# Biochemical Characterization of a Caspase-3 Far-red Fluorescent Probe for Non-invasive Optical Imaging of Neuronal Apoptosis

Valérie Jolivel, Sébastien Arthaud, Béatrice Botia, Christophe Portal, Bruno

Delest, Guillaume Clavé, Jérôme Leprince, Anthony Romieu, Pierre-Yves

Renard, Omar Touzani, et al.

► To cite this version:

Valérie Jolivel, Sébastien Arthaud, Béatrice Botia, Christophe Portal, Bruno Delest, et al. Biochemical Characterization of a Caspase-3 Far-red Fluorescent Probe for Non-invasive Optical Imaging of Neuronal Apoptosis. Journal of Molecular Neuroscience, 2014, 54 (3), pp.451-462. 10.1007/s12031-014-0325-4. http://hal-01196843

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# Biochemical Characterization of a Caspase-3 Far-red Fluorescent Probe for Non-invasive Optical Imaging of Neuronal Apoptosis

Valérie Jolivel

Sébastien Arthaud

Béatrice Botia

Christophe Portal

Bruno Delest

Guillaume Clavé

Jérôme Leprince

Anthony Romieu

Pierre-Yves Renard

Omar Touzani

Heidi Ligeret

Pauline Noack

Marc Massonneau

Alain Fournier

Hubert Vaudry

David Vaudry

## Abstract

Apoptosis is a regulated process, leading to cell death, which is involved in several pathologies including neurodegenerative diseases and stroke. Caspase-3 is a key enzyme of the apoptotic pathway and is considered as a major target for the treatment of abnormal cell death. Sensitive and non-invasive methods to monitor caspase-3 activity in cells and in the brain of living animals are needed to test the efficiency of novel therapeutic strategies. In the present study, we have biochemically characterized
acaspase-3 far-red fluorescent probe, QCASP3.2, that can be used to detect apoptosis in vivo. The specificity of cleavage of QCASP3.2 was demonstrated using recombinant caspases and protease inhibitors. The functionality of the probe was also established in cerebellar neurons cultured in apoptotic conditions. QCASP3.2 did not exhibit any toxicity and appeared to accurately reflect the induction and inhibition of caspase activity by H₂O₂ and PACAP, respectively, both in cell lysates and in cultured neurons. Finally, intravenous injection of the probe after cerebral ischemia revealed activation of caspase-3 in the infarcted hemisphere. Thus, the present study demonstrates that QCASP3.2 is a suitable probe to monitor apoptosis both in vitro and in vivo and illustrates some of the possible applications of this caspase-3 fluorescent probe.

Keywords

Apoptosis Caspase-3 Stroke Imaging

Introduction

Cerebrovascular accidents represent the third cause of death in industrialized countries just after cardiovascular diseases and cancers. In 87 % of the cases, these accidents are due to occlusion of a cerebral artery that causes abrupt deprivation of oxygen and consequently provokes massive neuronal cell death in a brain area (Lloyd-Jones et al. 2009). After ischemia, cells located at the centre of the lesion die by necrosis, whereas in the peripheral zone, cells degenerate through an apoptotic process (Zheng et al. 2003). Apoptosis is a universal programmed cell death mechanism that plays a pivotal role in normal development and homeostasis (Jacobson et al. 1997). Dysregulation of apoptosis is involved in various pathologies such as cancers, neurodegenerative diseases and stroke. Apoptosis is characterized by a series of cellular events including cytoplasm shrinkage, DNA fragmentation and membrane blebbing (Elmore 2007). At the molecular level, these morphological changes have been ascribed to a complex cascade of biochemical pathways leading to the activation of specific and highly conserved proteases, the cysteine-dependent aspartate-specific proteases (caspases) (Alnemri et al. 1996). The term caspase designates a family of proteases that are synthesized as inactive zymogens and get activated through proteolytic cleavage at specific internal aspartate residues (Liu et al. 2005). Active caspases are heterotetramers composed of two large and two short subunits (Rotonda et al. 1996). Most caspases are involved in apoptosis and can be divided into two subfamilies. The first group includes the initiator caspases (caspase-2, caspase-8, caspase-9 and caspase-10) which exhibit an N-terminal adapter domain involved in the auto-cleavage process, while the second group corresponds to the effector caspases (caspase-3, caspase-6 and caspase-7) which lack the N-terminal adapter domain and get activated by initiator caspases. Each caspase recognizes a specific sequence, generally composed of four amino acids, and cleaves at the C-terminus of the last aspartate residue (Hengartner 2000). Activation of caspases initiates a series of events that ultimately lead to morphological alterations characteristic of the apoptotic cell death. Caspase-3 (EC 3.4.22.56) is considered as a key effector enzyme of the apoptotic cascade (Lakhani et al. 2006) and is involved in neuronal cell death in vitro, following exposure to toxic molecules (Vaudry et al. 2002; Takadera et al. 2007), and in vivo, after for instance cerebral ischemia (Love et al. 2000; Zhu et al. 2004). Characterization of the natural target
of caspase-3 has revealed that this enzyme has a high specificity of cleavage for the tetrapeptide Asp-Glu-Val-Asp (DEVD) (Stennicke and Salvesen 1997).

