title: 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 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 µm2 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.
authors.affiliation: Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Walter
authors.initials: W
authors.lastname: Georgescu
authors.affiliation: Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Alma
authors.initials: A
authors.lastname: Osseiran
authors.affiliation: Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Maria
authors.initials: M
authors.lastname: Rojec
authors.affiliation: Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, United States of America.
authors.forename: Yueyong
authors.initials: Y
authors.lastname: Liu
authors.affiliation: CNRS, UMR 6158, LIMOS, F-63173, Aubiere, France.
authors.forename: Maxime
authors.initials: M
authors.lastname: Bombrun
authors.affiliation: Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Tang
authors.affiliation: Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Sylvain V
authors.initials: SV
authors.lastname: Costes
mesh_terms: D000465:Algorithms; D001940:Breast / Q000166:cytology; D002460:Cell Line; D002467:Cell Nucleus / Q000378:metabolism; D058948:Cell Tracking / Q000295:instrumentation / Q000379:methods*; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D004847:Epithelial Cells / Q000166:cytology* / Q000378:metabolism; D005260:Female; D006657:Histones / Q000378:metabolism*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D047908:Intracellular Signaling Peptides and Proteins / Q000378:metabolism; D007700:Kinetics; D008164:Luminescent Proteins / Q000737:chemistry; D008856:Microscopy, Fluorescence / Q000295:instrumentation / Q000379:methods*; D016011:Normal Distribution; D011839:Radiation, Ionizing; D000071857:Tumor Suppressor p53-Binding Protein 1; D014965:X-Rays; D000097573:Red Fluorescent Protein
chemical_list: D006657:Histones; D047908:Intracellular Signaling Peptides and Proteins; D008164:Luminescent Proteins; D000071857:Tumor Suppressor p53-Binding Protein 1; D000097573:Red Fluorescent Protein; C498301:TP53BP1 protein, human