Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis
Abstract
Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolvemore »
- Authors:
-
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Harvard Medical School, Boston, MA (United States)
- CNRS, Aubiere (France)
- Univ. of Hong Kong (Hong Kong)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1212447
- Alternate Identifier(s):
- OSTI ID: 1469157
- Report Number(s):
- LBNL-185582
Journal ID: ISSN 1932-6203
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 6; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; ionizing radiation; cell death; DNA repair; DNA damage; epithelial cells; image processing; linear programming; nuclear bodies
Citation Formats
Georgescu, Walter, Osseiran, Alma, Rojec, Maria, Liu, Yueyong, Bombrun, Maxime, Tang, Jonathan, Costes, Sylvain V., and Huen, Michael Shing-Yan. Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis. United States: N. p., 2015.
Web. doi:10.1371/journal.pone.0129438.
Georgescu, Walter, Osseiran, Alma, Rojec, Maria, Liu, Yueyong, Bombrun, Maxime, Tang, Jonathan, Costes, Sylvain V., & Huen, Michael Shing-Yan. Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis. United States. https://doi.org/10.1371/journal.pone.0129438
Georgescu, Walter, Osseiran, Alma, Rojec, Maria, Liu, Yueyong, Bombrun, Maxime, Tang, Jonathan, Costes, Sylvain V., and Huen, Michael Shing-Yan. Wed .
"Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis". United States. https://doi.org/10.1371/journal.pone.0129438. https://www.osti.gov/servlets/purl/1212447.
@article{osti_1212447,
title = {Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis},
author = {Georgescu, Walter and Osseiran, Alma and Rojec, Maria and Liu, Yueyong and Bombrun, Maxime and Tang, Jonathan and Costes, Sylvain V. and Huen, Michael Shing-Yan},
abstractNote = {Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 microm2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when too many DSB occur at once. High doses of ionizing radiation lead to RIF merging into repair domains which in turn increases DSB proximity and misrepair. Such finding may therefore be critical to explain the supralinear dose dependence for chromosomal rearrangement and cell death measured after exposure to ionizing radiation.},
doi = {10.1371/journal.pone.0129438},
journal = {PLoS ONE},
number = 6,
volume = 10,
place = {United States},
year = {Wed Jun 24 00:00:00 EDT 2015},
month = {Wed Jun 24 00:00:00 EDT 2015}
}
Web of Science
Figures / Tables:
Works referenced in this record:
Irradiation of Juvenile, but not Adult, Mammary Gland Increases Stem Cell Self-Renewal and Estrogen Receptor Negative Tumors: Radiation Induces Mammary Stem Cell Self-Renewal
journal, February 2014
- Tang, Jonathan; Fernandez-Garcia, Ignacio; Vijayakumar, Sangeetha
- STEM CELLS, Vol. 32, Issue 3
Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre
journal, May 2003
- Lisby, Michael; Mortensen, Uffe H.; Rothstein, Rodney
- Nature Cell Biology, Vol. 5, Issue 6, p. 572-577
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images
journal, May 2010
- Ruusuvuori, Pekka; Äijö, Tarmo; Chowdhury, Sharif
- BMC Bioinformatics, Vol. 11, Issue 1
Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains
journal, January 2007
- Costes, Sylvain V.; Ponomarev, Artem; Chen, James L.
- PLoS Computational Biology, Vol. 3, Issue 8, Article No. e155
Chromatin mobility is increased at sites of DNA double-strand breaks
journal, February 2012
- Krawczyk, P. M.; Borovski, T.; Stap, J.
- Journal of Cell Science, Vol. 125, Issue 9
Cellular responses to DNA double-strand breaks after low-dose γ-irradiation
journal, April 2009
- Asaithamby, Aroumougame; Chen, David J.
- Nucleic Acids Research, Vol. 37, Issue 12, p. 3912-3923
Live cell microscopy analysis of radiation-induced DNA double-strand break motion
journal, February 2009
- Jakob, B.; Splinter, J.; Durante, M.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 9, p. 3172-3177
Increased chromosome mobility facilitates homology search during recombination
journal, April 2012
- Miné-Hattab, Judith; Rothstein, Rodney
- Nature Cell Biology, Vol. 14, Issue 5
Chromosome breakage after G2 checkpoint release
journal, March 2007
- Deckbar, Dorothee; Birraux, Julie; Krempler, Andrea
- The Journal of Cell Biology, Vol. 176, Issue 6
Identification of genetic loci that control mammary tumor susceptibility through the host microenvironment
journal, March 2015
- Zhang, Pengju; Lo, Alvin; Huang, Yurong
- Scientific Reports, Vol. 5, Issue 1
Common genetic determinants of vitamin D insufficiency: a genome-wide association study
journal, July 2010
- Wang, Thomas J.; Zhang, Feng; Richards, J. Brent
- The Lancet, Vol. 376, Issue 9736
DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin
journal, April 2011
- Jakob, Burkhard; Splinter, Jörn; Conrad, Sandro
- Nucleic Acids Research, Vol. 39, Issue 15, p. 6489-6499
Dynamics of DNA Double-Strand Breaks Revealed by Clustering of Damaged Chromosome Domains
journal, January 2004
- Aten, Jacob A.; Stap, Jan; Krawczyk, Przemek M.
