The p53 response in single cells is linearly correlated to the number of DNA breaks without a distinct threshold
© Loewer et al.; licensee BioMed Central Ltd. 2013
Received: 1 August 2013
Accepted: 13 November 2013
Published: 19 November 2013
The tumor suppressor protein p53 is activated by cellular stress. DNA double strand breaks (DSBs) induce the activation of the kinase ATM, which stabilizes p53 and activates its transcriptional activity. Single cell analysis revealed that DSBs induced by gamma irradiation trigger p53 accumulation in a series of pulses that vary in number from cell to cell. Higher levels of irradiation increase the number of p53 pulses suggesting that they arise from periodic examination of the damage by ATM. If damage persists, additional pulses of p53 are triggered. The threshold of damage required for activating a p53 pulse is unclear. Previous studies that averaged the response across cell populations suggested that one or two DNA breaks are sufficient for activating ATM and p53. However, it is possible that by averaging over a population of cells important features of the dependency between DNA breaks and p53 dynamics are missed.
Using fluorescent reporters we developed a system for following in individual cells the number of DSBs, the kinetics of repair and the p53 response. We found a large variation in the initial number of DSBs and the rate of repair between individual cells. Cells with higher number of DSBs had higher probability of showing a p53 pulse. However, there was no distinct threshold number of breaks for inducing a p53 pulse. We present evidence that the decision to activate p53 given a specific number of breaks is not entirely stochastic, but instead is influenced by both cell-intrinsic factors and previous exposure to DNA damage. We also show that the natural variations in the initial amount of p53, rate of DSB repair and cell cycle phase do not affect the probability of activating p53 in response to DNA damage.
The use of fluorescent reporters to quantify DNA damage and p53 levels in live cells provided a quantitative analysis of the complex interrelationships between both processes. Our study shows that p53 activation differs even between cells that have a similar number of DNA breaks. Understanding the origin and consequences of such variability in normal and cancerous cells is crucial for developing efficient and selective therapeutic interventions.
The tumor suppressor p53 mediates the cellular response to DNA damage by triggering cell cycle arrest and DNA repair or by evoking cellular senescence and apoptosis . These functions of p53 are essential for preserving genomic integrity and preventing neoplastic transformation. Loss of p53 activity, either by functional inactivation of its pathway or by gene mutation, is a frequent event in the onset and progression of many human malignancies [2, 3]. p53 function is also critical to the efficacy of cancer therapies that generate DNA damage, such as radiation and chemotherapy, and defects in p53 are often associated with therapy resistance [1, 4].
Within cells, levels of p53 protein are tightly controlled by several regulatory feedback loops that direct its stability and degradation. One major regulator of p53 is the E3 ubiquitin ligase Mdm2. p53 transcriptionally activates Mdm2 expression and Mdm2 targets p53 for degradation by the proteasome [5–8]. This interaction keeps p53 levels low under unstressed conditions. In response to cellular stress, p53 is activated through upstream kinases that induce post-translational modifications and disrupt the p53-Mdm2 interaction, allowing p53 to accumulate in the nucleus and induce the expression of target genes that mediate the cellular stress response .
DNA double strand breaks (DSBs) are particularly dangerous lesions for metazoan cells, as they can promote tumorigenesis by inducing chromosomal translocations and genomic instability upon misrepair . A complex molecular machinery recognizes the presence of free DNA ends and induces the rapid activation of the kinase ataxia-telangiectasia mutated (ATM) [11–13] (reviewed in ). Among the substrates of ATM is the histone variant H2AX, which is phosphorylated around the break site and serves as a binding platform for mediator proteins that propagate the DNA damage signal.
