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Population context determines cell-to-cell variability in endocytosis and virus infection


Single-cell heterogeneity in cell populations arises from a combination of intrinsic and extrinsic factors1,2,3. This heterogeneity has been measured for gene transcription, phosphorylation, cell morphology and drug perturbations, and used to explain various aspects of cellular physiology4,5,6. In all cases, however, the causes of heterogeneity were not studied. Here we analyse, for the first time, the heterogeneous patterns of related cellular activities, namely virus infection, endocytosis and membrane lipid composition in adherent human cells. We reveal correlations with specific cellular states that are defined by the population context of a cell, and we derive probabilistic models that can explain and predict most cellular heterogeneity of these activities, solely on the basis of each cell’s population context. We find that accounting for population-determined heterogeneity is essential for interpreting differences between the activity levels of cell populations. Finally, we reveal that synergy between two molecular components, focal adhesion kinase and the sphingolipid GM1, enhances the population-determined pattern of simian virus 40 (SV40) infection. Our findings provide an explanation for the origin of heterogeneity patterns of cellular activities in adherent cell populations.

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Figure 1: Modelling and predicting diverse activity patterns in heterogeneous human cell populations.
Figure 2: Most variation observed in cellular activities is population determined and must be accounted for.
Figure 3: SV40 infection and cell size are co-regulated by GM1 and active FAK, depending on the local cell density.

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We acknowledge H. Verheije and L. Burleigh for providing images of MHV and dengue virus infection, G. Jurisic for providing primary cells and help with experiments, and all members of the laboratory for comments on the manuscript. P.R. is supported by the European Molecular Biology Organisation and the Human Frontiers Science Program, E.-M.D. by Oncosuisse and P.L. by the Federation of European Biochemical Societies. L.P. is supported by the ETH Zürich,, the Swiss National Science Foundation and the European Union.

Author Contributions L.P. supervised and conceived the project. R.S., B.S., E.-M.D. and P.L. performed experiments, B.S. and P.R. developed computational image analysis methods, B.S. performed all computational image analysis, B.S. and P.R. conceived the statistical analysis methods, B.S. performed all statistical analysis, L.P. and B.S. wrote the manuscript.

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Correspondence to Lucas Pelkmans.

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This file contains Supplementary Figures 1-10 with Legends, Supplementary Movie 1 Legend, Supplementary Methods, Supplementary Data, Supplementary Table 1 and Supplementary References. (PDF 6784 kb)

Supplementary Movie 1

This movie file shows that population properties are determined during growth of adherent human cells - see file s1 for full Legend. (MOV 9511 kb)

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Snijder, B., Sacher, R., Rämö, P. et al. Population context determines cell-to-cell variability in endocytosis and virus infection. Nature 461, 520–523 (2009).

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