinformatics↗

bioRxiv2024

Dynamic Wt1 expression in the gastrulation-stage mouse embryo specifies vascular and visceral smooth muscle cell fate independently from mesothelial fate.

1.The Wilms Tumour protein (WT1) was previously linked to the mesothelial and vascular smooth muscle cell (vSMC) lineage in the mouse intestine, with evidence suggesting that intestinal vSMCs arise from the mesothelium. Here, we report that WT1 is already expressed, unexpectedly, during gastrulation, in cells that specify a population of SMC precursor cells in the lateral plate mesoderm (LPM). Tamoxifen-induced genetic lineage tracing of Wt1-expressing cells revealed that vSMC and visceral smooth muscle cells (visSMCs) of the foetal mid-gut, but not mesothelial cells, were labelled after Tamoxifen administration at E7.5 or E8.5. Analysis of single cell RNA sequencing (scRNAseq) datasets of gastrulation-stage mouse embryos and confocal microscopy demonstrated Wt1 expression in epiblast, primitive streak, emerging mesoderm and, from E7.5 onwards, in the LPM. Co-expression of signature smooth muscle markers in Wt1-expressing cells in gastrulation-stage embryos revealed that vSMC and visSMC fate is specified independently from visceral mesothelium formation. Furthermore, Tamoxifen-induced Wt1 knock-out at E7.5 affected vascularisation in the E12.5 intestine. Taken together, our study provides novel insight into the developmental lineage of smooth muscle specified by WT1 expression during gastrulation. Summary StatementThis study provides novel insight into the developmental lineage of smooth muscle cells in the intestine and mesentery, specified by WT1 expression during gastrulation.

developmental biology↗

bioRxiv2023

Negative feedback on Retinoic Acid by Brachyury guides gastruloid symmetry-breaking

Establishment of the vertebrate body plan requires a combination of extra-embryonic signalling to establish morphogen gradients, and an underlying self-assembly mechanism that contributes to pattern regulation and robustness. Gastruloids are aggregates of mouse embryonic stem cells that break morphological symmetry and polarise Brachyury (Bra) expression in the absence of extra-embryonic signals. However, the mechanism by which symmetry breaking occurs is not yet known. During gastrulation and body axis elongation, retinoic acid (RA) and Cyp26a1 are polarised along the anteroposterior axis, and this is critical for balancing the decision of cells to self-renew or differentiate. We found that symmetry-breaking in gastruloids is coincident with the separation of Aldh1a2 and Cyp26a1 expression, and that feedback from Bra is critical for maintaining polarised Cyp26a1 gene expression in the gastruloid posterior region. Furthermore, we reveal a short temporal window where RA signalling can negatively influence both Bra and Cyp26a1 expression. These observations lead us to suggest a mechanism of how initial gastruloid patterning, subsequent elongation, and evolving network topologies can create defined boundaries of RA signalling that permits proper axial patterning and gastruloid growth.

developmental biology↗