Activated ATM subsequently phosphorylates and stabilizes p53, which shows a series of highly regulated, undamped pulses in single cells upon induction of DSBs. The amplitude and duration of p53 pulses is independent of the damage dose, whereas the number of pulses increases with higher damage . These dynamics are a consequence of the feedback architecture of the p53 network. In addition to the p53-Mdm2 feedback, a second feedback mediated by the phosphatase Wip1 leads to periodic inactivation of ATM after a pulse of p53 accumulation . This allows cells to evaluate the state of their genome and re-initiate the response if damage persists . Moreover, p53 pulses after DSB induction are excitable: a complete p53 pulse of uniform amplitude and duration is induced independent of the strength of the damage signal [18, 19]. Several theoretical studies have suggested potential physiological roles for p53 pulses [20–22]. Recently we have shown that, indeed, the dynamical behavior of p53 carries information that controls cell fate. Cells that experience p53 pulses undergo temporary cell cycle arrest and recover from the damage, while cells in which p53 shows a non-oscillatory, sustained response undergo apoptosis or senescence .
Although much insight has been gained into the molecular mechanisms that regulate p53 pulses in response to DSBs  and their functional role , little is known about the quantitative relationship of DNA damage and p53 induction. Specifically, is there a fixed threshold of damage that is necessary for activating a p53 response? Western blot analysis of ATM phosphorylation in irradiated cells suggested that ATM is activated in a highly sensitive manner. Damage doses estimated to generate one or two DSBs were sufficient for a partial activation of ATM, and doses that generated more than twenty DSBs evoked a complete ATM response [12, 24]. Similarly, it was shown that cells are released from an ATM-mediated G2 checkpoint when less than approximately 20 DSBs remain . The sensitivity of the p53 pathway was measured by introducing serial dilutions of restriction enzymes or linearized double-stranded DNA molecules into cells that were subsequently assayed for p53 function. From these studies, it was estimated that a solitary DSB might suffice to activate a p53 response .
However, measurements in previous studies averaged over populations of cells or estimated dynamics from fixed cells. Remarkably, identical cells in a uniformly damaged population exhibit a large heterogeneity in their p53 response, with cells showing a variable number of pulses [15, 27]. It is conceivable that this variation arises from differences in the cells’ number of breaks or rates of repair. To gain a quantitative understanding of the relationship between the number of DSBs and p53 activation and to investigate the cause of heterogeneity in the p53 response, we established a cellular system that expresses fluorescent reporters to quantify both DNA damage and p53 dynamics in the same living cell.
Quantification of DSBs and their rate of repair in individual living cells
Determining the quantitative relationship between DSBs and activation of p53
Our quantification of DSBs in individual cells showed a large heterogeneity in the induction and rate of repair between cells exposed to the same damage dose (Figure 1). Is there a comparable heterogeneity in the p53 response? To test this, we treated cells with varying doses of the radiomimetic drug neocarcinostatin (NCS) and quantified the number of p53 pulses. As previously reported, higher levels of damage led on average to higher numbers of p53 pulses. However, even at high damage doses, cells showed a large variability in the p53 response (Figure 3D and [15, 18]).
To analyze in more detail the relationship between DNA damage and the induction of a new p53 pulse during the repair process, we quantified the number of DSBs after a p53 pulse in each individual cell and correlated it with the presence or absence of a subsequent pulse in the expected time frame (Figure 4E). We found that cells showing a subsequent p53 pulse tended to have higher levels of DNA damage (Figure 4F). However, the distributions of retained damage between cells that showed a subsequent p53 pulse and cells that did not were broadly overlapping, and we were unable to observe a fixed threshold number of DSBs that determine whether p53 will pulse or not.
To analyze the relationship between DNA breaks and the induction of p53, we measured the number of DSBs and p53 pulses in more than 350 cells post DNA damage. Cells were binned according to the number of DSBs, and the fraction of cells that induced a p53 pulse in each bin was plotted (Figure 5B). We expected to see a clear distinction between non-responding and responding cells at a defined threshold level of DSBs. Surprisingly, what we observed instead was a linear relationship between DNA damage and the p53 response: with higher amounts of damage, the fraction of cells responding with a p53 pulse increased continuously. This observation suggested that the amount of DNA damage in each cell determines the probability of activating a p53 response. For intermediate levels of breaks the p53 response is heterogeneous between cells; for example, only about 50% of cells with 20 breaks show a p53 pulse.
