美国华盛顿大学Cole Trapnell和David Kimelman共同合作，近期取得重要工作进展。他们研究开发了单细胞分辨率下的胚胎规模反向遗传学方法。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，单细胞转录组技术的成熟促进了从整个胚胎中生成全面的细胞图谱。然而，这些数据中的大多数都是从野生型胚胎中收集的，而没有对发育中存在的潜在变异进行评估。
研究人员展示了“受干扰胚胎的斑马鱼单细胞图谱”：1812个单独解析发育中的斑马鱼类胚胎的单细胞转录组数据，包括19个时间点、23个遗传干扰和3.2 百万个细胞。这一研究中的高度复制（每个条件下有八个或更多胚胎）使研究人员能够评估整个生物体内细胞类型丰度的变化，并检测细胞类型组成相对于野生型胚胎的扰动依赖性偏差。这一方法对罕见的细胞类型很敏感，可以解析脑神经节神经元的发育轨迹和遗传依赖性，脑神经节神经元是一个占胚胎不到1%的细胞群体。
此外，对单个突变体的时间序列分析发现了一组与脊索鞘细胞具有惊人相似转录组的短距离独立细胞，这导致了关于头骨早期起源的新假设。研究人员预计，从大量个体胚胎中标准化收集高分辨率、生物体规模的单细胞数据，将有助于绘制斑马鱼细胞类型的遗传依赖性，同时也解决发育遗传学中的长期挑战，包括个体表型多样性背后的细胞和转录可塑性。
附：英文原文
Title: Embryo-scale reverse genetics at single-cell resolution
Author: Saunders, Lauren M., Srivatsan, Sanjay R., Duran, Madeleine, Dorrity, Michael W., Ewing, Brent, Linbo, Tor H., Shendure, Jay, Raible, David W., Moens, Cecilia B., Kimelman, David, Trapnell, Cole
Issue&Volume: 2023-11-15
Abstract: The maturation of single-cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos1,2,3,4. A majority of these data, however, has been collected from wild-type embryos without an appreciation for the latent variation that is present in development. Here we present the ‘zebrafish single-cell atlas of perturbed embryos’: single-cell transcriptomic data from 1,812 individually resolved developing zebrafish embryos, encompassing 19 timepoints, 23 genetic perturbations and a total of 3.2million cells. The high degree of replication in our study (eight or more embryos per condition) enables us to estimate the variance in cell type abundance organism-wide and to detect perturbation-dependent deviance in cell type composition relative to wild-type embryos. Our approach is sensitive to rare cell types, resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons, a cell population that comprises less than 1% of the embryo. Additionally, time-series profiling of individual mutants identified a group of brachyury-independent cells with strikingly similar transcriptomes to notochord sheath cells, leading to new hypotheses about early origins of the skull. We anticipate that standardized collection of high-resolution, organism-scale single-cell data from large numbers of individual embryos will enable mapping of the genetic dependencies of zebrafish cell types, while also addressing longstanding challenges in developmental genetics, including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals.
DOI: 10.1038/s41586-023-06720-2
Source: https://www.nature.com/articles/s41586-023-06720-2
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
本期文章：《自然》：Online/在线发表
