Asami Soichiro, Yin Chenshuo, Garza Luis A, Kalhor Reza
Department of Biomedical Engineering, Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Department of Dermatology, Department of Cell Biology, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
bioRxiv. 2024 Sep 24:2024.09.24.614640. doi: 10.1101/2024.09.24.614640.
Organ development is guided by a space-time landscape that constraints cell behavior. This landscape is challenging to characterize for the hair follicle - the most abundant mini organ - due to its complex microscopic structure and asynchronous development. We developed 3DEEP, a tissue clearing and spatial transcriptomic strategy for characterizing tissue blocks up to 400 µm in thickness. We captured 371 hair follicles at different stages of organogenesis in 1 mm of skin of a 12-hour-old mouse with 6 million transcripts from 81 genes. From this single time point, we deconvoluted follicles by age based on whole-organ molecular pseudotimes to animate a stop-motion 3D atlas of follicle development along its trajectory. We defined molecular stages for hair follicle organogenesis and characterized the order of emergence for its structures, differential signaling dynamics at its top and bottom, morphogen shifts preceding and accompanying structural changes, and series of structural changes leading to the formation of its canal and opening. We further found that hair follicle stem cells and their niche are established and stratified early in organogenesis, before the formation of the hair bulb. Overall, this work demonstrates the power of increased depth of spatial transcriptomics to provide a four-dimensional analysis of organogenesis.
器官发育由一种限制细胞行为的时空格局引导。由于毛囊这种最丰富的微型器官具有复杂的微观结构和异步发育过程，因此难以对其时空格局进行表征。我们开发了3DEEP，这是一种用于表征厚度达400微米的组织块的组织透明化和空间转录组学策略。我们在一只12小时大的小鼠1毫米厚的皮肤中捕获了371个处于器官发生不同阶段的毛囊，得到了来自81个基因的600万个转录本。从这个单一时间点出发，我们根据全器官分子伪时间按年龄对毛囊进行反卷积，以制作一部沿其轨迹的毛囊发育定格3D图谱动画。我们定义了毛囊器官发生的分子阶段，并表征了其结构出现的顺序、顶部和底部的差异信号动态、结构变化之前和伴随的形态发生素转变，以及导致其管道和开口形成的一系列结构变化。我们还进一步发现，毛囊干细胞及其微环境在器官发生早期、毛球形成之前就已建立并分层。总的来说，这项工作展示了增加空间转录组学深度以提供器官发生的四维分析的能力。
