title: 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 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.
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
authors.forename: Berend
authors.initials: B
authors.lastname: Snijder
authors.forename: Raphael
authors.initials: R
authors.lastname: Sacher
authors.forename: Pauli
authors.initials: P
authors.lastname: Rämö
authors.forename: Prisca
authors.initials: P
authors.lastname: Liberali
authors.forename: Karin
authors.initials: K
authors.lastname: Mench
authors.forename: Nina
authors.initials: N
authors.lastname: Wolfrum
authors.forename: Laura
authors.initials: L
authors.lastname: Burleigh
authors.forename: Cameron C
authors.initials: CC
authors.lastname: Scott
authors.forename: Monique H
authors.initials: MH
authors.lastname: Verheije
authors.forename: Jason
authors.initials: J
authors.lastname: Mercer
authors.forename: Stefan
authors.initials: S
authors.lastname: Moese
authors.forename: Thomas
authors.initials: T
authors.lastname: Heger
authors.forename: Kristina
authors.initials: K
authors.lastname: Theusner
authors.forename: Andreas
authors.initials: A
authors.lastname: Jurgeit
authors.forename: David
authors.initials: D
authors.lastname: Lamparter
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Balistreri
authors.forename: Mario
authors.initials: M
authors.lastname: Schelhaas
authors.forename: Cornelis A M
authors.initials: CA
authors.lastname: De Haan
authors.forename: Varpu
authors.initials: V
authors.lastname: Marjomäki
authors.forename: Timo
authors.initials: T
authors.lastname: Hyypiä
authors.forename: Peter J M
authors.initials: PJ
authors.lastname: Rottier
authors.forename: Beate
authors.initials: B
authors.lastname: Sodeik
authors.forename: Mark
authors.initials: M
authors.lastname: Marsh
authors.forename: Jean
authors.initials: J
authors.lastname: Gruenberg
authors.forename: Ali
authors.initials: A
authors.lastname: Amara
authors.forename: Urs
authors.initials: U
authors.lastname: Greber
authors.forename: Ari
authors.initials: A
authors.lastname: Helenius
authors.forename: Lucas
authors.initials: L
authors.lastname: Pelkmans
mesh_terms: D001499:Bayes Theorem; D060833:Cellular Microenvironment; D003198:Computer Simulation; D023281:Genomics / Q000379:methods; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D008954:Models, Biological; D034622:RNA Interference; D034741:RNA, Small Interfering; D012367:RNA, Viral / Q000302:isolation & purification; D015203:Reproducibility of Results; D059010:Single-Cell Analysis / Q000379:methods*; D049490:Systems Biology / Q000379:methods; D014764:Viral Proteins / Q000235:genetics / Q000302:isolation & purification; D014777:Virus Diseases / Q000235:genetics* / Q000378:metabolism; D014780:Viruses / Q000302:isolation & purification / Q000472:pathogenicity
chemical_list: D034741:RNA, Small Interfering; D012367:RNA, Viral; D014764:Viral Proteins