Ayyappan Vinay, Triandafillou Catherine G, Sarma Kavitha, Raj Arjun
Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
The Wistar Institute, Gene Expression and Regulation Program, Philadelphia, PA, USA.
bioRxiv. 2025 Jul 14:2025.07.12.664536. doi: 10.1101/2025.07.12.664536.
Embryonic development typically requires precise coordination among cells to achieve reproducible outcomes, leading to the assumption that cellular heterogeneity must be minimized or buffered against. Using fluorescence-based lineage tracing in combination with spatial transcriptomics, we show that, in the gastruloid model of early development, pre-existing heterogeneity promotes proper axial organization through division of labor among stem cell clones. Individual clones isolated from a common population exhibit consistent spatial propensities for anterior or posterior fates. While pure clones generate elongated structures less frequently than a polyclonal population, mixing clones restores proper axial elongation. Spatial transcriptomics reveals that pure clones show disrupted gene expression with inappropriate coexpression of anterior and posterior markers, while clone combinations restore proper spatial organization. Using RNA-seq, ATAC-seq, and perturbations to key developmental signaling pathways, we further profile differences among clones and suggest a model whereby developmental precision emerges from the coordinated action of intrinsically biased clonal populations.
胚胎发育通常需要细胞间精确协调以实现可重复的结果，这导致一种假设，即细胞异质性必须被最小化或缓冲。通过基于荧光的谱系追踪与空间转录组学相结合，我们发现，在早期发育的类原肠胚模型中，预先存在的异质性通过干细胞克隆间的分工促进了正确的轴向组织。从共同群体中分离出的单个克隆对前后命运表现出一致的空间倾向。虽然纯克隆产生细长结构的频率低于多克隆群体，但混合克隆可恢复正确的轴向伸长。空间转录组学显示，纯克隆表现出基因表达紊乱，前后标记物出现不适当的共表达，而克隆组合可恢复正确的空间组织。利用RNA测序、ATAC测序以及对关键发育信号通路的扰动，我们进一步分析了克隆间的差异，并提出了一个模型，即发育精度源于内在有偏向性的克隆群体的协同作用。
