Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry

Summary

The present protocol describes two methods to measure caspase activity through a fluorogenic substrate using flow cytometry or a spectrofluorometer.

Abstract

The activation of cysteine proteases, known as caspases, remains an important process in multiple forms of cell death. Caspases are critical initiators and executioners of apoptosis, the most studied form of programmed cell death. Apoptosis occurs during developmental processes and is a necessary event in tissue homeostasis. Pyroptosis is another form of cell death that utilizes caspases and is a critical process in activating the immune system through the activation of the inflammasome, which results in the release of members of the interleukin-1 (IL-1) family. To assess caspase activity, target substrates can be assessed. However, sensitivity can be an issue when examining single cells or low-level activity. We demonstrate how a fluorogenic substrate can be used with a population-based assay or single-cell assay by flow cytometry. With proper controls, different amino acid sequences can be used to identify which caspases are active. Using these assays, the simultaneous loss of the inhibitors of apoptosis proteins upon tumor necrosis factor (TNF) stimulation has been identified, which primarily induces apoptosis in macrophages rather than other forms of cell death.

Introduction

Caspases are involved in several forms of programmed cell death. Apoptosis is the most studied form of programmed cell death and is associated with caspase activity¹. All caspases possess a large and small catalytic subunit. Caspase-1, caspase-4, caspase-5, caspase-9, and caspase-11 possess a caspase activation and recruitment domain (CARD), and caspase-8 and caspase-10 contain death effector domains (DED)^2,3,4,5 (Table 1). Apoptosis can be initiated by two major pathways: the extrinsic pathway and the intrinsic pathway. The extrinsic apoptotic pathway is triggered by death receptors, which are part of the tumor necrosis factor superfamily (TNFSF). Death receptors possess DED domains, facilitating caspase-8 activity⁶. The intrinsic apoptotic pathway involves the activation of caspase-9 after the formation of the apoptosome, requiring the release of cytochrome c and Apaf-1⁷. The activation of either initiator caspase, caspase-8 or caspase-9, leads to the cleavage and subsequent activation of the executioner caspases, which are caspase-3, caspase-6, and caspase-7. Identifying that the executioner caspases are active indicates that the cells are undergoing apoptosis, and this activation is considered an important factor in defining the mode of cell death.

Caspase activation is also a critical juncture for regulating inflammation and the induction of alternative forms of programmed cell death. For example, caspase-1 activation leads to the maturation of pro-inflammatory cytokines of the interleukin-1 family⁸. The release and activation of cytokines from this family, particularly IL-1β and IL-18, result from gasdermin D cleavage and pore formation at the plasma membrane^9,10. Inadequate membrane repair of gasdermin D pores can result in a type of cell death known as pyroptosis¹¹. Moreover, caspase-8 activity results in the inhibition of a caspase-independent cell death known as necroptosis¹². Receptor-interacting serine/threonine protein kinase 1 (RIPK1) is one of the critical factors in necroptosis and in driving inflammation regulated by NF-kB. Models have shown that RIPK1 is cleaved by caspase-8, resulting in limiting NF-kB signaling, apoptosis, and necroptosis^13,14. Therefore, identifying the activity of different caspases can aid in understanding the resulting inflammation and cell death modality.

Independent of the function of caspases in regulating cell death modalities, caspase activity can also regulate other cytokine families, such as interferon (IFN), in response to infection^15,16. Additionally, caspases are involved in non-cell death functions, including cell fate decisions, tissue repair and regeneration, tumorigenesis through DNA repair, and neuronal synapse function. The activity of caspases in these non-lethal roles is thought to be limited by the cellular localization and amount of caspases. Therefore, quantifying the level of caspase activity may well define whether a cell undergoes cell death or whether the caspase plays a role in a non-cell death function^4,17,18.

Caspase activity can be assessed by multiple methods. Western blotting for cleaved caspases and their substrates has been used as an indicator of activity, but these assays are qualitative at best. To determine whether caspase activity is associated with cell death, a quantitative measurement is ideal. Since caspases cleave substrates at a recognition site consisting of four amino acids, colorimetric, luminescence, or fluorometric methods have been developed. However, caspases appear to have plasticity in their substrate recognition^19,20. The recognition sequence is not associated with the protein domains (Table 1). The tetrapeptide sequence DEVD, however, can be used to detect caspase-3 and caspase-7 activity^20,21.

