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Automated Comet Assay Imaging and Dual-Mask Analysis to Determine DNA Damage on an Individual Comet BasisDownload
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July 07, 2016
Mammalian cells incur DNA damage and alterations as a result of internal factors, such as stress, environment, oxidation and metabolism, as well as exposure to external stimuli, such as chemical compounds, UV and cosmic radiation. Genotoxicity studies aim to identify and understand the mechanisms of DNA damage and repair, and also to seek methods of pathway regulation and dysregulation for improved therapeutic success. Beyond therapeutic implications, a number of industries, including cosmetics, food/beverage, chemical and mining/ oil/petroleum, incorporate genotoxicity testing to characterize the safety profile of their products.
The comet assay, or single cell gel electrophoresis (SCGE), is well established as a direct measure of DNA damage in genotoxicity studies. Typically, neutral comet is used to detect DNA doublestranded breaks while alkali comet detects a wider breadth of DNA lesions including DNA single-stranded breaks and abasic sites. Using this method, cells exposed to a test compound are embedded in agarose, lysed to remove membranes and histones, treated with an alkali solution to unwind and denature the DNA (in the case of alkali comet), and subjected to an electric field to separate DNA fragments from intact DNA molecules based on differences in charge to mass ratio. Upon fluorescent staining and imaging, the result appears similar to a comet, where DNA fragments (comet tail) migrate through the gel matrix while intact/undamaged DNA remains static (comet head). Commonly generated metrics such as percentage of fragmented DNA in the comet tail and tail moment are a direct measure of cellular DNA damage following treatment.
Fluorescence microscopy is the standard method for measuring these parameters. Typically, detection requires operator intervention for image capture and analysis which tends to be a slow process, limiting sample throughput. Furthermore, operator subjectivity during analysis can also skew results as only comets that meet personal criteria are chosen for inclusion in the data set. Incorporating automated image acquisition and analysis into the assay workflow can help to enhance sample throughput, assay robustness and accuracy, while also increasing the overall laboratory efficiency.
The ability to generate data on a per-comet basis is also preferable when measuring the effect of a potential damaging or healing agent. While average percent DNA in the comet tail and tail moment data allows for assessment of a population captured within an image or set of images, it does not allow for the most efficient scrutiny of individual comets to ascertain why damage was seen at a particular level within the imaged sample set. Incorporating methods to calculate results from multiple areas linked to a particular comet provides population and individual comet data; providing a more complete data set.
Here we demonstrate a method to automate detection and analysis of high throughput cometbased genotoxicity data. Using a novel cell imaging multi-mode reader and high-density slides, 96 individual samples may be processed and analyzed simultaneously. Advanced analysis software with dual-mask capability links comet head and tail information per comet so that realtime population-level data, as well as individual comet data, are available for use in percent DNA in the tail and comet tail moment calculations.
Materials and Methods
U251 (human glioma) cells (Catalog No. 09063001) were purchased from Sigma Aldrich (Saint Louis, MO).
Assay and Experimental Components
LMAgarose (Catalog No. 4250-050-02), 96 well CometSlides (Catalog No. 4253-096-03), Lysis Buffer (Catalog No. 4250-050-01) and CometAssay Electrophoresis System (Catalog No. 4250-050-ES) were obtained from Trevigen, Inc. (Gaithersburg, MD). SYBR® Gold Nucleic Acid Gel Stain (Catalog No. S-11494, ThermoFisher, Carlsbad, CA), diluted to 1x, was also supplied by Trevigen, Inc. The known topoisomerase-1 inhibitor (cytotoxin), camptothecin (Catalog No. 208925) was purchased from EMD Millipore (Billerica, MA).
Cytation 5 is a modular multi-mode microplate reader combined with automated digital microscopy. Filter- and monochromator-based microplate reading are available, along with laser-based excitation for Alpha assays. The microscopy module provides up to 60x magnification in fluorescence, brightfield, color brightfield and phase contrast. With special emphasis on live-cell assays, Cytation 5 features shaking, temperature control to 65 °C, CO2/O2 gas control and dual injectors for kinetic assays. The instrument was used to image the stained DNA using the GFP imaging channel. Integrated Gen5™ Microplate Reader and Imager Software controls Cytation 5, and also automates image capture, analysis and processing. A two-part adapter (Catalog No. 1322144) was used when imaging the 96-well CometSlide to ensure consistent positioning.
