德国吕贝克大学和基尔大学Malte Spielmann，美国华盛顿大学Jay Shendure和美国洛克菲勒大学Junyue Cao共同合作，近期取得重要工作进展，他们对哺乳动物发育障碍的单细胞、全胚胎表型进行了研究分析。相关研究成果2023年11月15日在线发表于《自然》杂志上。

据介绍，小鼠模型是研究人类疾病，特别是发育障碍的重要工具。然而，传统的表型分型方法可能无法在整个发育过程中发现细微的缺陷。

研究人员着手建立整个胚胎的单细胞RNA测序，作为小鼠遗传模型系统表型的可扩展平台。在胚胎第13.5天，研究人员应用基于组合索引的单细胞RNA测序法对22种突变型和4种野生型基因型的101个胚胎进行了分析，总共分析了超过160万个细胞核。这22个突变体代表了一系列预期的表型，从已建立的多系统疾病到个体调控区的缺失。研究人员开发并应用了几种分析框架，用于检测52种细胞类型或轨迹的组成及基因表达差异。一些突变体表现出数十种轨迹的变化，而另一些突变体只表现出少数细胞类型的变化。

研究人员还确定了广泛使用的野生型品系之间的差异，比较了功能获得突变体和功能丧失突变体的表型，并表征了拓扑相关结构域边界的缺失。值得注意的是，突变体之间有一些共同的变化，这表明通过进一步扩大这种方法，发育多效性可能是“可分解的”。

总之，这一发现表明了整个胚胎的单细胞图谱如何能够以前所未有的广度和分辨率，对小鼠突变体进行系统的分子和细胞表型表征。

附：英文原文

Title: Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Author: Huang, Xingfan, Henck, Jana, Qiu, Chengxiang, Sreenivasan, Varun K. A., Balachandran, Saranya, Amarie, Oana V., Hrab de Angelis, Martin, Behncke, Rose Yinghan, Chan, Wing-Lee, Despang, Alexandra, Dickel, Diane E., Duran, Madeleine, Feuchtinger, Annette, Fuchs, Helmut, Gailus-Durner, Valerie, Haag, Natja, Hgerling, Rene, Hansmeier, Nils, Hennig, Friederike, Marshall, Cooper, Rajderkar, Sudha, Ringel, Alessa, Robson, Michael, Saunders, Lauren M., da Silva-Buttkus, Patricia, Spielmann, Nadine, Srivatsan, Sanjay R., Ulferts, Sascha, Wittler, Lars, Zhu, Yiwen, Kalscheuer, Vera M., Ibrahim, Daniel M., Kurth, Ingo, Kornak, Uwe, Visel, Axel, Pennacchio, Len A., Beier, David R., Trapnell, Cole, Cao, Junyue, Shendure, Jay, Spielmann, Malte

Issue&Volume: 2023-11-15

Abstract: Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing3 to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions4,5. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be ‘decomposable’ through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.

DOI: 10.1038/s41586-023-06548-w

Source: https://www.nature.com/articles/s41586-023-06548-w

期刊信息

Nature：《自然》，创刊于1869年。隶属于施普林格·自然出版集团，最新IF：69.504

官方网址：http://www.nature.com

投稿链接：http://www.nature.com/authors/submit_manuscript.html