Smac mimetics are compounds targeting the inhibitors of apoptosis proteins (IAPs). The use of Smac mimetics in a subset of cancer cells causes the cells to become sensitive to TNF-induced cell death²². In primary macrophages, Smac mimetics cause cell death without the exogenous addition of TNF^23,24. The loss of cIAP1 by Smac mimetic-induced degradation results in the production of TNF. If caspase activity is detected, this means the cells did not die by necroptosis but in an apoptotic manner. In this method, the detection of cleaved DEVD substrate is used to identify caspase-3/caspase-7 activity. Further experiments to confirm apoptotic cell death have been published previously²⁴.

Protocol

The present study was performed with the approval and following the guidelines of the animal ethical committee of the University of Zürich (#ZH149/19). Male C57Bl/6J mice aged 8-16 weeks, bred and housed in specific pathogen-free (SPF) conditions, were used for the present study. The intact bones can be kept on ice in sterile Hank's buffered saline solution (HBSS) with 2% heat-inactivated fetal bovine serum (FBS). Bone marrow was collected from the femur and tibia of the mouse²⁵ on the day of differentiation. Both methods for assessing caspase activity can be used for other cell types, including both primary and transformed.

1. Differentiating bone marrow-derived macrophages (BMDMs)

NOTE: Perform all the steps in a tissue culture laminar flow hood, and use sterile aseptic techniques.

1. Prepare a 1 mL syringe with a 21 G needle.
2. Add 5 mL of HBSS + 2% FBS to a 15 mL tube.
3. Using sterile forceps, take an excised femur, and insert the needle into the opening of the femur. Holding the femur in the HBSS + 2% FBS, flush the bone marrow out until the bone is white. Flush the tibia in the same manner. Continue to flush the solution to obtain a single-cell suspension.
4. Centrifuge the single-cell suspension at 200 x g for 4 min at room temperature (RT).
5. Remove the supernatant using a vacuum aspirator. Tap the tube to gently resuspend the pellet. Add 1 mL of red cell lysis buffer (see Table of Materials), and mix gently with a P1,000 pipette. Incubate at RT for 1 min.
6. Add 10 mL of HBSS + 2% FBS, and centrifuge at 200 x g for 4 min at RT.
7. Remove the supernatant, and resuspend in 10 mL of bone marrow-derived macrophage (BMDM) culture medium.
   NOTE: BMDM culture medium consists of low-glucose DMEM with the addition of 10% FBS, 20 ng/ml M-CSF, penicillin (50 U/mL), and streptomycin (50 μg/mL) (see Table of Materials). Alternatively, 20% L929 conditioned medium can be substituted for the M-CSF.
8. Add 15 mL of BMDM culture medium into two 15 cm Petri dishes. Add 5 mL of the single-cell solution to each plate.
   NOTE: Do not use tissue culture-treated plates. Tissue culture-treated plates limit the differentiation.
9. Place the dishes at 37 °C, 5% CO₂, for 6 days.
   ​NOTE: The BMDMs can be harvested after 5-7 days. Longer incubation times for differentiation lead to increased anti-apoptotic protein expression²⁶.

2. Harvesting, seeding, and treatment of cells

NOTE: Perform all the steps in a tissue culture laminar flow hood, and use sterile aseptic techniques. Fully differentiated macrophages adhere to the plate, allowing for easy separation, while floating cells can be discarded. Phosphate-buffered saline (PBS) can be used with or without Ca²⁺ and Mg²⁺.