In vivo molecular imaging is based on three major technologies making use of either contrast agents (magnetic resonance imaging), radio-emitting isotopes (positron emission tomography) or light-emitting species (optical imaging). Among these technologies, optical imaging presents the advantages of being rapid, inexpensive and safe. Therefore, optical imaging is emerging as a powerful diagnostic/prognostic approach for the detection of various diseases such as cancer (Weissleder and Pittet 2008), inflammation (Cortez-Retamozo et al. 2008) or degenerative disorders (Raymond et al. 2008).

Nevertheless, this technique exhibits some constraints such as the choice of the excitation and emission wavelengths which have to be in the near-infrared domain where the absorption by tissues is minimum (Weissleder and Ntziachristos 2003).

Non-invasive optical imaging of apoptosis has initially been carried out with fluorochrome-labelled annexin-5 which specifically targets phosphatidylserine moieties that are externalized when cells enter into apoptosis (Petrovsky et al. 2003). However, these probes have major limitations since they are unable to distinct apoptotic from necrotic cells, in as much as they penetrate into permeabilized necrotic cells and subsequently bind to phosphatidyl serines that are at the internal side of the cell membrane. More recently, other probes have been developed that directly target caspase-3 and become fluorescent only in the presence of active caspase-3, thus substantially increasing signal specificity (Bullok and Piwnica-Worms 2005; Lapeyre et al. 2006).

Functionality of these probes was demonstrated in human colon xenografts and in liver abscess mouse models (Bullok et al. 2007), in isolated heart reperfusion injury (Pantos et al. 2009) or after intra-dermal injection of caspase-3 (Zhang et al. 2009).

In this context, the aim of the present study was to characterize a fluorescent probe targeting caspase-3, and to validate the suitability of the probe by investigating the efficiency of protective molecules in in vitro and in vivo models of neuronal cell death.

# Material and Methods

## Chemicals and Reagents

Recombinant human caspase-3 was purchased from Sigma (Saint-Quentin Fallavier, France), murine caspase-1, caspase-3 and caspase-8 were from Biovision (Mountain View, CA, USA) and murine caspase-11 was from Biomol (Plymouth Meeting, PA, USA). Antipain, leupeptin, Z-VAD-FMK, Ac-YVAD-CHO, Ac-DEVD-CHO, fluorescein diacetate, H₂O₂ and all culture reagents were from Sigma. Multiwell plates and petri dishes were from Costar (Cambridge, MA, USA). Calcein was from Molecular Probe (Cergy Pontoise, France) and the Apo-ONE™ Homogeneous Caspase-3/7 Assay kit was from Promega (Charbonnières, France).

