Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Cell Stem Cell. 2023 Mar 2;30(3):312-332.e13. doi: 10.1016/j.stem.2023.01.010. Epub 2023 Feb 15.
Human genome variation contributes to diversity in neurodevelopmental outcomes and vulnerabilities; recognizing the underlying molecular and cellular mechanisms will require scalable approaches. Here, we describe a "cell village" experimental platform we used to analyze genetic, molecular, and phenotypic heterogeneity across neural progenitor cells from 44 human donors cultured in a shared in vitro environment using algorithms (Dropulation and Census-seq) to assign cells and phenotypes to individual donors. Through rapid induction of human stem cell-derived neural progenitor cells, measurements of natural genetic variation, and CRISPR-Cas9 genetic perturbations, we identified a common variant that regulates antiviral IFITM3 expression and explains most inter-individual variation in susceptibility to the Zika virus. We also detected expression QTLs corresponding to GWAS loci for brain traits and discovered novel disease-relevant regulators of progenitor proliferation and differentiation such as CACHD1. This approach provides scalable ways to elucidate the effects of genes and genetic variation on cellular phenotypes.
人类基因组变异导致神经发育结果和脆弱性的多样性；要识别潜在的分子和细胞机制，需要可扩展的方法。在这里，我们描述了一个“细胞村”实验平台，我们使用该平台来分析在共享的体外环境中培养的来自 44 位人类供体的神经祖细胞中的遗传、分子和表型异质性，使用算法（Dropulation 和 Census-seq）将细胞和表型分配给个体供体。通过快速诱导人干细胞衍生的神经祖细胞、测量自然遗传变异和 CRISPR-Cas9 遗传干扰，我们鉴定出一个调节抗病毒 IFITM3 表达的常见变体，该变体解释了对寨卡病毒易感性的大多数个体间变异。我们还检测到与大脑特征的 GWAS 位点相对应的表达 QTL，并发现了 CACHD1 等新型与祖细胞增殖和分化相关的疾病相关调节剂。这种方法提供了阐明基因和遗传变异对细胞表型影响的可扩展方法。