1. After 6 days of incubation, remove the floating cells and medium from the plate using an aspirator.
2. Add 5 mL of PBS to each 15 cm plate. Remove the PBS from the plate using an aspirator.
3. Add 2 mL of trypsin (see Table of Materials) to each plate. Incubate the plate until gentle tapping of the plate dislodges the cells. Take 5 mL of BMDM culture medium, and harvest the cells off the plate.
   1. Transfer to the second 15 cm plate, and harvest the cells off the plate. Remove the cell suspension from the plate into a 50 mL tube. Take an additional 5 mL of BMDM culture medium, and wash both plates to ensure all the cells have been collected. Place the cell suspension into the same 50 mL tube.
4. Take 10 μL of the cell suspension, and count using a hemacytometer using a 1:1 dilution with trypan blue.
   NOTE: Automatic cell counters can be used as well when calibrated for the size of the macrophages.
5. Seed the macrophages at a density of 1 x 10⁶ cells/mL. BMDMs seeded at 2 x 10⁶ cells/well in a 6-well plate provide approximately 2 mg/mL total protein. Allow the cells to adhere to the plate for a minimum of 6 h before treatment.
   NOTE: For other cell types, the optimal concentration must be determined.
6. Treat the macrophages with Smac mimetic (Compound A, see Table of Materials)²² at 250 nM and 500 nM for 16 h.
   ​NOTE: Include a positive control to induce apoptosis and caspase-3 cleavage to ensure the assay is working. Common apoptosis inducers include staurosporine and etoposide. For many cell lines to undergo apoptosis, 0.1-10 μM for 16 h of stimulation is sufficient.

3. Preparing cell lysates from treated cells

NOTE: This step must be done on ice, and the reagents and materials must be pre-cooled.

1. Transfer the plates containing the treated cells onto the ice. Collect the medium from the cell culture into a 1.5 mL tube, centrifuge at 300 x g for 5 min at 4 °C, aspirate the medium, and put the tube on ice. This allows the collection of the cells that have detached from the plate.
2. Add 1 mL of cold PBS to the cell culture plate for washing the cells, and aspirate all the PBS. Add 100 μL of trypsin to the cells (if working with a 6-well dish). Allow the trypsin to lift the cells off the plate, and collect them into the 1.5 mL tube. Use 1 mL of cold PBS to ensure all the cells have been collected.
   NOTE: If working with suspension cells, gently transfer the medium and cells to a 1.5 mL tube.
3. Centrifuge the cells at 300 x g for 5 min at 4 °C. Remove the supernatant, and resuspend in 100 μL DISC lysis buffer (150 mM sodium chloride, 2 mM EDTA, 1% Triton X-100, 10% glycerol, 20 mM Tris, pH 7.5, see Table of Materials).
4. Incubate the samples on ice for 20 min.
5. Centrifuge the lysates at ~12,000 x g for 10 min at 4 °C to pellet the insoluble fraction.
6. Transfer 25 μL of the lysate into a white flat-bottomed 96-well plate for the caspase-3/caspase-7 activity assay (step 5).
   NOTE: Do not disturb the pellet. This is the insoluble fraction of the cell lysate.
7. Transfer 10 μL of the remaining lysate into a transparent flat-bottomed 96-well plate for the bicinchoninic acid (BCA) assay (step 4). This will be used for the normalization of the samples.
8. Keep both plates on ice for further processing.
   ​NOTE: At this stage, the plates can be sealed with an adhesive cover and stored at −20 °C for approximately 4 weeks.

4. Protein quantification using the BCA assay

NOTE: Other reagents or assays can be used to quantitate the amount of protein in each sample. In the population-based assay, the samples can be compared by normalizing the amount of protein used in the assay.

1. Prepare standard protein concentrations between 0 μg/mL and 2,000 μg/mL (0 μg/mL, 25 μg/mL, 125 μg/mL, 250 μg/mL, 500 μg/mL, 750 μg/mL, 100 μg/mL, 1,500 μg/mL, 2,000 μg/mL) with bovine serum albumin (BSA). Prepare blanks with lysis buffer only.
2. Add 10 μL of each standard into the flat-bottomed 96-well plate containing the samples, mentioned in step 3.7.
3. Mix BCA reagent 1 with BCA reagent 2 in a 50:1 ratio (see Table of Materials). Add 200 μL of mixed BCA reagent to each sample and standard.
4. Incubate at 37 °C for 30 min.
5. Measure the absorbance at 562 nm on a fluorometric instrument, and quantify the protein concentration with the standard curve.

5. Population-based assay for caspase-3/caspase-7 activity

NOTE: Do not allow the cell lysates in the plate to sit on ice for more than 3 h. If caspase activity is present, this increases over time despite the sample being on ice. If the samples were frozen, thaw them on ice, and proceed immediately once the lysates have thawed.