Pituitary adenylate cyclase-activating polypeptide 38 (PACAP38) was synthesized using the fluorenylmethyloxycarbonyl (Fmoc) chemistry methodology using a semi-automatic multireactor system. A rink amide resin was used as a solid support and amino acids were introduced under their Fmoc-N-protected form. Couplings were performed in *N*,*N*-dimethylformamide in the presence of diisopropylethylamine using benzotriazol-1-yl-
oxy-trishexafluorophosphate as a coupling reagent. N-terminal deprotection was achieved with 40 % piperidine in DMF, and PACAP38 was cleaved from the solid support using trifluoroacetic acid (TFA) containing ethanedithiol, phenol and water as scavengers. After evaporation of TFA, the remaining material was precipitated. Crude PACAP38, dissolved in aqueous TFA (0.06 %), was purified by HPLC and the molecular weight of the peptide was verified by MALDI-TOF mass spectrometry.

Three probes were used for the study: QCASP3.2, a control probe corresponding to QCASP3.2 in which theL-Val was replaced by the antipodal D-Ala and a probe corresponding to cleaved QCASP3.2.

## In Vitro Characterization of QCASP3.2

For the determination of biochemical values, QCASP3.2 was diluted in caspase-3 buffer (100 mM NaCl, 40 mM HEPES, 10 mM DTT, 1 mM ethylenediaminetetraacetic acid (EDTA), 10 % (w/v) sucrose and 0.1 % (w/v) CHAPS, pH 7.4) in the presence of 10 % DMSO, which has previously been reported not to affect caspase activity (Kume et al. 2006), at concentrations ranging from 0.125 to 16 µM. Each dilution of QCASP3.2 was then incubated with 20 nM of caspase-3 at 37 °C for 2 h and recorded every 30 s on a FlexStation II microplate reader (Molecular Devices Corporation, Sunnydale, CA, USA; $λ_{excitation}$ = 645 nm, $λ_{emission}$ = 670 nm, cut-off filter = 665 nm). A standard curve using the probe equivalent to cleaved QCASP3.2 was used to convert fluorescence units into moles of formed product. The inner-filter effect was corrected as previously described (Liu et al. 1999). The $V_i$ was measured for each substrate concentration and $K_M$, $V_{max}$, $k_{cat}$ and $k_{cat}/K_M$ values were determined by means of the double-inverse relation of Lineweaver-Burk.

Recombinant human caspase-3, murine caspase-1, caspase-3, caspase-8 and caspase-11 or 10 µL of mouse plasma were incubated in caspase buffer for 75 min at 37 °C to determine QCASP3.2 specificity. The final concentration of each caspase was adjusted to obtain a volumic activity of 0.5 pmol/min/µL per well. QCASP3.2 was then added (1 µM), and the kinetics of cleavage in each condition was monitored at 37 °C for 5 h on the microplate reader. In some wells, 0.25 µM of the caspase-3 inhibitor Ac-DEVD-CHO was added 1 h prior to QCASP3.2.

## Animals

Wistar rats were obtained from Charles River Laboratories (L'Arbresle, France) and C57BL/6 mice from Janvier (Le Genest-Saint-Isle, France). Animals were kept in a temperature-controlled environment (21 ± 1 °C) under an established photoperiod (lights on 0700-1900 hours) with free access to food and tap water. Animal procedures were performed under the supervision of authorized investigators in accordance with the European Union normative for care and use of experimental animals.

## Cell Culture, Treatments and in Cellulo Investigations

Primary cerebellar granule cells (CGC) were isolated from cerebella of 8-day-old Wistar rats and cultured as previously described (Gonzalez et al. 1997; Vaudry et al. 2002).
Neurons were treated, 24 h after plating, with medium, H₂O₂ (10 to 160 µM) and/or PACAP (100 nM). To investigate caspase activity, 6 h after treatment, cells seeded in 35-mm-diameter dishes (300,000 cells/cm²) were scrapped and incubated with the Apo-ONE Caspase-3/7 Assay kit. Fluorescence intensity was measured over a 3-h period with the microplate reader (λ<sub>exCitation</sub> = 485 nm, λ<sub>emission</sub> = 530 nm). For cell survival experiments, 24 h after treatment, cells seeded in 24-multiwell plates were incubated with fluorescein diacetate as previously described (Vaudry et al. 2002).

