A genome-wide atlas of human cell morphology.
A genome-wide atlas of human cell morphology.
复制标题
人类细胞形态的全基因组图谱。
DOI：
10.1101/2023.08.06.552164
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
中科院分区：
文献类型：
--
作者：
Ramezani,Meraj;Bauman,Julia;Singh,Avtar;Weisbart,Erin;Yong,John;Lozada,Maria;Way,GregoryP;Kavari,SanamL;Diaz,Celeste;Haghighi,Marzieh;Batista,ThiagoM;Pérez-Schindler,Joaquín;Claussnitzer,Melina;Singh,Shantanu;Cimini,BethA;
现代基因组学时代的一个关键挑战是开发基因功能的经验数据驱动的表示。在这里，我们提出了人类细胞中第一个基于形态学的无偏差全基因组扰动图谱，其中包含三个全基因组基因型-表型图谱，其中包括基于 CRISPR-Cas9 的 3000 万个以上细胞中超过 20,000 个基因的敲除。我们的光学混合细胞分析平台 (PERISCOPE) 将可脱色的高维表型分析面板（基于 Cell Painting）与分子条形码的光学测序和可扩展的开源分析管道相结合，以促进混合扰动文库的大规模并行筛选。该扰动图谱包含单个细胞的高维表型特征，具有足够的分辨率来聚类数千个人类基因，重建已知的途径和蛋白质-蛋白质相互作用网络，询问亚细胞过程并识别培养基特异性反应。使用该图谱，我们将与疾病相关的 TMEM251/LYSET 识别为一种高尔基驻留跨膜蛋白，对于 6-磷酸甘露糖依赖性溶酶体酶运输至关重要。总之，这个扰动图谱和筛选平台代表了大规模连接基因与细胞功能的丰富且可访问的资源。
A key challenge of the modern genomics era is developing empirical data-driven representations of gene function. Here we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-wide genotype–phenotype maps comprising CRISPR–Cas9-based knockouts of >20,000 genes in >30 million cells. Our optical pooled cell profiling platform (PERISCOPE) combines a destainable high-dimensional phenotyping panel (based on Cell Painting) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This perturbation atlas comprises high-dimensional phenotypic profiles of individual cells with sufficient resolution to cluster thousands of human genes, reconstruct known pathways and protein–protein interaction networks, interrogate subcellular processes and identify culture media-specific responses. Using this atlas, we identify the poorly characterized disease-associated TMEM251/LYSET as a Golgi-resident transmembrane protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes. In sum, this perturbation atlas and screening platform represents a rich and accessible resource for connecting genes to cellular functions at scale.