- Science, Vol. 303, Issue 5654, p. 92-95
Combinatorial DNA Damage Pairing Model Based on X-Ray-Induced Foci Predicts the Dose and LET Dependence of Cell Death in Human Breast Cells
journal, September 2014
- Vadhavkar, Nikhil; Pham, Christopher; Georgescu, Walter
- Radiation Research, Vol. 182, Issue 3
Fiji: an open-source platform for biological-image analysis
journal, June 2012
- Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin
- Nature Methods, Vol. 9, Issue 7
Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair
journal, March 2011
- Chiolo, Irene; Minoda, Aki; Colmenares, Serafin U.
- Cell, Vol. 144, Issue 5, p. 732-744
Positional stability of single double-strand breaks in mammalian cells
journal, May 2007
- Soutoglou, Evi; Dorn, Jonas F.; Sengupta, Kundan
- Nature Cell Biology, Vol. 9, Issue 6
CellAnimation: an open source MATLAB framework for microscopy assays
journal, November 2011
- Georgescu, Walter; Wikswo, John P.; Quaranta, Vito
- Bioinformatics, Vol. 28, Issue 1
Evidence for formation of DNA repair centers and dose-response nonlinearity in human cells
journal, December 2011
- Neumaier, T.; Swenson, J.; Pham, C.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 2, p. 443-448
Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery
journal, April 2012
- Dion, Vincent; Kalck, Véronique; Horigome, Chihiro
- Nature Cell Biology, Vol. 14, Issue 5
Nuclear dynamics of radiation-induced foci in euchromatin and heterochromatin
journal, October 2013
- Chiolo, Irene; Tang, Jonathan; Georgescu, Walter
- Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 750, Issue 1-2
DNA double-strand break repair: From mechanistic understanding to cancer treatment
journal, July 2007
- Helleday, T.; Lo, J.; Vangent, D.
- DNA Repair, Vol. 6, Issue 7
Cancer risks attributable to low doses of ionizing radiation: Assessing what we really know
journal, November 2003
- Brenner, D. J.; Doll, R.; Goodhead, D. T.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 24
Persistence of γ-H2AX and 53BP1 foci in proliferating and non-proliferating human mammary epithelial cells after exposure to γ-rays or iron ions
journal, January 2011
- Groesser, Torsten; Chang, Hang; Fontenay, Gerald
- International Journal of Radiation Biology, Vol. 87, Issue 7
Binary Image Segmentation of Aggregates Based on Polygonal Approximation and Classification of Concavities
journal, October 1998
- Wang, W. X.
- Pattern Recognition, Vol. 31, Issue 10
Getting the dose–response wrong: why hormesis became marginalized and the threshold model accepted
journal, February 2009
- Calabrese, Edward J.
- Archives of Toxicology, Vol. 83, Issue 3
Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair
journal, March 2011
- Chiolo, Irene; Minoda, Aki; Colmenares, Serafin U.
- Cell, Vol. 144, Issue 5, p. 732-744
DNA double-strand break repair: From mechanistic understanding to cancer treatment
journal, July 2007
- Helleday, T.; Lo, J.; Vangent, D.
- DNA Repair, Vol. 6, Issue 7
Nuclear dynamics of radiation-induced foci in euchromatin and heterochromatin
journal, October 2013
- Chiolo, Irene; Tang, Jonathan; Georgescu, Walter
- Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 750, Issue 1-2
Testiculopathy and vitamin D insufficiency
journal, October 2010
- Foresta, Carlo; Selice, Riccardo; Di Mambro, Antonella
- The Lancet, Vol. 376, Issue 9749
Insight into sites
journal, November 1996
- Savage, John R. K.
