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Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells.

Publication ,  Journal Article
Kim, JJ; Bennett, NK; Devita, MS; Chahar, S; Viswanath, S; Lee, EA; Jung, G; Shao, PP; Childers, EP; Liu, S; Kulesa, A; Garcia, BA; Hwang, NS ...
Published in: Scientific reports
January 2017

While distinct stem cell phenotypes follow global changes in chromatin marks, single-cell chromatin technologies are unable to resolve or predict stem cell fates. We propose the first such use of optical high content nanoscopy of histone epigenetic marks (epi-marks) in stem cells to classify emergent cell states. By combining nanoscopy with epi-mark textural image informatics, we developed a novel approach, termed EDICTS (Epi-mark Descriptor Imaging of Cell Transitional States), to discern chromatin organizational changes, demarcate lineage gradations across a range of stem cell types and robustly track lineage restriction kinetics. We demonstrate the utility of EDICTS by predicting the lineage progression of stem cells cultured on biomaterial substrates with graded nanotopographies and mechanical stiffness, thus parsing the role of specific biophysical cues as sensitive epigenetic drivers. We also demonstrate the unique power of EDICTS to resolve cellular states based on epi-marks that cannot be detected via mass spectrometry based methods for quantifying the abundance of histone post-translational modifications. Overall, EDICTS represents a powerful new methodology to predict single cell lineage decisions by integrating high content super-resolution nanoscopy and imaging informatics of the nuclear organization of epi-marks.

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Published In

Scientific reports

DOI

EISSN

2045-2322

ISSN

2045-2322

Publication Date

January 2017

Volume

7

Start / End Page

39406

Related Subject Headings

  • Optical Imaging
  • Mesenchymal Stem Cells
  • Image Processing, Computer-Assisted
  • Humans
  • Epigenesis, Genetic
  • Cytological Techniques
  • Chromatin
  • Cell Nucleus
  • Biological Variation, Population
 

Citation

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MLA
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Kim, J. J., Bennett, N. K., Devita, M. S., Chahar, S., Viswanath, S., Lee, E. A., … Moghe, P. V. (2017). Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells. Scientific Reports, 7, 39406. https://doi.org/10.1038/srep39406
Kim, Joseph J., Neal K. Bennett, Mitchel S. Devita, Sanjay Chahar, Satish Viswanath, Eunjee A. Lee, Giyoung Jung, et al. “Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells.Scientific Reports 7 (January 2017): 39406. https://doi.org/10.1038/srep39406.
Kim JJ, Bennett NK, Devita MS, Chahar S, Viswanath S, Lee EA, et al. Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells. Scientific reports. 2017 Jan;7:39406.
Kim, Joseph J., et al. “Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells.Scientific Reports, vol. 7, Jan. 2017, p. 39406. Epmc, doi:10.1038/srep39406.
Kim JJ, Bennett NK, Devita MS, Chahar S, Viswanath S, Lee EA, Jung G, Shao PP, Childers EP, Liu S, Kulesa A, Garcia BA, Becker ML, Hwang NS, Madabhushi A, Verzi MP, Moghe PV. Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells. Scientific reports. 2017 Jan;7:39406.

Published In

Scientific reports

DOI

EISSN

2045-2322

ISSN

2045-2322

Publication Date

January 2017

Volume

7

Start / End Page

39406

Related Subject Headings

  • Optical Imaging
  • Mesenchymal Stem Cells
  • Image Processing, Computer-Assisted
  • Humans
  • Epigenesis, Genetic
  • Cytological Techniques
  • Chromatin
  • Cell Nucleus
  • Biological Variation, Population