To investigate QCASP3.2 cleavage, 6 h after treatment, cells seeded in 35-mm-diameter dishes were scrapped and diluted in caspase-3 buffer in the presence of QCASP3.2 (1 µM). Fluorescence was then measured with the microplate reader and for each condition, Vᵢ was determined after subtracting QCASP3.2 background fluorescence observed in the absence of cells. To evaluate QCASP3.2 cleavage in living neurons, cells were seeded in 96-multiwell plates. Six hours after treatment, QCASP3.2 (5 µM) was added, and fluorescence intensity was measured to calculate in each well the Vᵢ. To establish whether QCASP3.2 was cleaved into cells or not, the probe was also incubated with cell culture supernatants.

To assess QCASP3.2 specificity, 6 h after induction of apoptosis by H₂O₂, cells seeded in 24-multiwell plates were scrapped and incubated in 96-well plates with caspase-3 buffer in the presence of graded concentrations of inhibitors (10 pM to 10 µM). After 15 min at 37 °C, QCASP3.2 (1 µM) was added in each well, and the fluorescence intensity was measured over a 3-h period to determine for each inhibitor the Vᵢ and the IC₅₀ values. The Kᵢ were also calculated by means of the Cheng-Pruschoff relation with [S] = 1 µM.

For confocal microscopy and flow cytometry analysis, cells were seeded at densities of 187,000 and 375,000 cells/cm², respectively. Six hours after treatment, cells were incubated with 1.2 µM calcein and 4 µM QCASP3.2 for 30 min at 37 °C. Neurons were then washed with phosphate-buffered saline (PBS) and either directly observed by confocal microscopy (SP2, Leica) or detached with 500 µL PBS-EDTA for flow cytometry analysis (FACSCalibur, Becton Dickinson).

In Vivo Investigations

Four-month-old male C57BL/6 mice underwent permanent focal cerebral ischemia using the electrocoagulation technique. Briefly, mice were anesthetized by an intraperitoneal injection of ketamine (100 mg/kg, Imalgene)/xylazine (10 mg/kg, Rompun). After shaving the temporal side of the head, a skin incision was made between the eye and the ear. The temporalis muscle was incised and retracted. Then, a hole was made with a microdrill in the skull to perform electrocoagulation of the right middle cerebral artery. After surgery, all animals were placed in a warmed ventilated rack (Charles River Laboratories) maintained at 26 °C with a dark/light cycle (light between 7.00 a.m. and 7.00 p.m.). Twenty-four hours after ischemia, animals received an intravenous injection of 2 nmol of QCASP3.2, and 24 hours later, animals were euthanized. Brains were dissected out, frozen in isopentane cooled at -30 °C with dry ice and stored at -80 °C until use.

Frozen brains were cut into 60-µm-thick tissue sections mounted on gelatin glass slides and stored at -20 °C. For histological analysis, the brain sections were fixed in 4 %
paraformaldehyde for 20 min and stained with acetate thionine. Each section was photographed with a scale bar. The areas of infarction were delineated based on the lack of staining in the ischemic area and measured by using NIH ImageJ software. Infarct area in each section was determined as follows: total area of the contralateral hemisphere – (total area of the ischemic hemisphere – infarcted area). The infarct volume was calculated as follows: total infarct areas over all affected brain slices × distance between two consecutive slices. Infarct volume was further corrected for edema volume as described earlier (Lin et al. 1993). For immunohistochemical analysis, the brain sections were fixed in 4 % paraformaldehyde and incubated overnight at 4 °C in buffer containing 1 % BSA and 3 % Triton X-100 with the primary antibody against cleaved caspase-3 (1/200, Cell Signaling). Tissue slices were rinsed in PBS and incubated at room temperature for 90 min with the secondary antibody. Finally, the slices were mounted with PBS-glycerol (50/50 %). To study in vivo cleavage of QCASP3.2 after cerebral ischemia, the brain sections were fixed for 30 min with 4 % paraformaldehyde, rinsed in PBS and mounted with PBS-glycerol (50/50 %) before microscopic observation.

## Statistical Analysis

All data were analyzed using the PRISM4 software. Data are presented as mean ± SEM from at least three independent experiments performed in triplicate. Statistical analysis of the data was conducted using a non-parametric test (Mann-Withney or Kruskal-Wallis tests) followed by a Dunn's multiple comparison test.