The decision to activate a p53 pulse depends on previous exposure to DNA damage and additional cell-intrinsic factors
Which internal cellular factors may affect the decision to pulse or not?
We previously showed that p53 is frequently activated in proliferating cells . As these spontaneous pulses of p53 activate negative feedback mechanisms, the sensitivity of the p53 network may depend on its previous activation state. Indeed, we saw here that previous exposure to DNA damage desensitizes the p53 response (Figure 6C). We, therefore, analyzed whether p53 absolute levels pre-damage influence the activation of p53 pulses post-damage. We found that cells with high initial p53 levels prior to NCS tended to have a lower probability of inducing a p53 pulse post-damage (Figure 7B). However, the limited correlation between both parameters indicates that basal p53 levels per se are not a good predictor for the subsequent p53 response. Note that since p53 initial levels were determined by measuring a single time point prior to NCS, cells with low levels of p53 might have just completed a p53 pulse and may still be in a desensitized state.
Finally, we tested if activation of p53 post-damage is determined by the cell cycle phase . It is possible that cells in different cell cycle phases vary in their sensitivity to DNA damage and have distinct thresholds of DSBs necessary for activating p53. To investigate this, we imaged damaged cells to quantify the dynamics of their DSB repair and p53 activation. We then calculated the cell cycle phase of the imaged cells by measuring their DNA content using diamidino-2-phenylindole (DAPI) staining (see Methods section for details). We found that cells that induce a p53 pulse and cells that do not activate a p53 response had similar cell cycle distributions (P-value 0.6337, Kolmogorov-Smirnov test, Figure 7C). To explore if different cell cycle phases vary in the threshold number of DSBs required to induce p53, we binned cells according to their initial numbers of DSBs and plotted both the fraction of cells inducing a p53 pulse and the proportion of S/G2 cells for each bin (Figure 7D). We found a uniform proportion of S/G2 cells across all bins indicating that cells in different cell cycle phases do not differ in their thresholds for activating a p53 pulse.
Our data indicate a linear relationship between the amount of DSBs in a cell and the probability that p53 will pulse. However, even for a fixed number of breaks, some cells show a pulse and others do not. Such heterogeneity in the response of individual cells has been frequently observed in other biological systems. For example, in response to low doses of the tumor necrosis factor, TNFα, nuclear localization of the transcription factor NFκB is only observed in a few cells. With higher doses of TNFα, more and more cells respond to the input . While the factors responsible for cell-cell variability were successfully identified for some biological systems [46, 47], in many cases the origin of heterogeneous cellular responses remains elusive.
One potential cause of heterogeneity between cells in the cellular response is that cells receive varying amounts of input, for example, ligands or drugs. Here, we directly measure the input each cell receives by enumerating the number of DSB. However, we found large variations in the induction of p53 even between cells that have similar numbers of DSBs, suggesting that it is not the level of DSB per se that explains the cell-cell variability in the decision to activate a p53 pulse.
By looking at the same cell in response to two rounds of DNA damage we showed that the p53 pathway does not reset after the response to the first stimulus, even when most of the damage is repaired. This indicates that the decision to activate a p53 pulse is affected by previous exposure to damage. In addition, the probability to show a second pulse was higher in cells that also had a pulse in response to the first stimulus suggesting that the decision whether to activate p53 in response to low amounts of DSBs is not entirely stochastic, but is likely affected by the internal state of individual cells. Although our analysis of the three cellular processes most likely to affect the sensitivity of the p53 network (rate of DNA repair, cell cycle phase and initial levels of p53) did not reveal a major influence, there are other factors that may contribute to setting individual thresholds for p53 activation. Such factors might include the expression of key proteins that regulate p53, such as the negative regulator Mdm2. The stimulus provided by DSBs may not be sufficient to initiate a p53 pulse in cells that express high levels of Mdm2. Interestingly, it was recently reported that tumor growth factor β (TGFβ) signaling attenuates the p53-mediated stress response . Other signaling pathways may interact with p53 as well. Using our experimental system, it would now be feasible to alter the signal state of cells systematically and determine the sensitivity of the p53 response.