- Mutation Research/Reviews in Genetic Toxicology, Vol. 366, Issue 2, p. 81-95
Positional stability of single double-strand breaks in mammalian cells
journal, May 2007
- Soutoglou, Evi; Dorn, Jonas F.; Sengupta, Kundan
- Nature Cell Biology, Vol. 9, Issue 6
Increased chromosome mobility facilitates homology search during recombination
journal, April 2012
- Miné-Hattab, Judith; Rothstein, Rodney
- Nature Cell Biology, Vol. 14, Issue 5
Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre
journal, May 2003
- Lisby, Michael; Mortensen, Uffe H.; Rothstein, Rodney
- Nature Cell Biology, Vol. 5, Issue 6, p. 572-577
Identification of genetic loci that control mammary tumor susceptibility through the host microenvironment
journal, March 2015
- Zhang, Pengju; Lo, Alvin; Huang, Yurong
- Scientific Reports, Vol. 5, Issue 1
Live cell microscopy analysis of radiation-induced DNA double-strand break motion
journal, February 2009
- Jakob, B.; Splinter, J.; Durante, M.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 9, p. 3172-3177
Cancer risks attributable to low doses of ionizing radiation: Assessing what we really know
journal, November 2003
- Brenner, D. J.; Doll, R.; Goodhead, D. T.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 24
CellAnimation: an open source MATLAB framework for microscopy assays
journal, November 2011
- Georgescu, Walter; Wikswo, John P.; Quaranta, Vito
- Bioinformatics, Vol. 28, Issue 1
Cellular responses to DNA double-strand breaks after low-dose γ-irradiation
journal, April 2009
- Asaithamby, Aroumougame; Chen, David J.
- Nucleic Acids Research, Vol. 37, Issue 12, p. 3912-3923
Chromatin mobility is increased at sites of DNA double-strand breaks
journal, February 2012
- Krawczyk, P. M.; Borovski, T.; Stap, J.
- Journal of Cell Science, Vol. 125, Issue 9
Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains
journal, January 2007
- Costes, Sylvain V.; Ponomarev, Artem; Chen, James L.
- PLoS Computational Biology, Vol. 3, Issue 8, Article No. e155
Solid Cancer Incidence in Atomic Bomb Survivors: 1958–1998
journal, July 2007
- Preston, D. L.; Ron, E.; Tokuoka, S.
- Radiation Research, Vol. 168, Issue 1
Positional Stability of Damaged Chromatin Domains along Radiation Tracks in Mammalian Cells
journal, April 2009
- Jakob, B.; Splinter, J.; Taucher-Scholz, G.
- Radiation Research, Vol. 171, Issue 4, p. 405-418
Comparison of Several Radiation Effects in Human MCF10A Mammary Epithelial Cells Cultured as 2D Monolayers or 3D Acinar Stuctures in Matrigel
journal, June 2009
- Lin, Yu-Fen; Nagasawa, Hatsumi; Peng, Yuanlin
- Radiation Research, Vol. 171, Issue 6
Imaging Features that Discriminate between Foci Induced by High- and Low-LET Radiation in Human Fibroblasts
journal, May 2006
- Costes, Sylvain V.; Boissière, Arnaud; Ravani, Shraddha
- Radiation Research, Vol. 165, Issue 5, p. 505-515
DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin
text, January 2022
- Jakob, Burkhard; Splinter, Jörn; Conrad, Sandro
- Oxford University Press
Persistence of γ-H2AX and 53BP1 foci in proliferating and non-proliferating human mammary epithelial cells after exposure to γ-rays or iron ions
journal, January 2011
- Groesser, Torsten; Chang, Hang; Fontenay, Gerald
- International Journal of Radiation Biology, Vol. 87, Issue 7
Works referencing / citing this record:
Predicting DNA damage foci and their experimental readout with 2D microscopy: a unified approach applied to photon and neutron exposures
journal, September 2019
- Barbieri, Sofia; Babini, Gabriele; Morini, Jacopo
- Scientific Reports, Vol. 9, Issue 1
Live cell imaging combined with high-energy single-ion microbeam
journal, March 2016
- Guo, Na; Du, Guanghua; Liu, Wenjing
- Review of Scientific Instruments, Vol. 87, Issue 3
Heterogeneity of γH2AX Foci Increases in Ex Vivo Biopsies Relative to In Vivo Tumors
journal, September 2018
- Rassamegevanon, Treewut; Löck, Steffen; Baumann, Michael
- International Journal of Molecular Sciences, Vol. 19, Issue 9
Evaluating biomarkers to model cancer risk post cosmic ray exposure
journal, June 2016
- Sridharan, Deepa M.; Asaithamby, Aroumougame; Blattnig, Steve R.
- Life Sciences in Space Research, Vol. 9
Optimizing radiotherapy protocols using computer automata to model tumour cell death as a function of oxygen diffusion processes
journal, May 2017
- Paul-Gilloteaux, Perrine; Potiron, Vincent; Delpon, Grégory
- Scientific Reports, Vol. 7, Issue 1
Predicting DNA damage foci and their experimental readout with 2D microscopy: a unified approach applied to photon and neutron exposures
journal, September 2019
- Barbieri, Sofia; Babini, Gabriele; Morini, Jacopo
- Scientific Reports, Vol. 9, Issue 1
Vive la radiorésistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization
journal, February 2018
- Cortese, Franco; Klokov, Dmitry; Osipov, Andreyan
- Oncotarget, Vol. 9, Issue 18