Systems survey of endocytosis by multiparametric image analysis

• Published in: Nature (London) Vol. 464; no. 7286; pp. 243 - 249
• Main Authors: Collinet, Claudio, Stöter, Martin, Bradshaw, Charles R., Samusik, Nikolay, Rink, Jochen C., Kenski, Denise, Habermann, Bianca, Buchholz, Frank, Henschel, Robert, Mueller, Matthias S., Nagel, Wolfgang E., Fava, Eugenio, Kalaidzidis, Yannis, Zerial, Marino
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 11.03.2010; Nature Publishing Group
• Subjects: 631/1647/245; 631/80/313/1461; 631/80/86; Cellular; Computing Methodologies; Endocytosis; Endocytosis - physiology; Endosomes; Endosomes - metabolism; Epidermal growth factor; Epidermal Growth Factor - metabolism; Gene Expression Profiling - methods; Genes; Genome-Wide Association Study; Genomes; Growth factors; Human; Humanities and Social Sciences; Humans; Image analysis; Image Processing, Computer-Assisted; Metabolic Networks and Pathways - physiology; Microscopy, Confocal; multidisciplinary; Phenotype; Physiological aspects; Protein Transport - physiology; Proteins; R&D; Research & development; RNA Interference; Science; Science (multidisciplinary); Signal Transduction - physiology; Signalling; Surveys; Systems analysis; Transferrin; Transferrin - metabolism; Transforming growth factors
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/nature08779

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. Systems analysis of endocytosis Endocytosis, the process that cells use to internalize proteins and other molecules by engulfment in the cell membrane, is central to many cellular and development functions. By combining genome-wide RNAi screening, automated high-resolution confocal microscopy and quantitative multi-parametric image analysis, Collinet et al . obtain an accurate profile of the activity of human genes in endocytosis. Several novel components of endocytosis and endosome trafficking are revealed, and systems analysis indicates that the number, size and concentration of cargo within endosomes are not determined randomly but are subject to specific regulation within the cell. A new strategy is presented to accurately profile the activity of human genes in endocytosis by combining genome-wide RNAi, automated high-resolution confocal microscopy and quantitative multi-parametric image analysis. Several novel components of endocytosis and endosome trafficking were uncovered; a systems analysis further revealed that the cell regulates the number, size and concentration of cargo within endosomes.