Our analyses showed that some cells do not activate p53 even at high levels of DNA damage. One possibility for this observation is that the induction of p53 in response to DSBs is highly deregulated in cancer cells. It will be important to determine if normal, non-transformed cells are more uniform in their p53 response and show activation of p53 at a low number of DSBs. Similar investigations carried out in multiple tumor cell lines will enable an understanding of their potential to uniformly induce p53 in response to DNA damage and will provide insights into their sensitivity to radiation and chemotherapeutic treatments.
In this work we looked at the relationship between DSB and p53 induction, and the variation between cells, in an unperturbed system. One question that arises from our study is whether this relationship can be altered when DNA repair is inhibited. This is especially important as major pharmaceutical companies have begun significant projects attempting to inhibit specific proteins in DNA repair pathways, with the goal of using DNA repair inhibitors in combination with DNA-damaging treatments to prevent repair and trigger death or cell cycle arrest. The same question can be asked in the opposite direction – how does perturbation of p53 dynamics affect the rate of repair? Recent studies from our group and others have shown that the dynamical behavior of p53 encodes critical cell-fate decisions [23, 39]; hence, understanding how perturbations of p53 and key repair proteins will provide new and important insights for the treatment of tumors with different genetic profiles and repair deficiencies.
In this study we combined a reporter for DSBs with a fluorescent reporter for p53 and quantified the level of damage and the dynamics of p53 in the same, living cell. We found a linear correlation between the number of DSBs and the probability for activating a p53 pulse; more DSBs increase the probability that a cell will have a p53 pulse. However, there was no distinct threshold of damage for inducing a p53 response. By re-damaging cells we showed that the decision to activate p53 is not entirely stochastic but is determined by both previous exposure to DNA damage and additional internal cell-specific factors. However, cell cycle phase, the initial levels of p53 and the rate of repair are not major determinants of this decision. The use of fluorescent reporters to quantify DNA damage and p53 levels in live cells now presents powerful tools for providing an integrated quantitative understanding of their complex interrelationships in normal and cancerous cells.
Human breast cancer epithelial MCF7 and A549 cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 μg/mL streptomycin and 250 ng/mL fungizone (Gemini Bio-Products, West Sacramento, CA, USA). RPE1-hTERT cells were grown in (D)MEM/F12 medium supplemented with 10% fetal calf serum, penicillin, streptomycin and fungizone. When required, the medium was supplemented with selective antibiotics (400 μg/mL G418, 5 μg/mL blasticidin, 50 μg/mL hygromycin). When indicated, medium was replaced with fresh medium supplemented with neocarzinostatin (National Cancer Institute, Bethesda, MD, USA) or with the DNA-PK inhibitor NU7026 (used at 10 μM, Sigma-Aldrich, St. Louis, MO, USA) during experiments. Irradiation treatments were carried out in a 60Co irradiator. Cell cycle distributions were analyzed by DAPI staining.
Cell line construction
The original pCMV-EGFP-53BP1 construct was kindly provided by Prof. Yasuhisa Adachi (Jullien et al. ). We generated our pEF1α-mCherry-53BP1 plasmid by replacing GFP with mCherry and combining this fluorescent protein-cDNA fragment with the EF1α promoter in a vector harboring a blasticidin resistance cassette using standard molecular biology techniques. This plasmid was stably transfected into MCF7 cells using FuGENE6 (Hoffmann-La Roche, USA), which were maintained in selective media and sorted into single cells using fluorescence activated cell sorting to generate a clonal population. Our pMT-p53-Venus plasmid has been previously reported . Stable, clonal cell lines were established as described above.
For constructing the pUbC-H2B-CFP vector, the H2B coding sequence was amplified by PCR from the vector pBOS-H2BGFP (BD Bioscience, San Jose, CA, USA). Using Multiside Gateway technology (Invitrogen, Eugene, OR, USA), the PCR product was combined with the Ubiquitin C promoter and CFP tag in a lentiviral vector harboring a hygromycin resistance cassette. This plasmid was transfected into 293T cells together with the corresponding packaging plasmids to generate replication-defective viral particles using standard protocols, which were used to stably infect the engineered MCF7 cell line.