## Results

### Structure of QCASP3.2 and the Control Probe

A protease-activable near-infrared fluorescent probe, designated QCASP3.2, was engineered to be sensitive and specific for caspase-3 activity by using the peptide substrate Asp-Glu-Val-Asp (DEVD), flanked by two anchoring amino acids with an N-acetylcystein at the N-terminal and a lysine-amide at the C-terminal extremity (Fig. 1). The Cy5.0 was grafted at the N-terminal side of the peptide structure and the quenching group QSY®21 at the other side (Fig. 1). The resulting far-red fluorogenic QCASP3.2 probe revealed quenching values of 96.5 and 88.3 % in caspase-3 buffer and mouse plasma, respectively (in conditions avoiding inter-molecular quenching phenomenon). The probe exhibited a relatively good solubility in basic aqueous buffers (caspase-3 buffer, PBS or NaHCO₃ solution), acidic buffers (ultrapure water or 0.1 % TFA) and biological media (culture medium, physiological saline or plasma) at concentrations below 50 µM. Above this concentration, probe aggregation could be observed, especially in acidic buffers. To test the specificity of the enzymatic reaction, a control probe was synthetized using a modified peptide sequence where the L-Val was replaced by the antipodal D-Ala (Fig. 1).
<figure><img src="image_2.png" /><figcaption>**Fig. 1**</figcaption></figure>

Schematic structure of the far-red fluorogenic caspase-3 probe QCASP3.2 and the control probe. The two probes are composed of a peptidic backbone grafted at the N-terminal side with Cy5.0 and at the C-terminal side with the quenching group QSY®21

Biochemical Characterization of QCASP3.2

As determined by the increase of its fluorescence, QCASP3.2 was cleaved by recombinant human or murine caspase-3 but not by murine caspase-1, caspase-8 and caspase-11 or plasma (Fig. 2a). Moreover, probe activation was efficiently inhibited by the addition of Ac-DEVD-CHO, a caspase-3 inhibitor (Fig. 2a). The incubation of the control probe with human or murine recombinant caspase-3 did not lead to any fluorescent emission (Fig. 2b).
A

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**Fig. 2**

Biochemical characterization of QCASP3.2. **a** Typical time-course effect of caspases and plasma on far-red QCASP3.2 probe fluorescence emission. QCASP3.2 (1 µM) was incubated in the presence of recombinant murine caspase-1, caspase-3, caspase-8 or caspase-11 and human caspase-3 or caspase-7 in caspase assay buffer. Caspases-3 were pre-incubated or not with Ac-DEVD-CHO (0.25 µM). The fluorescence signal was monitored over time with excitation at 645 nm and emission at 670 nm. **b** Typical time-course effect of caspases-3 and plasma on fluorescence emission of QCASP3.2 and the control probe containing the antipodal D-Ala. **c** Michaelis-Menten representation of the initial velocities ($V_i$) corrected for the inner-filter effect corresponding to each QCASP3.2 concentration used. Lineweaver-Burk representation (inset); the intersection of the straight line and the abscissa axis equals $-1/K_M$. **d** Signal/background fluorescence ratio of QCASP3.2 determined at the end of the catalytic reaction. **e** Linearity of QCASP3.2 cleavage by graded concentrations of recombinant human caspase-3

The representation of the initial velocities ($V_i$) for each concentration of substrate followed a hyperbolic curve indicating that recombinant caspase-3 cleaves QCASP3.2 according to the Michaelis-Menten model (Fig. 2c). Using the double-inverse relation of Lineweaver-Burk, the kinetic parameters of QCASP3.2 cleavage were determined. The calculated Michaelis constant ($K_M$) was 9.35 ± 1.78 µM which reflects a high affinity between the enzyme and QCASP3.2. Furthermore, the catalytic turnover ($k_{cat}$) was 0.298 ± 0.035 s⁻¹ which leads to a $k_{cat}/K_M$ ratio of 31.8 × 10³ s⁻¹ M⁻¹. The final fluorescence intensity compared to the background signal strongly increased as probe concentration was raised, to reach a maximum in the presence of 8 µM of QCASP3.2 (Fig. 2d). Finally, the $V_i$ observed after cleavage of QCASP3.2 at either 1 or 5 µM in the presence of graded concentrations of human recombinant caspase-3 followed a linear relationship (Fig. 2e).

