Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_time]

Understanding the interplay between cell fate specification and morphogenetic changes remains a central challenge in developmental biology. Gastruloids, self-organizing pseudo-embryos that mimic post-implantation mammalian development, provide a powerful platform to address this question. Here, we show that physical parameters, particularly system size, critically influence the timing and outcomes of morphogenetic processes. Larger gastruloids exhibit delayed symmetry breaking, increased multipolarity, and prolonged axial elongation, with morphogenesis driven by system size. Despite these variations, transcriptional programs and cell fate composition remain remarkably stable across a broad size range. Notably, extreme sizes show distinct transcriptional modules and clear shifts in gene expression patterns. Intriguingly, size perturbation experiments rescued the morphogenetic and pattern phenotypes observed in extreme sizes, demonstrating the remarkable adaptability of gastruloids to their effective system size. These findings establish gastruloids as versatile models for studying spatiotemporal dynamics in mammalian embryogenesis and reveal how physical constraints decouple transcriptional from morphogenetic programs. Overall design: RNA-seq on hydrogel embedded gastruloids (1mM and 1.5mM, at 72h vs 96h)

解析细胞命运特化与形态发生变化之间的相互作用，始终是发育生物学领域的核心难题之一。类原肠胚（Gastruloids）是一类可模拟哺乳动物着床后发育过程的自组织伪胚胎，为解答该问题提供了强有力的研究平台。本研究证实，物理参数——尤其是系统尺寸——会显著影响形态发生过程的时序与结局。尺寸更大的类原肠胚会出现对称性破缺延迟、多极化程度升高以及轴向伸长延长的现象，其形态发生过程由系统尺寸主导调控。尽管存在上述差异，在较宽的尺寸范围内，转录程序与细胞命运组成仍保持极高的稳定性。值得注意的是，尺寸处于极端区间的类原肠胚则会表现出独特的转录模块与显著的基因表达模式偏移。有趣的是，尺寸扰动实验可挽救极端尺寸类原肠胚中出现的形态发生与模式表型，这证实了类原肠胚对其有效系统尺寸具备极强的适应能力。本研究结果确立了类原肠胚作为研究哺乳动物胚胎发生时空动态的通用模型的地位，并揭示了物理约束如何将转录程序与形态发生程序解耦。实验设计：对水凝胶包埋的类原肠胚进行RNA测序（RNA-seq），样本涵盖1mM与1.5mM两种条件，分别采集72小时及96小时的样本。