Systems survey of endocytosis by multiparametric image analysis

Claudio Collinet 1, Martin Stöter 2, Charles R. Bradshaw 1, Nikolay Samusik 1, Jochen C. Rink †, Denise Kenski †, Bianca Habermann 1, Frank Buchholz 1, Robert Henschel 3, Matthias S. Mueller 3, Wolfgang E. Nagel 3, Eugenio Fava 2, Yannis Kalaidzidis 1,4 & Marino Zerial 1

Endocytosis is a complex process fulfilling many cellular and developmental functions. Understanding how it is regulated and integrated with other cellular processes requires a comprehensive analysis of its molecular constituents and general design principles. Here, we developed a new strategy to phenotypically profile the human genome with respect to transferrin (TF) and epidermal growth factor (EGF) endocytosis by combining RNA interference, automated high-resolution confocal microscopy, quantitative multiparametric image analysis and high-performance computing. We identified several novel components of endocytic trafficking, including genes implicated in human diseases. We found that signalling pathways such as Wnt, integrin/cell adhesion, transforming growth factor (TGF)-β and Notch regulate the endocytic system, and identified new genes involved in cargo sorting to a subset of signalling endosomes. A systems analysis by Bayesian networks further showed that the number, size, concentration of cargo and intracellular position of endosomes are not determined randomly but are subject to specific regulation, thus uncovering novel properties of the endocytic system.

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1 Max Planck Institute for Molecular Cell Biology and Genetics,
2 High-Throughput Technology Development Studio, MPI-CBG, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
3 Center for Information Services and High Performance Computing (ZIH), Dresden University of Technology, D-01062 Dresden, Germany.
4 Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119899, Moscow, Russia.
† Present addresses: University of Utah School of Medicine, 401 MREB, 20 North 1900 East, Salt Lake City, Utah 84132-3401, USA (J.C.R.); Sirna Therapeutics Inc., San Francisco, California 94158, USA (D.K.).