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Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility

Nature Biomedical Engineering volume 3, pages 1009–1019 (2019)Cite this article

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Abstract

In breast cancer, the increased stiffness of the extracellular matrix is a key driver of malignancy. Yet little is known about the epigenomic changes that underlie the tumorigenic impact of extracellular matrix mechanics. Here, we show in a three-dimensional culture model of breast cancer that stiff extracellular matrix induces a tumorigenic phenotype through changes in chromatin state. We found that increased stiffness yielded cells with more wrinkled nuclei and with increased lamina-associated chromatin, that cells cultured in stiff matrices displayed more accessible chromatin sites, which exhibited footprints of Sp1 binding, and that this transcription factor acts along with the histone deacetylases 3 and 8 to regulate the induction of stiffness-mediated tumorigenicity. Just as cell culture on soft environments or in them rather than on tissue-culture plastic better recapitulates the acinar morphology observed in mammary epithelium in vivo, mammary epithelial cells cultured on soft microenvironments or in them also more closely replicate the in vivo chromatin state. Our results emphasize the importance of culture conditions for epigenomic studies, and reveal that chromatin state is a critical mediator of mechanotransduction.

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Fig. 1: Nuclear and chromatin alterations accompany phenotypic changes induced by ECM stiffness.
Fig. 2: Chromatin accessibility changes are associated with normal and tumorigenic phenotypes.
Fig. 3: Sp1 mediates the stiffness-induced tumorigenic phenotype.
Fig. 4: HDACs 3 and 8 regulate the stiffness-induced tumorigenic phenotype.
Fig. 5: Soft hydrogel culture produces more physiologically representative chromatin accessibility profiles than standard tissue culture.

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Data availability

The authors declare that the main data supporting the results in this study are available within the paper and its Supplementary Information. ATAC-seq data generated in this study are available through the Gene Expression Omnibus under accession code GSE131968. Additional datasets are available from the corresponding author upon reasonable request.

Code availability

Custom analysis pipelines are available at https://github.com/kundajelab.

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Acknowledgements

The authors acknowledge helpful discussions with the Chaudhuri laboratory, C. Hsueh for assistance with nuclear curvature analysis, M. Black for assistance with chromatin thickness analysis, the Bollyky laboratory for use of the Licor imager, the Stanford Genome Sequencing Service Center for sequencing (NIH S10OD020141), and the Stanford Cell Science Imaging Facility for assistance with confocal image analysis and TEM preparation and imaging (NIH 1S10RR026780-01). This work was supported by an NIH F32 fellowship to R.S.S. (F32CA210431), and an American Cancer Society grant (RSG-16-028-01) and NIH grant (R37-CA214136) to O.C.

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Authors and Affiliations

  1. Department of Mechanical Engineering, Stanford University, Stanford, CA, USA

    Ryan S. Stowers, Sungmin Nam & Ovijit Chaudhuri

  2. Department of Biological Data Science, Stanford University, Stanford, CA, USA

    Anna Shcherbina

  3. Department of Genetics, Stanford University, Stanford, CA, USA

    Johnny Israeli, Joshua J. Gruber, Michael P. Snyder & Anshul Kundaje

  4. Department of Physics, Stanford University, Stanford, CA, USA

    Johnny Israeli

  5. Department of Medicine, Oncology Division, Stanford University, Stanford, CA, USA

    Joshua J. Gruber

  6. Department of Bioengineering, Stanford University, Stanford, CA, USA

    Julie Chang

  7. Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA

    Atefeh Rabiee & Mary N. Teruel

  8. Department of Computer Science, Stanford University, Stanford, CA, USA

    Anshul Kundaje

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Contributions

R.S.S. and O.C. conceived the study. R.S.S., A.S., A.K. and O.C. wrote the manuscript. R.S.S., J.J.G., J.C., A.R., M.N.T., M.P.S. and O.C. designed the experiments. R.S.S., J.J.G., J.C., A.R. and S.N. conducted experiments. R.S.S., A.S., J.I., J.C., A.K. and O.C. analysed the data.

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Correspondence to Ovijit Chaudhuri.

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Stowers, R.S., Shcherbina, A., Israeli, J. et al. Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility. Nat Biomed Eng 3, 1009–1019 (2019). https://doi.org/10.1038/s41551-019-0420-5

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