Cells were plated in RMPI lacking riboflavin and phenol red in poly-D-lysine coated glass-bottom plates (MatTek Corporation, Ashland, MA, USA) 24 hours prior to microscopy}. The medium was supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 250 ng/mL fungizone (Gemini Bio-Products) and 10 mM HEPES. Cells were imaged on a Nikon Eclipse Ti inverted microscope with a Plan Apo 60X oil objective (NA 1.4), Hamamatsu Orca ER camera and a Perfect Focus System. The microscope was surrounded by a custom enclosure to maintain constant temperature and atmosphere. The filter sets used were CFP: 436/20 nm; 455 nm; 480/40 nm (excitation; beam splitter; emission filter, respectively), YFP: 500/20 nm; 515 nm; 535/30 nm; and mCherry: 560/40 nm; 585 nm; 630/75 nm (Chroma, Bellows Falls, VT, USA). Images were acquired every 15 to 20 minutes in the phase, YFP and CFP channels and every 15 to 40 minutes in the mCherry channel for 8 to 12 hours. We acquired seven z-sections with a step size of 1 μm in the mCherry channel. Image acquisition was controlled by MetaMorph software (Molecular Devices, Sunnyvale, CA, USA).
For analyzing cell cycle distribution, cells were imaged for six hours post-damage as described above, fixed with 2% paraformaldehyde, permeabilized with 0.2% Triton/PBS and stained with Hoechst (Molecular Probes, Eugene, OR, USA). We imaged thousands of cells and quantified the integrated fluorescence intensity of the Hoechst signal by image analysis using automated thresholding and watershed algorithms to segment individual nuclei. Using the nuclear intensity of the DNA dye, we established a histogram of the distribution of DNA content that allowed assigning a cell cycle phase to each cell. We identified cells analyzed in the preceding time-lapse experiment using gridded cover slips.
Custom written algorithms in Matlab (Mathworks) were used to analyze 53BP1 foci. In brief, image stacks were first enhanced using blind deconvolution (AutoQuant) and were then converted to two-dimensional maximum projections. Nuclei were segmented using the H2B-CFP signal. For each nucleus, the background signal was first reduced by a Tophat transformation, following which the edges were detected using the Canny method. Foci were determined from the edges using morphological transformations and optimal thresholding. To determine the effect of thresholding on our foci measurements, we increased and decreased the threshold by a factor of up to 0.3 and 1.6, respectively, and determined the effect on foci quantification. Touching foci were separated by a marker-directed watershed algorithm. We analyzed p53 trajectories in single cells using previously described algorithms . The raw data are available on request.
Cells were grown on number 1.5 glass coverslips coated with poly-L-lysine (Sigma-Aldrich, St. Louis, MO, USA). They were fixed with 2% paraformaldehyde, permeabilized with 0.2% Triton/PBS and blocked with 5% goat serum supplemented with 1% bovine serum albumin. Cells were treated with primary antibody to detect γ-H2AX (mouse monoclonal JBW301, Upstate Millipore, Billerica, MA, USA, 1:700 dilution), washed and treated with secondary antibody conjugated with Alexa Fluor 647 (Molecular Probes). After washing, cells were stained with Hoechst (Molecular Probes) and embedded in Prolong Antifade (Invitrogen). Immunofluorescence preparations were imaged on the microscope described for live cell imaging and automated segmentation was performed in Matlab (MathWorks) with algorithms from CellProfiler .
We thank Yasuhisa Adachi for providing the GFP-53BP1 construct; Yangqing Xu, Jared Toettcher and Ran Kafri for help with image analysis; Megha Padi, Giorgio Gaglia, Jose Reyes and Kyle Karhohs for help with the RPE1 line expressing the p53 fluorescent reporter; the Nikon Imaging Center at Harvard Medical School for support with live-cell imaging and deconvolution; and members of the Lahav and Loewer labs for helpful discussions. This research was supported by National Institutes of Health grant GM083303.
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