1. Start the fluorometric instrument (see Table of Materials) and heat the machine to 37 °C. Prepare the script as mentioned:
   1. Perform individual readings every minute for 40 min in order to determine the kinetics of the reaction.
   2. Set the excitation at 360 nm and the emission at 465 nm. Ten flashes per well are sufficient.
2. Prepare the positive control of recombinant caspase-3 (see Table of Materials). Mix 1 U of the recombinant caspase-3 enzyme in 50 μL of lysis buffer (tube 1). Add 25 μL of lysis buffer to an additional three tubes. Transfer 25 μL from tube 1 to tube 2. Mix by pipetting.
   1. Repeat for tube 3 and tube 4. Tube 5 will contain only 50 μL of lysis buffer. Add 25 μL of each standard into the white flat-bottomed 96-well plate for the caspase-3 activity assay, mentioned in step 3.6.
3. Prepare a master reaction mix for caspase activity assay on ice. For one reaction, mix 50 μL of 2x caspase cleavage buffer (0.2M HEPES pH 7.5; 20% sucrose or PEG; 0.2% CHAPS), 5 μL of 1 mM DEVD-AMC (caspase-3 tetrapeptide substrate), 2 μL of 500 mM DTT, and 18 μL of deionized water (see Table of Materials).
4. Add 75 μL of the reaction mix to each sample and standard to obtain a total reaction volume of 100 μL.
5. Immediately measure the fluorescence using the fluorometric instrument set up in step 5.1.
6. For each fluorescent measurement, subtract the fluorescence reading for the blank (lysis buffer only) from the sample's fluorescence. Normalize the reading by dividing by the protein concentration of the sample (calculated in step 4.5)²⁷:
   
7. Calculate the rate of caspase activity by determining the slope of the normalized fluorescence on the y-axis and time on the x-axis.

6. Single-cell assay (flow cytometry analysis) for caspase-3/caspase-7 activity

1. Seed the cells as described in section 2.
2. Harvest the cells into a 5 mL polystyrene tube. If working with adherent cells, collect the medium into the 5 mL tube. Add 1 mL of cold PBS to the cell culture plate, and collect the PBS into the 5 mL tube. Add trypsin to the cells (100 μL if working with 6-well dishes). Allow the trypsin to lift the cells off the plate, and collect into the 5 mL tube. Use 1 mL of cold PBS to ensure all the cells have been collected.
   NOTE: If working with suspension cells, gently transfer the medium and cells to a 5 mL tube.
3. Centrifuge the samples at 300 x g for 5 min, 4 °C. Remove the supernatant using a vacuum aspirator.
4. Prepare the staining mix. The optimal staining concentration is 1 x 10⁶-2 x 10⁶ cells in 50 μL. Dilute the fluorogenic substrate as per the manufacturer's instructions (see Table of Materials, flow cytometry). Take 1 μL of the stock substrate, and dilute in 150 μL of PBS. Add 50 uL per sample.
5. Incubate the samples at 37 °C for 30 min protected from light, with mixing every 15 min.
6. With the flow cytometer utilized in this study, use the red laser at 640 nm, and detect using 675/25 nm. Run the unstained control sample first, and acquire a minimum of 10,000 events of the desired population. Exclude the debris using a gate (P1) on an FSC-A and SSC-A dot plot.
   1. Use a histogram displaying the events in the P1 gate and detection for the caspase substrate (y-axis) to determine the median fluorescence intensity (MFI).
      NOTE: The caspase substrate described in this method requires an excitation at 590 nm and emits at 628 nm.

Representative Results

Primary mouse macrophages were differentiated for 6 days. After 6 days, the cells were harvested, counted, and seeded. The following treatments were used: no treatment and Smac mimetic (Compound A)²² at 250 nM and 500 nM for 16 h (Figure 1). The experiment was performed in duplicate to allow caspase-3/caspase-7 activation to be assessed either by a population-based assay or single-cell analysis using flow cytometry.

The protein concentration of the cell lysates was quantified using the BCA assay (Supplementary Table 1). This is necessary to ensure the amount of protein used in the caspase-3/caspase-7 activity assay is the same between samples. In this population-based assay, the data can be presented in two ways. The first is to show the kinetics by plotting the adjusted fluorescence (y-axis) versus time (x-axis) (Figure 2A). Alternatively, the slope can be calculated to directly compare the samples (Figure 2B). The increase in slope upon 500 nM Smac mimetic treatment was not significant based on an ordinary one-way ANOVA with multiple comparisons (Dunnett's multiple comparison test²⁸).

