title: Exploiting cell-to-cell variability to detect cellular perturbations.
abstract: Any single-cell-resolved measurement generates a population distribution of phenotypes, characterized by a mean, a variance, and a shape. Here we show that changes in the shape of a phenotypic distribution can signal perturbations to cellular processes, providing a way to screen for underlying molecular machinery. We analyzed images of a Drosophila S2R+ cell line perturbed by RNA interference, and tracked 27 single-cell features which report on endocytic activity, and cell and nuclear morphology. In replicate measurements feature distributions had erratic means and variances, but reproducible shapes; RNAi down-regulation reliably induced shape deviations in at least one feature for 1072 out of 7131 genes surveyed, as revealed by a Kolmogorov-Smirnov-like statistic. We were able to use these shape deviations to identify a spectrum of genes that influenced cell morphology, nuclear morphology, and multiple pathways of endocytosis. By preserving single-cell data, our method was even able to detect effects invisible to a population-averaged analysis. These results demonstrate that cell-to-cell variability contains accessible and useful biological information, which can be exploited in existing cell-based assays.
authors.affiliation: Stanford University, Palo Alto, California, United States of America.
authors.forename: Gautam
authors.initials: G
authors.lastname: Dey
authors.affiliation: Samuel Lunenfeld Research Institute, Toronto, Canada.
authors.forename: Gagan D
authors.initials: GD
authors.lastname: Gupta
authors.affiliation: Centre for Cellular and Molecular Platforms (C-CAMP), Bangalore, India.
authors.forename: Balaji
authors.initials: B
authors.lastname: Ramalingam
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India.
authors.forename: Mugdha
authors.initials: M
authors.lastname: Sathe
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India.
authors.forename: Satyajit
authors.initials: S
authors.lastname: Mayor
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS/GKVK Campus, Bangalore, India.
authors.forename: Mukund
authors.initials: M
authors.lastname: Thattai
mesh_terms: D000818:Animals; D048430:Cell Shape; D004330:Drosophila / Q000166:cytology* / Q000235:genetics*; D004705:Endocytosis; D010641:Phenotype; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering