Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens

• Atray Dixit ^[1] ; Oren Parnas ; Biyu LI
  1. [1] Broad Institute of MIT and Harvard
• Localización: Cell, ISSN 0092-8674, Vol. 167, Nº. 7, 2016, págs. 1853-1866
• Idioma: inglés
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• Resumen

  • Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes—such as transcriptional profiles—at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays.