Abstract
Cell-matrix adhesions are of great interest because of their contribution to numerous biological processes, including cell migration, differentiation, proliferation, survival, tissue morphogenesis, wound healing, and tumorigenesis. Adhesions are dynamic structures that are classically defined on two-dimensional (2D) substrates, though the need to analyze adhesions in more physiologic three-dimensional (3D) environments is being increasingly recognized. However, progress has been greatly hampered by the lack of available tools to analyze adhesions in 3D environments. To address this need, we have developed a platform for the automated analysis, segmentation, and tracking of adhesions (PAASTA) based on an open source MATLAB framework, CellAnimation. PAASTA enables the rapid analysis of adhesion dynamics and many other adhesion characteristics, such as lifetime, size, and location, in 3D environments and on traditional 2D substrates. We manually validate PAASTA and utilize it to quantify rate constants for adhesion assembly and disassembly as well as adhesion lifetime and size in 3D matrices. PAASTA will be a valuable tool for characterizing adhesions and for deciphering the molecular mechanisms that regulate adhesion dynamics in 3D environments.
Highlights
Cell-matrix adhesions are of great interest because of their contribution to numerous biological processes, including cell migration, differentiation, proliferation, survival, tissue morphogenesis, wound healing, and tumorigenesis
We have developed a platform for the automated analysis, segmentation, and tracking of adhesions (PAASTA) based on an open source MATLAB framework, CellAnimation
Adhesions are composed of a number of different proteins, including integrin transmembrane receptors, which bind to the extracellular matrix (ECM), and intracellular signaling and structural proteins, such as paxillin, vinculin, talin, and focal adhesion kinase (FAK), that link integrins to the actin cytoskeleton[12,13,14,15]
Summary
Cell-matrix adhesions are of great interest because of their contribution to numerous biological processes, including cell migration, differentiation, proliferation, survival, tissue morphogenesis, wound healing, and tumorigenesis. Little mechanistic data for the regulation of adhesion assembly, maturation, and disassembly in 3D matrices is currently available Progress in this rapidly emerging field has been greatly hampered by the lack of available tools to analyze adhesion dynamics in 3D environments. To address this need, we have created an automated platform, PAASTA, for analyzing adhesion dynamics in cells migrating on both 2D substrates and in 3D environments, that is based on an open source MATLAB framework, CellAnimation[30]. We manually validate our platform using an established adhesion analysis method[9] and use PAASTA to quantify adhesion dynamics in 3D matrices
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