For the analysis of caspase-3/caspase-7 activity using flow cytometry, the cells and supernatant were harvested. Unstained cells or fluorescence minus one were used as a negative control, as well as the untreated cells. A histogram of the cells collected by flow cytometry showed a shift in fluorescence for the cells treated with Smac mimetics in comparison to the untreated cells (Figure 2C). The data can be shown either as median fluorescence intensity (Figure 2D) or as a fold change over the untreated cells (Figure 2E).

Figure 1: Flow chart of the study. (A) Femurs and tibias were excised from C57Bl/6 mice. The bones were flushed and differentiated in 20 ng/mL M-CSF for 6 days. (B) On day 6, macrophages were harvested and reseeded for treatment. One set of cells was harvested for lysates and assessed by fluorogenic activity, while the other set was harvested, incubated with the fluorogenic substrate, and assessed by flow cytometry. Please click here to view a larger version of this figure.

Figure 2: Kinetic assay for caspase-3/caspase-7 activity and substrate cleavage by flow cytometry. (A,B) Representative data of the kinetic assay for caspase-3/caspase-7 activity (C-E) and substrate cleavage by flow cytometry. The macrophages were treated with two concentrations of Smac mimetic (Compound A; 250 nM and 500 nM) for 16 h. (A) Detection of the cleaved DEVD AFC substrate over time. The data were normalized to the protein concentration in the sample. (B) The rate of cleavage (slope) of DEVD AFC for each sample was normalized to the untreated slope and presented as the fold change over the untreated cells. (C) Flow cytometric histograms of the cells incubated with the caspase-3 substrate. (D,E) MFI comparison and fold change in the MFI compared to the untreated sample. Each data point represents an independent sample; mean ± standard error of the mean are shown; *p < 0.05 using a one-way ANOVA and multiple comparison tests (Dunnett's multiple comparison test). Please click here to view a larger version of this figure.

Caspase	Species	Substrate sequence	Protein domains
Caspase-1	Hs, Mm	(W/L)EHD	CARD, large domain, small catalytic domain
Caspase-2	Hs, Mm	DEXD	CARD, large domain, small catalytic domain
Caspase-4	Hs	(W/L)EHD	CARD, large domain, small catalytic domain
Caspase-5	Hs	(W/L)EHD	CARD, large domain, small catalytic domain
Caspase-9	Hs, Mm	(I/V/L)E(H/T)D	CARD, large domain, small catalytic domain
Caspase-11	Mm	(W/L)EHD	CARD, large domain, small catalytic domain
Caspase-12	Mm	ATAD	CARD, large domain, small catalytic domain
Caspase-8	Hs, Mm	(I/V/L)E(H/T)D	DED, large domain, small catalytic domain
Caspase-10	Hs	(I/V/L)E(H/T)D	DED, large domain, small catalytic domain
Caspase-3	Hs, Mm	DEXD	large domain, small catalytic domain
Caspase-6	Hs, Mm	(I/V/L)E(H/T)D	large domain, small catalytic domain
Caspase-7	Hs, Mm	DEXD	large domain, small catalytic domain
caspase-14	hs, mm	(W/L)EHD	large domain, small catalytic domain
CARD	caspase activation and recruitment domain
DED	death effector domain
Hs	homo sapien
Mm	mus musculus

Table 1: Substrate specificity and the protein domains of the caspases. The table is adapted from McStay et al.²⁰; Shalini et al.³; and van Opdenbosch and Lamkanfi⁴.

Supplementary Table 1: DEVD kinetic analysis. Please click here to download this Table.

Discussion

In this method, a fluorogenic substrate is used in a population-based assay or single-cell analysis to measure caspase-3/caspase-7 activity. Both methods measure the caspase activity in a quantitative manner based on the cleavage of a substrate. One advantage is the ability to utilize these methods for numerous samples. With these methods, caspase-3/caspase-7 activity is detected in primary macrophages treated with Smac mimetics.

