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Statistical analysis of cell migration in 3D using the anisotropic persistent random walk model

Nature Protocols volume 10, pages 517–527 (2015)Cite this article

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Abstract

Cell migration through 3D extracellular matrices (ECMs) is crucial to the normal development of tissues and organs and in disease processes, yet adequate analytical tools to characterize 3D migration are lacking. The motility of eukaryotic cells on 2D substrates in the absence of gradients has long been described using persistent random walks (PRWs). Recent work shows that 3D migration is anisotropic and features an exponential mean cell velocity distribution, rendering the PRW model invalid. Here we present a protocol for the analysis of 3D cell motility using the anisotropic PRW model. The software, which is implemented in MATLAB, enables statistical profiling of experimentally observed 2D and 3D cell trajectories, and it extracts the persistence and speed of cells along primary and nonprimary directions and an anisotropic index of migration. Basic computer skills and experience with MATLAB software are recommended for successful use of the protocol. This protocol is highly automated and fast, taking <30 min to analyze trajectory data per biological condition.

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Figure 1: Characterization of cell migration inside a 3D matrix.
Figure 2: Computer simulations of cell trajectories using the APRW and PRW models.
Figure 3: Statistical analysis of simulated trajectories.
Figure 4: 3D cell migration parameters obtained via the APRW and PRW models.

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Acknowledgements

This work was supported in part by the US National Institutes of Health grant U54CA143868.

Author information

Author notes

  1. Pei-Hsun Wu and Anjil Giri: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, USA

    Pei-Hsun Wu, Anjil Giri & Denis Wirtz

  2. Johns Hopkins Physical Science Oncology Center, The Johns Hopkins University, Baltimore, Maryland, USA

    Pei-Hsun Wu, Anjil Giri & Denis Wirtz

  3. Department of Pathology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA

    Denis Wirtz

  4. Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA

    Denis Wirtz

  5. Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA

    Denis Wirtz

Authors
  1. Pei-Hsun Wu
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  3. Denis Wirtz
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Contributions

A.G. conducted the experiments; P.-H.W. developed, tested, applied and validated the APRW model; and A.G., P.-H.W. and D.W. designed the experiments, analyzed the results and wrote the paper.

Corresponding authors

Correspondence to Pei-Hsun Wu or Denis Wirtz.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Methods (PDF 188 kb)

Supplementary Software

Contains MATLAB scripts. (ZIP 21 kb)

Supplementary Data

Contains example excel sheets (ZIP 3455 kb)

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Wu, PH., Giri, A. & Wirtz, D. Statistical analysis of cell migration in 3D using the anisotropic persistent random walk model. Nat Protoc 10, 517–527 (2015). https://doi.org/10.1038/nprot.2015.030

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