Cell-derived matrices for studying cell proliferation and directional migration in a complex 3D microenvironment


2D surfaces offer simple analysis of cells in culture, yet these often yield different cell morphologies and responses from those observed in vivo. Considerable effort has therefore been expended on the generation of more tissue-like environments for the study of cell behavior in vitro. Purified matrix proteins provide a 3D scaffold that better mimics the in vivo situation; however, these are far removed from the complex tissue composition seen in vivo. Cell-derived matrices (CDMs) offer a more physiologically relevant alternative for studying in vivo-like cell behavior in vitro. In the protocol described here, fibroblasts cultured on gelatin-coated surfaces are maintained in the presence of ascorbic acid to strengthen matrix deposition over 1–3 weeks. The resulting fibrillar CDMs are denuded of cells, and other cells are subsequently cultured on them, after which their behavior is monitored. We also demonstrate how to use CDMs as an in vivo-relevant reductionist model for studying tumor-stroma-induced changes in carcinoma cell proliferation and migration.

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Figure 1: Cell morphology on different in vitro matrices and in vivo.
Figure 2: Workflow diagram.
Figure 3: Common problems associated with CDM production.
Figure 4: Immunofluorescence imaging of collagen I and fibronectin in CDMs.
Figure 5: Comparison of HeLa-H2B-GFP cell proliferation on CDMs and on plastic.
Figure 6: Analysis of cell migration on CDMs.


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M. Georgiadou (University of Turku Centre for Biotechnology) is acknowledged for providing the bright-field images of CDMs presented in Figure 3. J. Norman (Beatson Institute for Cancer Research) is acknowledged for providing the TIFs. P. Caswell (University of Manchester) and J.F. Marshall (Barts Cancer Institute) are acknowledged for the A2780 and the MCF10 DCIS.COM cell lines, respectively. The Turku Centre for Biotechnology Imaging Core facility is acknowledged for help with the imaging. We gratefully acknowledge the following funding sources: Academy of Finland, European Research Council Consolidator Grant (no. 615258), the Sigrid Juselius Foundation and the Finnish Cancer Organization to J.I. R.K. was funded by the University of Turku/TUBS TuDMM doctoral program and G.J. was funded by an EMBO LTF.

Author information

J.I., G.J., H.H. and R.K. organized and wrote the manuscript. H.H. provided the illustrated workflow and edited the manuscript. G.J. and R.K. produced the data. R.K. produced the video-guided material with help from G.J and J.I.

Correspondence to Johanna Ivaska.

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The authors declare no competing financial interests.

Supplementary information


This video outlines the entire workflow used to generate CDMs. (MP4 2139 kb)

Coverslip preparation

This video shows how to prepare gelatin-coated coverslips (Steps 1–6 of the protocol). (MP4 6555 kb)

Plating of fibroblasts

This video shows how to plate fibroblasts for CDM production (Steps 7–10 of the protocol). (MP4 21761 kb)

Extraction of CDMs.

This video shows how to extract CDMs (Steps 11–17 of the protocol). (MP4 21408 kb)

Staining of CDMs.

This video shows how to stain CDMs using immunofluorescence (Step 18A of the protocol). (MP4 8054 kb)

Analysis of cell proliferation.

This video shows how to analyze cell proliferation on CDMs using an IncuCyte Zoom live-cell incubator (Step 18B of the protocol). (MP4 7943 kb)

Quantification of cell migration.

This video shows how to quantify cell migration on CDMs using ImageJ and the Chemotaxis tool (Step 18C of the protocol). (MP4 4202 kb)

Migration of an ovarian carcinoma cell.

This video shows an ovarian carcinoma cell transiently expressing Lifeact RFP (to visualize the actin cytoskeleton) migrating on TIF CDMs (labeled in green using Alexa Fluor 488 recombinant fibronectin). Images were acquired on a spinning-disk microscope using a 63× objective. (MP4 4849 kb)

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Kaukonen, R., Jacquemet, G., Hamidi, H. et al. Cell-derived matrices for studying cell proliferation and directional migration in a complex 3D microenvironment. Nat Protoc 12, 2376–2390 (2017). https://doi.org/10.1038/nprot.2017.107

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