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How signals are processed by interact-ing cells is largely unknown. In a new study in Science, Pawson, Linding and colleagues have dissected cell-specific signalling networks during the inter-action between cells expressing trans-membrane Eph receptor Tyr kinases (EphRs) and cells expressing their membrane-bound ephrin ligands. They found that the receptor- and ligand-expressing cells use different Tyr kinases and phosphorylation targets to process signals induced by cell–cell contacts.

To study bidirectional EphR–ephrin signalling in the context of direct cell–cell interactions, the authors labelled cells expressing EphB2 or ephrin B1 using different amino acid isotopes, which enable relative quantification of Tyr phos-phorylation peptides (and therefore

signalling events) by mass spectrom-etry in a cell line-specific manner. They found that global changes in Tyr phosphorylation induced by cell–cell contact differ between the two cell types. The comparison of cell-specific modulation of the 100 Tyr phosphor-ylation sites present in both cell types identified asymmetric regulation of proteins that have a wide range of molecular and cellular functions. For example, the phosphorylation of adaptor proteins is preferentially increased in EphB2-expressing cells, suggesting that they have cell-specific regulatory roles.

When cells expressing EphB2 and ephrin B1 contact each other in cell culture they segregate and form distinct colonies with well-defined boundaries. To study the role of selected signalling proteins during this process, a small interfering RNA (siRNA) screen was performed. Among the 200 targets that affected EphB2–ephrin B1 cell segregation, 37 were significantly modulated in EphB2-expressing cells and 26 were significantly modulated in ephrin-expressing cells. The siRNA data were combined with the quantified modulation of Tyr phosphorylation in the two cell types. The authors then used the NetPhorest and NetworKIN algorithms to derive a computational model of cell-specific dynamic signalling networks during

cell segregation. The analysis revealed that the asymmetric regulation of Tyr phosphorylation events in EphB2- and ephrin B1-expressing cells is achieved through the alternative use of kinases and adaptor proteins.

Cells expressing a variant of ephrin B1 that lacks the cytoplasmic region (ephrin B1ΔIC) elicit a unidi-rectional signal in EphB2-expressing cells but do not induce signalling in the cell in which they are expressed. Notably, the analysis of EphB2–ephrin B1ΔIC signalling revealed that the cytoplasmic region of ephrin B1 is required for cell sorting and also affects signalling in neighbouring cells that express EphB2. This shows that EphR–ephrin signalling is not entirely cell autonomous.

Using proteomic and computa-tional approaches, this study provides important new insights into cell-specific signalling networks in two populations of cells, while they contact each other. Similar integrative net-work biology approaches will enable more accurate studies of the effects of cell–cell interactions and signalling networks during normal and pathological processes.

Francesca Cesari

ORIGINAL RESEARCH PAPER Jørgensen, C. et al. Cell-specific information processing in segregating populations of Eph receptor ephrin–expressing cells. Science 326, 1502–1509 (2009)

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NATURE REvIEWS | Molecular cell BIology voLUmE 11 | FEBRUARy 2010

Nature Reviews Molecular Cell Biology | AoP, published online 13 January 2010; doi:10.1038/nrm2837

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