Single‐cell analysis of population context advances RNAi screening at multiple levels

Single‐cell analysis of population context advances RNAi screening at multiple levels

Abstract Isogenic cells in culture show strong variability, which arises from dynamic adaptations to the microenvironment of individual cells. Here we study the influence of the cell population context, which determines a single cell's microenvironment, in image‐based RNAi screens. We developed...

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Main Authors: Berend Snijder, Raphael Sacher, Pauli Rämö, Prisca Liberali, Karin Mench, Nina Wolfrum, Laura Burleigh, Cameron C Scott, Monique H Verheije, Jason Mercer, Stefan Moese, Thomas Heger, Kristina Theusner, Andreas Jurgeit, David Lamparter, Giuseppe Balistreri, Mario Schelhaas, Cornelis A M De Haan, Varpu Marjomäki, Timo Hyypiä, Peter J M Rottier, Beate Sodeik, Mark Marsh, Jean Gruenberg, Ali Amara, Urs Greber, Ari Helenius, Lucas Pelkmans
Format: Article
Language:English
Published: Springer Nature 2012-04-01
Series:Molecular Systems Biology
Subjects:
cell‐to‐cell variability
image analysis
population context
RNAi
virus infection
Online Access:https://doi.org/10.1038/msb.2012.9
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Summary:Abstract Isogenic cells in culture show strong variability, which arises from dynamic adaptations to the microenvironment of individual cells. Here we study the influence of the cell population context, which determines a single cell's microenvironment, in image‐based RNAi screens. We developed a comprehensive computational approach that employs Bayesian and multivariate methods at the single‐cell level. We applied these methods to 45 RNA interference screens of various sizes, including 7 druggable genome and 2 genome‐wide screens, analysing 17 different mammalian virus infections and four related cell physiological processes. Analysing cell‐based screens at this depth reveals widespread RNAi‐induced changes in the population context of individual cells leading to indirect RNAi effects, as well as perturbations of cell‐to‐cell variability regulators. We find that accounting for indirect effects improves the consistency between siRNAs targeted against the same gene, and between replicate RNAi screens performed in different cell lines, in different labs, and with different siRNA libraries. In an era where large‐scale RNAi screens are increasingly performed to reach a systems‐level understanding of cellular processes, we show that this is often improved by analyses that account for and incorporate the single‐cell microenvironment.
ISSN:1744-4292

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