The Casp3 assay as presented in this protocol is meant to be straightforward, and if performed as instructed herein, should give rise to a robust signal-to-noise ratio. The critical steps of this protocol include the use of fresh 1x PDT buffer for all washes, sufficient length of wash steps in PDT buffer following incubation of embryos in the primary antibody, gentle handling of embryos, and meticulous accounting for all embryos within tubes or transfer pipets during all steps of the protocol.
In our experience, the following are the most common reasons for lack of a signal on positive controls: 1) 1x PBST is substituted for 1x PDT during washing steps, 2) 1x PDT buffer is older than one month, 3) the wrong secondary antibody was used, 4) embryos are older than 32 hpf and/or 5) more than 40 embryos were analyzed in one tube. When inconsistent results or variability arises within samples, this is usually because 1) care was not taken to ensure that all embryos remained within liquid at all times during the procedure, and/or 2) embryos were not incubated under sufficient rocking. High levels of background noise are often visualized as a general fluorescent haze arising throughout the animal tissue of the embryo (see Figure 4, “background fluorescence”). A poor signal-to-noise ratio can arise when 1) embryos were not washed for sufficient time following the primary antibody, and/or 2) embryos were left in PFA or methanol for longer than the recommended time. If embryos fail to remain intact by the end of the assay: 1) solutions were not added drop-wise following fixation with PFA, and/or 2) rocker speed during incubation steps was set too high.
The whole-mount visualization inherent in the Casp3 assay is helpful for spatial localization of apoptotic cells. However, tissue-specificity is approximate and will likely rely on colabeling techniques (see Figure 5) and/or embryo sectioning to pinpoint the exact identity of cells undergoing apoptosis. In the protocol described here, colabeling is limited by the requirement for the specific rabbit-derived antibody used in our assay. We have not identified a commercially available nonrabbit-derived anti-activated Caspase 3 antibody that specifically labels apoptotic cells by whole-mount immunofluorescence in zebrafish embryos. Thus, cell-type specific antibodies that are raised in rabbits will not be compatible with the Casp3 assay for colabeling experiments. One alternative is to perform a TUNEL assay which requires a mouse-derived antibody to label apoptotic cells6. However, we have found that the whole-mount TUNEL assay performed on zebrafish embryos is very sensitive to a number of variables in the reaction, including the concentration of TdT enzyme, duration of embryo incubation in TdT enzyme, and the number of embryos present per tube (our unpublished observations). Thus, it is challenging to find a balance of enzyme that gives consistent interpretation of results. Therefore, a preferable alternative is to analyze apoptotic cells in transgenic zebrafish embryos that express a fluorophore (with commercially available robust antibodies) like GFP in a specific cell type. Then, colabeling experiments can be performed using a primary mouse anti-Gfp antibody followed by a green-fluorescing anti-mouse secondary antibody. See Figure 5 for an example.
While the Casp3 protocol gives robust, reliable staining of apoptotic cells in embryos from the 4-cell stage through 32 hpf, it has limited application beyond 32 hpf due to the inability of the antibodies to penetrate the skin of older embryos. Additional techniques to permeabilize the embryos, including treatment with collagenase, trypsin, acetone, or ethanol, could potentially be optimized to adapt this assay to the analysis of older embryos. Staining with AO, however, can be performed on live zebrafish up to at least 5 days-old9. Thus, the AO assay circumvents the embryonic stage restriction and represents a rapid assay to analyze apoptotic cells (1-2 hr). By contrast, the Casp3 assay requires overnight fixation of embryos and takes 2-4 days to complete. The disadvantages of the AO assay include that efficient photographic documentation of embryos can be challenging with multiple samples since embryos are alive and apoptotic cells are rapidly formed and cleared. This can be especially problematic if embryos need to be mounted to obtain a specific orientation for documentation. Additionally, we have found that AO staining diminishes after fixation with PFA, so it is not compatible with colabeling experiments involving immunofluorescence.
Quantitative analysis of activated-Caspase 3 can be performed utilizing software programs that measure fluorescence intensity of documented images. We have quantified IR-induced apoptosis in the neural tissue, a method we have described in detail elsewhere10. Depending on the experiment, quantitative analysis of activated-Caspase 3 may require further manipulation of embryos, such as flat-mounting, to obtain proper orientation for optimal tissue analysis. In addition, the linearity of the analysis will depend on the thickness of the tissue being analyzed. For instance, we analyzed IR-induced apoptosis in neural tissue by measuring active-Caspase 3 immunofluorescence in the shallow neural tissue of the spinal cord rather than the neuron-dense tissue of the brain4,10.
In our experience, the Casp3 assay is the most robust and reliable assay available to analyze apoptosis in zebrafish embryos between the 4-cell stage and 32 hpf when analysis requires ample time for documentation. When appropriate antibodies or transgenic lines are available to identify specific cells, this assay is also highly amenable to colabeling to identify the specific cell types undergoing apoptosis.