Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Transient nuclear deformation primes epigenetic state and promotes cell reprogramming

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

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

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/).

References

  1. Aydin, B. & Mazzoni, E. O. Cell reprogramming: the many roads to success. Annu. Rev. Cell Dev. Biol. 35, 433–452 (2019).

    Article  CAS  Google Scholar 

  2. Karagiannis, P. et al. Induced pluripotent stem cells and their use in human models of disease and development. Physiol. Rev. 99, 79–114 (2019).

    Article  CAS  Google Scholar 

  3. Wang, H., Yang, Y., Liu, J. & Qian, L. Direct cell reprogramming: approaches, mechanisms and progress. Nat. Rev. Mol. Cell Biol. 22, 410–424 (2021).

    Article  Google Scholar 

  4. Pang, Z. P. et al. Induction of human neuronal cells by defined transcription factors. Nature 476, 220–223 (2011).

    Article  CAS  Google Scholar 

  5. Ieda, M. et al. Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142, 375–386 (2010).

    Article  CAS  Google Scholar 

  6. Pagliuca, F. W. et al. Generation of functional human pancreatic β cells in vitro. Cell 159, 428–439 (2014).

    Article  CAS  Google Scholar 

  7. Szabo, E. et al. Direct conversion of human fibroblasts to multilineage blood progenitors. Nature 468, 521–526 (2010).

    Article  CAS  Google Scholar 

  8. Huang, P. et al. Direct reprogramming of human fibroblasts to functional and expandable hepatocytes. Cell Stem Cell 14, 370–384 (2014).

    Article  CAS  Google Scholar 

  9. Vierbuchen, T. et al. Direct conversion of fibroblasts to functional neurons by defined factors. Nature 463, 1035–1041 (2010).

    Article  CAS  Google Scholar 

  10. Hu, W. et al. Direct conversion of normal and Alzheimer’s disease human fibroblasts into neuronal cells by small molecules. Cell Stem Cell 17, 204–212 (2015).

    Article  CAS  Google Scholar 

  11. Takahashi, K. & Yamanaka, S. A decade of transcription factor-mediated reprogramming to pluripotency. Nat. Rev. Mol. Cell Biol. 17, 183–193 (2016).

    Article  CAS  Google Scholar 

  12. Song, Y., Soto, J., Chen, B., Yang, L. & Li, S. Cell engineering: biophysical regulation of the nucleus. Biomaterials 234, 119743 (2020).

  13. Uhler, C. & Shivashankar, G. V. Regulation of genome organization and gene expression by nuclear mechanotransduction. Nat. Rev. Mol. Cell Biol. 18, 717–727 (2017).

    Article  CAS  Google Scholar 

  14. Li, Y. et al. Biophysical regulation of histone acetylation in mesenchymal stem cells. Biophys. J. 100, 1902–1909 (2011).

    Article  CAS  Google Scholar 

  15. Song, Y., Soto, J. & Li, S. Mechanical regulation of histone modifications and cell plasticity. Curr. Opin. Solid State Mater. Sci. 24, 100872 (2020).

    Article  CAS  Google Scholar 

  16. Discher, D. E. et al. Matrix mechanosensing: from scaling concepts in ’omics data to mechanisms in the nucleus, regeneration, and cancer. Annu. Rev. Biophys. 46, 295–315 (2017).

    Article  CAS  Google Scholar 

  17. Miroshnikova, Y. A., Nava, M. M. & Wickström, S. A. Emerging roles of mechanical forces in chromatin regulation. J. Cell Sci. 130, 2243–2250 (2017).

    CAS  Google Scholar 

  18. Downing, T. L. et al. Biophysical regulation of epigenetic state and cell reprogramming. Nat. Mater. 12, 1154–1162 (2013).

    Article  CAS  Google Scholar 

  19. Wang, P. et al. WDR5 modulates cell motility and morphology and controls nuclear changes induced by a 3D environment. Proc. Natl Acad. Sci. USA 115, 8581–8586 (2018).

    Article  CAS  Google Scholar 

  20. Tan, Y. et al. Matrix softness regulates plasticity of tumour-repopulating cells via H3K9 demethylation and Sox2 expression. Nat. Commun. 5, 4619 (2014).

    Article  CAS  Google Scholar 

  21. Nava, M. M. et al. Heterochromatin-driven nuclear softening protects the genome against mechanical stress-induced damage. Cell 181, 800–817 (2020).

    Article  CAS  Google Scholar 

  22. Damodaran, K. et al. Compressive force induces reversible chromatin condensation and cell geometry–dependent transcriptional response. Mol. Biol. Cell 29, 3039–3051 (2018).

    Article  CAS  Google Scholar 

  23. Ding, X. et al. High-throughput nuclear delivery and rapid expression of DNA via mechanical and electrical cell-membrane disruption. Nat. Biomed. Eng. 1, 0039 (2017).

    Article  CAS  Google Scholar 

  24. Denais, C. M. et al. Nuclear envelope rupture and repair during cancer cell migration. Science 352, 353–358 (2016).

    Article  CAS  Google Scholar 

  25. Paul, C. D., Mistriotis, P. & Konstantopoulos, K. Cancer cell motility: lessons from migration in confined spaces. Nat. Rev. Cancer 17, 131–140 (2017).

    Article  CAS  Google Scholar 

  26. Gossett, D. R. et al. Hydrodynamic stretching of single cells for large population mechanical phenotyping. Proc. Natl Acad. Sci. USA 109, 7630–7635 (2012).