CGC as a Model to Investigate Neuronal Apoptosis

In the present study, cultured CGC were used as a model for the determination of caspase activity in neurons (Vaudry et al. 2000, 2003), to test and characterize QCASP3.2. Treatment of granule neurons with graded concentrations of H₂O₂ induced a dose-dependent increase of caspase-3 activity as measured with the Apo-ONE Caspase-3/7 Assay commercial kit (Fig. 3a). The maximum effect on caspase-3 activity (+73 %) was observed in the presence of 40 µM H₂O₂ (Fig. 3a) and can be correlated with subsequent CGC death (Fig. 3b). Application of PACAP (100 nM) alone on cultured neurons only slightly reduced caspase-3 activity but a concomitant administration of PACAP with H₂O₂ reversed the effect of both 20 and 40 µM H₂O₂ by decreasing caspase-3 activity of 31 and 33 %, respectively (Fig. 3c). Consequently, PACAP completely blocked the neurotoxic effect of both 20 and 40 µM H₂O₂ (Fig. 3d).
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<figure><img src="image_11.png" /><figcaption>Fig. 3</figcaption></figure>

Induction of apoptosis in cerebellar granule cells. **a, b** Effect of graded concentrations of H₂O₂ on caspase-3 activity and cell survival. **c, d** Effect of PACAP (100 nM) on H₂O₂-induced caspase-3 activation and cell death. Caspase-3 activity (**a, c**) and cultured granule cell viability (**b, d**) were determined 6 and 24 h after the beginning of the treatment, respectively. Results are expressed as percentage of control. Each value is the mean ± SEM of at least three independent experiments performed in triplicate. \*p < 0.05; \*\*p < 0.01; \*\*\*p < 0.001 versus control; §p < 0.05; §§p < 0.01 versus H₂O₂ (Kruskal-Wallis test followed by Mann-Whitney test)

## QCASP3.2 Cleavage by Neuronal Lysates

Incubation of QCASP3.2 with a lysate from control CGC led to a rapid increase of near-infrared fluorescence signal, indicating the presence in the neurons of active enzymes able to cleave the probe (Fig. 4a). Pre-incubation of the cells with 20 µM Z-VAD-FMK, a general cell permeant caspase inhibitor, markedly reduced QCASP3.2 cleavage (Fig. 4a,b). Incubation of QCASP3.2 with a lysate from PACAP (100 nM)-treated cells significantly reduced the fluorescence signal (Fig. 4c). In contrast, incubation of QCASP3.2 with a lysate from H₂O₂ (40 µM)-treated cells provoked a 58% increase in the fluorescence intensity. Finally, incubation of QCASP3.2 with a lysate from cells that had been co-treated with H₂O₂ and PACAP did not modify cleavage of the probe
(Fig. 4c). A direct effect of H₂O₂ on QCASP3.2 fluorescence was excluded as incubation of the probe with graded concentrations of H₂O₂ (20–400 µM) did not modify the fluorescent signal.

<figure><img src="image_12.png" /><figcaption>Fig. 4</figcaption></figure>

Cleavage of the QCASP3.2 probe by neuronal lysates. a Time course of QCASP3.2 cleavage with neuronal lysates. Effect of pre-incubation of cells with b Z-VAD-FMK and c PACAP and/or H₂O₂ on initial velocities (Vᵢ) of QCASP3.2 cleavage by neuronal lysates. d Effect of increasing concentrations of protease inhibitors (Ac-DEVD-CHO, Ac-YVAD-CHO, Z-VAD-FMK, antipain and leupeptin) on Vᵢ of QCASP3.2 cleavage in
neuronal lysate. Each value is the mean ± SEM of at least three independent experiments performed in triplicates. *p < 0.05 versus control; §p < 0.05 versus H₂O₂ (Kruskal-Wallis test followed by Mann-Whitney test)