A critical aspect of the population-based fluorometric assay is the time from lysis to reading the fluorescence. The samples must be kept on ice throughout the procedure, particularly prior to "reading" the assay. This prevents premature cleavage and fluorescence of the substrate. Using the population-based assay, less optimization may be required. The amount of protein used in the assay is normalized, allowing the samples to be directly compared. One caveat is that at a late stage of apoptotic cell death, the total protein amount is reduced; hence, the detection of caspase activity may not be possible. Different kinetics or different treatment doses are recommended to circumvent this problem. In addition, other software can be used to accurately assess the rate of caspase activity besides the software described in this method.

For the flow cytometric assay, enough events or cells are required to gate the populations confidently. In addition, more optimization in the flow-based assay may be required to achieve the optimal ratio of substrate to cell number. However, with flow cytometry, this method lends itself to measuring additional parameters, such as cell surface markers for cell type identification.

Both the population and single-cell methods could be used for other caspases. However, it is important to remember that the recognition sequence is less discriminated for other caspases. As such, other methods for caspase activity must be used. This includes the inhibition of caspase activity, CRISPR or knock-down of specific caspases, and western blotting to detect the cleavage of known substrates.

One alternative method for detecting caspase activity is time-lapse imaging. The same permeable caspase substrate could be used along with other markers of viability, such as annexin V, to provide information on the kinetics of cell death. Imaging would also separate the caspase activity and cell survival, allowing for the detection of sublethal amounts of caspase activity in a cell population. The non-lethal functions of caspase-3/caspase-7 are linked to antiviral regulation in innate immune cells²⁹, particularly the activation of type I IFN via mitochondrial DNA release^15,16. Thus, these assays to measure caspase activity are critical for identifying different modes of cell death and may be useful in assessing non-cell death functions.

Materials

Name	Company	Catalog Number	Comments
1.5 mL microfuge tubes	Sarstedt	72.706.400
15 cm Petri plates	Sarstedt	82.1184.500
37 degree incubator shaker	IKA shaker KS 4000i	97014-816	distributed by VWR
6-well cell culture dish	Sarstedt	83.392
96 well flat bottom, white polystyrene, non-sterile	Sigma	CLS3600
96 well flat plate	Sarstedt	82.1581
Ac-DEVD-AFC	Enzo Life Sciences	ALX-260-032-M005	Caspase-3 substrate
BD Fortessa	BD		any flow cytometer with the appropriate excitation and emission detector will work
b-glycerolphosphate	Sigma	G9422-10G
caspase-3 recombinant	Enzo Life Sciences	ALX-201-059-U025
CHAPS	Sigma	1.11662
DMEM, low glucose, pyruvate	Thermoscientific	31885023
DMSO	Sigma	D8418-250ML
EDTA	Sigma	03685-1KG
EGTA	Sigma	324626-25GM
Etoposide	MedChem Express	HY-13629
FBS	Thermoscientific	26140
Flow cytometry tubes	Falcon	352008
Flowjo	Flowjo		A license in required but any program that can analyze .fcs files will suffice
Glycerol	Sigma	G5516-500ML
HEPES	Sigma	H4034
Magic Red caspase-3/7 assay kit; flow cytometry or imaging	Immunochemistry Technologies	935
M-CSF	ebioscience	14-8983-80	now a subsidiary of Thermoscientific
M-Plex	Tecan		any fluorometric reader will work with the appropriate excitation and emission detectors
NaCl	Roth	3957.1
PBS pH 7.4	Thermoscientific	10010023
Penicillin-Streptomycin-Glutamine (100X)	Thermoscientific	10378016
Pierce BCA Protein Assay Kit	ThermoFisher Scientific	23225	protein concentration assay
protease inhibitors	Biomol	P9070.100
Smac mimetic, Compound A	Tetralogics		also known as 12911; structure shown in supplementary figures of Vince et al., Cell 2007
Sodium Fluoride	Sigma	S7920-100G
sodium orthovanadate	Sigma	S6508-10G
sodium pyrophosphate	Sigma	P8010-500G
Staurosporine	MedChem Express	HY-15141
sucrose	Sigma	1.07687
Tris Base	Sigma	T1503-1KG
Triton X100	Sigma	T8787-50ML
TrypLE	Thermoscientific	A1285901	In the protocol, it is listed as Trypsin