    Article  CAS  Google Scholar 

  27. Naim, B. et al. Passive and facilitated transport in nuclear pore complexes is largely uncoupled. J. Biol. Chem. 282, 3881–3888 (2007).

    Article  CAS  Google Scholar 

  28. Raab, M. et al. ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death. Science 352, 359–362 (2016).

    Article  CAS  Google Scholar 

  29. Irianto, J. et al. DNA damage follows repair factor depletion and portends genome variation in cancer cells after pore migration. Curr. Biol. 27, 210–223 (2017).

    Article  CAS  Google Scholar 

  30. Wapinski, O. L. et al. Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons. Cell 155, 621–635 (2013).

    Article  CAS  Google Scholar 

  31. Wapinski, O. L. et al. Rapid chromatin switch in the direct reprogramming of fibroblasts to neurons. Cell Rep. 20, 3236–3247 (2017).

    Article  CAS  Google Scholar 

  32. Wang, S., Riahi, R., Li, N., Zhang, D. D. & Wong, P. K. Single cell nanobiosensors for dynamic gene expression profiling in native tissue microenvironments. Adv. Mater. 27, 6034–6038 (2015).

    Article  CAS  Google Scholar 

  33. Song, Y. et al. Asymmetric cell division of fibroblasts is an early deterministic step to generate elite cells during cell reprogramming. Adv. Sci. 8, 2003516 (2021).

  34. De Carvalho, D. D., You, J. S. & Jones, P. A. DNA methylation and cellular reprogramming. Trends Cell Biol. 20, 609–617 (2010).

    Article  Google Scholar 

  35. Cho, S. et al. Mechanosensing by the lamina protects against nuclear rupture, DNA damage, and cell-cycle arrest. Dev. Cell 49, 920–935 (2019).

    Article  CAS  Google Scholar 

  36. Nmezi, B. et al. Concentric organization of A- and B-type lamins predicts their distinct roles in the spatial organization and stability of the nuclear lamina. Proc. Natl Acad. Sci. USA 116, 4307–4315 (2019).

    Article  CAS  Google Scholar 

  37. Lammerding, J. et al. Lamins A and C but not lamin B1 regulate nuclear mechanics. J. Biol. Chem. 281, 25768–25780 (2006).

    Article  CAS  Google Scholar 

  38. van Steensel, B. & Belmont, A. S. Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell 169, 780–791 (2017).

    Article  Google Scholar 

  39. Collas, P., Ali, T. M. L., Brunet, A. & Germier, T. Finding friends in the crowd: three-dimensional cliques of topological genomic domains. Front. Genet. 10, 602 (2019).

    Article  CAS  Google Scholar 

  40. Kind, J. et al. Single-cell dynamics of genome-nuclear lamina interactions. Cell 153, 178–192 (2013).

    Article  CAS  Google Scholar 

  41. Li, X. et al. Small-molecule-driven direct reprogramming of mouse fibroblasts into functional neurons. Cell Stem Cell 17, 195–203 (2015).

    Article  CAS  Google Scholar 

  42. Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948–951 (2008).

    Article  CAS  Google Scholar 

  43. Becker, J. S., Nicetto, D. & Zaret, K. S. H3K9me3-dependent heterochromatin: barrier to cell fate changes. Trends Genet. 32, 29–41 (2016).

    Article  CAS  Google Scholar 

  44. Sun, J., Chen, J., Mohagheghian, E. & Wang, N. Force-induced gene up-regulation does not follow the weak power law but depends on H3K9 demethylation. Sci. Adv. 6, eaay9095 (2020).

    Article  CAS  Google Scholar 

  45. Elosegui-Artola, A. et al. Force triggers YAP nuclear entry by regulating transport across nuclear pores. Cell 171, 1397–1410 (2017).

    Article  CAS  Google Scholar 

  46. Monroe, T. O. et al. YAP partially reprograms chromatin accessibility to directly induce adult cardiogenesis in vivo. Dev. Cell 48, 765–779 (2019).

    Article  CAS  Google Scholar 

  47. Gill, N. K. et al. A scalable filtration method for high throughput screening based on cell deformability. Lab Chip 19, 343–357 (2019).

    Article  CAS  Google Scholar 

  48. Sia, J., Yu, P., Srivastava, D. & Li, S. Effect of biophysical cues on reprogramming to cardiomyocytes. Biomaterials 103, 1–11 (2016).

    Article  CAS  Google Scholar 

  49. Peng, Q. et al. Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. Proc. Natl Acad. Sci. USA 115, E11681–E11690 (2018).

    Article  CAS  Google Scholar 

  50. Liu, L. et al. Integration of FRET and sequencing to engineer kinase biosensors from mammalian cell libraries. Nat. Commun. 12, 5031 (2021).

    Article  CAS  Google Scholar 

Download references

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.

Author information

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

Authors
  1. Yang Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jennifer Soto
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Binru Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tyler Hoffman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Weikang Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ninghao Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Qin Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Longwei Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Chau Ly
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Pak Kin Wong
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Yingxiao Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Amy C. Rowat
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Siavash K. Kurdistani
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Song Li
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Corresponding author

Correspondence to Song Li.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

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

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

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

Reporting Summary

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.

Source data

Source Data Fig. 1

Statistical source data.

Source Data Fig. 2

Statistical source data.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 5

Statistical source data.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41563-022-01312-3

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research