Five protease inhibitors were also tested in order to investigate which enzyme was responsible for cleavage of QCASP3.2 in cultured neuronal lysate (Fig. 4d). Z-VAD-FMK and Ac-DEVD-CHO, a reversible caspase-3 inhibitor, totally abolished the catalytic reaction at concentrations of 10⁻⁶ and 10⁻⁸ M, respectively. The use of Ac-YVAD-CHO, a potent reversible caspase-1 inhibitor, decreased the velocity of the reaction but only at 10⁻⁵ M. In contrast, antipain and leupeptin, two serine protease inhibitors, had no effect.

## QCASP3.2 Cleavage by Living Cultured Neurons

As the probe was designed for in vivo imaging, its potential toxicity and ability to enter the cells were tested. Exposure of cultured neurons to QCASP3.2 for 24 h did not modify their survival either in control conditions or under H₂O₂ treatment (Fig. 5a). A 6-h incubation of living neurons with QCASP3.2 provoked a gradual increase of the fluorescent signal. Treatment of cells for 6 h with PACAP (100 nM; Vaudry et al. 2009) reduced the fluorescence intensity by 25% (Fig. 5b). In contrast, addition of H₂O₂ (40 µM) increased the fluorescence signal by 68%. Co-incubation with PACAP significantly attenuated the H₂O₂-induced fluorescence rise (Fig. 5b). Moreover, incubation of cells with Z-VAD-FMK reduced the cleavage rate of QCASP3.2 by more than 55% (Fig. 5c). The cleavage likely occurred inside the cells because conditioned supernatants only induced a very limited increase of the fluorescence intensity which was not affected by treatments (control, PACAP, H₂O₂ or PACAP + H₂O₂). Microscopic observation of cultured neurons incubated with QCASP3.2 confirmed that the probe can enter into cells and revealed different labelling patterns. Healthy neurons with long extensions were only labelled with calcein (Fig. 6a), a sensor of viability, and did not exhibit any QCASP3.2 signal (Fig. 6b). Some round cells also revealed a green uniform staining (Fig. 6c), whereas others showed a patchy appearance with both calcein and QCASP3.2 labelling, indicating that although the cells were still viable, they contained activated caspase-3 (Fig. 6d, e). These neurons also exhibited vacuolization which are characteristic of apoptotic cells (Fig. 6d, e). Finally, in our culture conditions, some cells, in a late apoptotic stage, were only labelled with QCASP3.2 (Fig. 6f). Quantification was performed by means of flow cytometry. Based on red and green fluorescence, different populations were isolated. PACAP (100 nM) alone had no effect on the proportion of cleaved QCASP3.2-positive cells (Fig. 6g). Treatment with H₂O₂ (40 µM) provoked a 284% massive increase of the number of QCASP3.2-labelled neurons. Co-incubation with H₂O₂ and PACAP slightly reduced the number of QCASP3.2-positive cells, but the difference was not statistically significant (Fig. 6g).
<figure><img src="image_13.png" /><figcaption>Fig. 5</figcaption></figure>

Cleavage of the QCASP3.2 probe in living neurons. a Effect of incubation with QCASP3.2 (5 µM) in the absence or presence of H₂O₂ (40 µM) on survival of cultured cerebellar granule cells. b Effect of PACAP (100 nM) and/or H₂O₂ (40 µM) or c the pan-caspase inhibitor Z-VAD-FMK (20 µM) on QCASP3.2 cleavage in cultured cerebellar granule cells. Each value is the mean ± SEM of at least three independent experiments performed in triplicates. \*p < 0.05; \*\*p < 0.01; \*\*\*p < 0.001 versus control; §p < 0.05 versus H₂O₂ (Kruskal-Wallis test followed by Mann-Whitney test)
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**Fig. 6**