Standard Alkaline Comet Assay Performance
Cultured U251 cells were treated with concentrations of camptothecin ranging from 0-10 μM, embedded in 1% low melting agarose, and immobilized on a specially treated 96-well slide to promote adherence. The slide was then immersed in Lysis Buffer for 30-60 minutes at 4 ºC to remove membranes and histones from the DNA, followed by a 30-minute room temperature equilibration in pH 13 alkaline electrophoresis buffer to unwind and denature the DNA. Alkaline electrophoresis was performed for 30-45 minutes at 4 ºC and 1V/cm using the CometAssay Electrophoresis System. Slides were neutralized and agarose dried down before staining the DNA with SYBR Gold. Stained slides were then imaged by the Cytation 5 using the parameters listed in Table 1.
Table 1. Automated comet imaging parameters.
Gen5 Dual Mask Comet Analysis
Primary mask cellular analysis criteria (Table 2) were applied to automatically place object masks around comet heads in each captured image. Auto threshold was selected and the slider bar moved to a value of -35. Secondary mask cellular analysis criteria (Table 3) were then also applied to place a linked additional mask around the entire comet.
Table 2. Comet head analysis parameters.
Table 3. Total comet analysis parameters.
Results and Discussion
Automated 96-Well Comet Imaging and Pre-Processing
U251 cells were exposed to various concentrations of camptothecin and processed using the 96-well CometSlide format. Cytation 5 automatically imaged the CometSlide using previously determined well locations in the plate layout for the incorporated slide, thus eliminating manual determination of comet locations. Exposure parameters were set such that fluorescence values per pixel were within the CCD camera’s quantifiable range, while autofocus and image montage creation were also performed.
Following image capture, multiple steps were automatically carried out in Gen5 Software to properly prepare each image for analysis. These steps improve robustness of the generated data from each test sample. The first step processed the image to remove background signal using the criteria in Table 4. The rolling ball diameter value of 1500 μm was chosen to ensure that adequate areas of the image were included in the determination of background signal from true comet signal. As the signal from the tail portion of the comet can be relatively weak, depending on the level of DNA damage, analysis of smaller portions of the image to determine background signal can skew results, causing signal from the comet tails to be falsely removed. Incorporation of the larger diameter creates pre-processed images with a reduced background, for more accurate identification of the fluorescent signal from actual comets without affecting final results.
Table 4. Image Pre-processing parameters.
Figure 1. Image background signal removal via pre-processing. Zoomed 2.5x images (A) before; (B) or after Table 4 pre-processing criteria applied using Gen5 Software. Inset graphs in (A) and (B) represent a cross-section of green fluorescence intensity across a single comet obtained using the Gen line analysis tool. The individual comet measured is visible immediately to the right of the inset graph. The length of the line used is represented by the x-axis of the inset graph.
In the second step, Gen5 automatically stitched together the two individually captured images in their original configuration so that comet placement in the final combined image was identical to that seen in the well.
Figure 2. Image stitching. 2.5x images of (A and B) individual image montage tiles; and (C) final stitched image using Gen5 Software.
The final images accurately portrayed the extent of DNA damage from each test condition, where untreated comets (Figure 3A) appeared as well-defined spheres, or comet heads, while those treated with camptothecin showed progressive DNA damage in the form of a distinct comet tail (Figures 3B and C).
Figure 3. Automated comet analyses based on user-programmed cellular analysis parameters. Images captured using a 2.5x objective, 1x2 montage images of stained comets from single well using U251 cells exposed to (A) 0 μM (untreated) camptothecin; (B) 0.1 μM camptothecin; (C) 10 μM camptothecin, using GFP imaging channel with fluorescent background removed.
Automated Dual-Mask Comet Analysis
Primary and secondary cellular analysis criteria (Tables 2 and 3) were applied to all images captured using Cytation 5's integrated Gen5 Microplate Reader and Imager Software. Primary cellular analysis automatically masked each comet head (Figure 4A), while secondary analysis automatically masked each comet tail (Figure 4B).
Figure 4. Automated 10 μM camptothecin treated comet analyses based on user-programmed cellular analysis parameters. Primary and secondary cellular analysis object masks showing (A) comet head and (B) comet tail in relation to the comet head, respectively. Images captured using a 2.5x objective, 1x2 image montage, and GFP imaging channel.
