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Transient nuclear deformation primes epigenetic state and promotes cell reprogramming

Nature Materials volume 21, pages 1191–1199 (2022)Cite this article

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Abstract

Cell reprogramming has wide applications in tissue regeneration, disease modelling and personalized medicine. In addition to biochemical cues, mechanical forces also contribute to the modulation of the epigenetic state and a variety of cell functions through distinct mechanisms that are not fully understood. Here we show that millisecond deformation of the cell nucleus caused by confinement into microfluidic channels results in wrinkling and transient disassembly of the nuclear lamina, local detachment of lamina-associated domains in chromatin and a decrease of histone methylation (histone H3 lysine 9 trimethylation) and DNA methylation. These global changes in chromatin at the early stage of cell reprogramming boost the conversion of fibroblasts into neurons and can be partially reproduced by inhibition of histone H3 lysine 9 and DNA methylation. This mechanopriming approach also triggers macrophage reprogramming into neurons and fibroblast conversion into induced pluripotent stem cells, being thus a promising mechanically based epigenetic state modulation method for cell engineering.

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Fig. 1: Microchannel-induced nuclear deformation.
Fig. 2: Microchannel-induced nuclear deformation boosted neuronal marker expression and enhanced iN reprogramming efficiency.
Fig. 3: Nuclear deformation induced the demethylation of histone and DNA.
Fig. 4: Lamin A/C-mediated microchannel-induced epigenetic changes and iN reprogramming.
Fig. 5: Development of mechanical reprogramming technologies by nuclear deformation.

Data availability

The authors declare that all data supporting the findings of this study are available within the paper, source data and Supplementary Information files. Additional images or videos are available from the corresponding author upon request. Source data are provided with this paper.

Code availability

Codes utilized for image analysis are available on the lab website (https://li-lab.seas.ucla.edu/requestform/).

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Acknowledgements

We thank M. Wernig at Stanford University for providing the constructs of BAM for reprogramming experiments and C.M. Ho for his suggestions on the design of microdevices. We were supported in part by a UCLA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Innovation Award and research grants from the National Institutes of Health (HL121450 and GM143485 to S.L. and GM140106 to S.K.K.) and the National Science Foundation (BMMB-1906165 to A.C.R.). We acknowledge the use of instruments at the Nano & Pico Characterization Lab and Advanced Light Microscopy and Spectroscopy Lab at the California NanoSystems Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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Authors and Affiliations

  1. Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA

    Yang Song, Jennifer Soto, Binru Chen, Tyler Hoffman, Weikang Zhao, Chau Ly, Amy C. Rowat & Song Li

  2. Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA

    Ninghao Zhu & Pak Kin Wong

  3. Department of Bioengineering, University of California San Diego, San Diego, CA, USA

    Qin Peng, Longwei Liu & Yingxiao Wang

  4. Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA, USA

    Amy C. Rowat

  5. Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA

    Siavash K. Kurdistani

  6. Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA

    Song Li

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Contributions

Y.S., S.L., P.K.W. and S.K.K. designed the experiments. Y.S., J.S., B.C., W.Z., N.Z., Q.P., L.L. and C.L. performed the experiments. Y.S., J.S., B.C., W.Z., T.H. and Q.P. analysed the data. Y.S., P.K.W., Y.W., A.C.R., C.L., S.K.K. and S.L. contributed to data interpretation and discussion. Y.S., J.S. and S.L. wrote the manuscript.

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Correspondence to Song Li.

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Nature Materials thanks Quasar Padiath and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary Figs. 1–57, Table 1 and Video 1 caption.

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Supplementary Video 1

Video of iN cells generated from mechanical squeezing treatment and labelled with the calcium indicator, Fluo-4 AM, after six weeks in culture.

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Song, Y., Soto, J., Chen, B. et al. Transient nuclear deformation primes epigenetic state and promotes cell reprogramming. Nat. Mater. 21, 1191–1199 (2022). https://doi.org/10.1038/s41563-022-01312-3

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