Cells in vivo exist
within the context of a multicellular
tissue, where their behavior is governed by homo- and heterotypic
cell–cell interactions, the material properties of the extracellular
matrix, and the distribution of various soluble and physical factors.
Most methods currently used to study and manipulate cellular behavior in vitro, however, sacrifice physiological relevance for
experimental expediency. The fallacy of such approaches has been highlighted
by the recent development and application of three-dimensional culture
models to cell biology, which has revealed striking phenotypic differences
in cell survival, migration, and differentiation in genetically identical
cells simply by varying culture conditions. These perplexing findings
beg the question of what constitutes a three-dimensional culture and
why cells behave so differently in two- and three-dimensional culture
formats. In the following review, we dissect the fundamental differences
between two- and three-dimensional culture conditions. We begin by
establishing a basic definition of what “three dimensions”
means at different biological scales and discuss how dimensionality
influences cell signaling across different length scales. We identify
which three-dimensional features most potently influence intracellular
signaling and distinguish between conserved biological principles
that are maintained across culture conditions and cellular behaviors
that are sensitive to microenvironmental context. Finally, we highlight
state-of-the-art molecular tools amenable to the study of signaling
in three dimensions under conditions that facilitate deconstruction
of signaling in a more physiologically relevant manner.