By using primary cellular analysis to mask the comet heads first, then a secondary mask for the comet tails, each individual comet was properly linked; reducing the occurrence of false results. Further subpopulation analysis may be applied to eliminate overlapping comets, anomalies and other false objects that might be overlooked via subjective methods. The final set of included objects yielded results with a high degree of accuracy and consistency, and allowed population level as well as individual single comet analysis.
Individual Comet Metric Calculations
Once the comet assay procedure and image preparation were complete, multiple calculations were immediately performed using Gen5 Microplate Reader and Imager Software, including commonly used assay metrics on an individual comet basis. The first metric was percent DNA in the tail. This value takes into account the total fluorescence within the comet head, containing undamaged DNA; and the comet tail, containing damaged DNA fragments (Figure 5). As explained above, DNA fragments, having a smaller size than intact DNA strands migrate faster through the gel matrix. When fluorescently stained and analyzed as one object, fluorescence increases outside the comet head as a function of the extent of the comet tail; and by proxy, the level of DNA damage.
Gen5™ Microplate Reader and Imager Software used the following formula and object metrics of interest (Table 5) to automatically calculate the percent DNA in the tail:
Table 5. Percent DNA in the tail formula metrics
When the fraction of comet head fluorescence, in terms of the total comet fluorescent signal, is subtracted from one, the fraction in the comet tail remains. When multiplied by 100, this value then represents the percent DNA in the comet tail.
The second metric was the comet tail moment. Here the percent DNA in the tail value previously calculated is combined with size measurements of the comet head and tail (Figure 5). With the integration of length measurements, not only is the total amount of damaged DNA taken into account, but also the extent of DNA strand damage. For the greater the number of times a strand is cut, the smaller the created fragments. And by proxy, the smaller the fragment the further the migration through the gel matrix, creating a longer comet tail and a larger tail moment.
Figure 5. Comet areas included in tail moment calculation.
Gen5 Microplate Reader and Imager Software used the following formula and object metrics of interest (Table 6) to calculate the tail moment value:
Table 6. Comet tail moment formula metrics.
The first portion of the formula calculates the aforementioned percent DNA in the comet tail. The second part of the formula calculates one half the length of the comet head, and the final portion of the formula calculates one half the length of the comet tail. By dividing each area by the comet head size, length values may be used in the final complete formula. As DNA damage increases, the length of the comet tail and percent DNA in the tail also increase, thereby creating a direct correlation between all three phenomena.
By including each formula into the calculated metrics for the cellular analysis step, percent DNA in the comet tail and tail moment may be determined for each comet included in every image taken (Figure 6).
Figure 6. Screenshot of comet assay image demonstrating individual comet assay metric calculation.
Dual-Mask Comet Assay Validation Data
Applying the formulas explained above, results for the comet population imaged from wells containing different camptothecin treatment levels were generated. As seen in Figure 7, both percent DNA in comet tail and tail moment values started low and increased appropriately as the concentration of camptothecin treatment increased, as was expected.
Figure 7. Percent DNA in comet tail and tail moment analyses using U251 cells exposed to various camptothecin concentrations. Four replicates tested at each compound concentration.
Data generated using the dual-mask analysis method was also compared to a previously validated method of comet assay analysis, which used a calculated metric based on the circularity of comets as DNA damage increases (Figure 8).
Figure 8. Comparison of generated (A) percent DNA in comet tail and (B) tail moment values using dual-mask or circularity analysis methods. U251 cells exposed to various concentrations of camptothecin. Four replicates tested at each compound concentration. Data from www.biotek.com/resources/articles/novelcomet- assay.html.
Results for both percent DNA in comet tail and tail moment agree across both methods, further validating the ability of the dual-mask method to deliver accurate, robust data on an individual comet and population basis. Using automated methods, both the percent DNA in the tail and comet tail moment calculations yielded consistent data across replicates, while reducing manual interpretations and sources of error, and saving time on manual calculations. The data may be compared to data from other analysis packages using circularity comet criteria.
Performing robust alkaline comet assays in a high throughput format, reduces laboratory workflow bottlenecks compared to manual methods. Automated comet imaging through Cytation™ 5 further enables high throughput efficiencies, with rapid imaging and a high degree of clarity to detect small changes in comet tail fluorescence. Dual masking enables population level analysis as well as single comet analysis, while common calculations, such as percent DNA in the tail and comet tail moment, are automatically and objectively determined in real time without requiring separate software, eliminating human subjectivity and error in the analysis that could potentially skew results. The combination of assay system along with automated imaging and analysis, create a robust, user-friendly method when performing genotoxicity studies.