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.

Organelles – understanding noise and heterogeneity in cell biology at an intermediate scale

“…Consequently, all cellular trafficking, biosynthetic and self-assembly processes are subject to noise and variation, and given that the structure of cells and organelles is the result of many such processes, it is to be expected that overall organelle and cellular structure may also exhibit heterogeneity. This hypothesis has been proven using live-cell imaging experiments, where stochastic fluctuations in growth rates have been observed for neurite outgrowth (Odde and Buettner, 1998) as well as endocytotic activity (Dey et al, 2014). Similar fluctuations are seen when cellular processes are reconstituted in vitro -for example, microtubules display momentary fluctuations in stability that influence microtubule growth and shrinkage rates (Duellberg et al, 2016).…”

Heterogeneity in the endocytic capacity of individual macrophage in a population determines its subsequent phagocytosis, infectivity and subcellular trafficking

“…It is now becoming abundantly clear that no two cells in a population are identical, 33,34 indeed cell‐to‐cell variability has been used as a tool to identify and understand cell biological processes 35 . Isogenic cells show substantial phenotypic heterogeneity in multiple assays in diverse contexts, 36‐39 including endocytic uptake 35 .…”

Building endocytic pits without clathrin

“…For example, several studies have noted the variability in the activity CIE pathways between cells within a population 22,35 ; this is not seen for clathrin-dependent endocytosis. In addition, CIE and the clathrin pathway show different sensitivities to experimental protocols that involve low-temperature treatments, which are a common feature of standard procedures to measure endocytosis (see Supplementary information S1 (table)).…”