Microscopic observation of neurons incubated with QCASP3.2. **a–f** Visualization of cerebellar granule neurons stained in *green* with calcein and in *red* with activated QCASP3.2. **a** Granule neurons cultured for 24 h in serum-free conditions exhibit mixed phenotypes with healthy cells (*green*) and dying cells (*red*). High magnification of a healthy neuron with extension (**b**), of a round healthy neuron (**c**, **f**, *green cell*) and of apoptotic neurons in early (**d**, **e**) or late stage (**f**, *red cell*). Scale bar = 30 µm (**a**), 5 µm (**b–f**). **g** Cytometric analysis of neurons incubated with QCASP3.2. Each value is the mean ± SEM of at least three independent experiments. \*p < 0.05 versus control (Kruskal-Wallis test followed by Mann-Whitney test) (Colour figure online)

In Vivo QCASP3.2 Cleavage

In order to test the QCASP3.2 probe in vivo, we used a rodent model of permanent middle cerebral artery occlusion (MCAO), which led after 48 h to a mean infarct volume of 20.2 ± 1.8 mm³. The lesion, corresponding to the unstained region of the brain, was located exclusively at the cortical level (Fig. 7a). Immunochemical labelling performed 24 h after ischemia with an antibody directed against the cleaved form of caspase-3 revealed the presence of positive cells in the ischemic hemisphere (Fig. 7b). Intravenous injection of QCASP3.2, 24 h after the focal ischemia (when caspase-3 was activated), led to a fluorescent signal detected in the right hemisphere of a brain tissue slice (Fig. 7d, g) while no fluorescence was recorded in the contralateral hemisphere of the mouse brain (Fig. 7c, f). High magnification observation showed that the fluorescence signal was associated with cell bodies and located mainly around nuclei (Fig. 7g). Several control experiments were conducted by injection of either a negative control probe, which cannot be cleaved by caspase-3 (Fig. 7e, h) or of vehicle alone (Fig. 7j, k). In these conditions, a very faint and diffuse fluorescent signal was detected at the level of the infarcted cerebral parenchyma, probably due to the presence of haemoglobin in the infarcted tissue (Saliba 2005). Nevertheless, at high magnification, no specific labelling associated to cell bodies could be observed in these control animals (Fig. 7h, k). Finally, no fluorescent signal was detected in sham animals injected with the probe (Fig. 7i).
<figure><img src="image_21.png" /><figcaption>Fig. 7</figcaption></figure>

Imaging of the brain infarct area with QCASP3.2 after permanent focal cerebral ischemia in the mouse. aThionine staining of a brain tissue slice 48 h after permanent MCAO allows detection of the uncolored infarct area. Rectangles correspond to region observed by fluorescence microscopy and illustrated in b-k. bActivated caspase-3 is detected after stroke in the ipsilateral hemisphere. After an intravenous injection of QCASP3.2, no
signal was recorded in the contralateral hemisphere (c, f) whereas a red fluorescence was
observed in the infarct area (d, g). No specific fluorescent signal was detected after the
injection of the control probe (e, h), or the vehicle (j, k) and neither in sham-operated
mice injected with QCASP3.2 (i). Nuclei were stained with DAPI
(blue). Cx cortex, St striatum. Scale bar = 1 mm (a), 500 µm (b–e, i, j), 50 µm (f–h, k)

Discussion

Biochemical Characterization of QCASP3.2

The protease-activable near-infrared fluorescent probe QCASP3.2 was engineered to be sensitive and specific of caspase-3 activity by using the peptide substrate Asp-Glu-Val-Asp (DEVD). Even though the DEVD tetrapeptide is recognized by both caspase-3 and caspase-7 (Alnemri et al. 1996), it is established that caspase-3 is actively well expressed in the brain while caspase-7 is present at very low or undetectable level in this tissue (Juan et al. 1997). Several recombinant caspases were tested to demonstrate the functionality of QCASP3.2, and as expected, only murine and human caspase-3 could cleave the DEVD motif. Moreover, the replacement of the L-Val by the antipodal D-Ala in the control probe assessed the selectivity of caspase-3 for the DEVD motif entirely composed of L-amino acids.

Kinetic analyses revealed that QCASP3.2 is cleaved by recombinant human caspase-3
according to a Michaelis-Menten model, suggesting that the two active sites of caspase-3
(Rotonda et al. 1996) act in an independent manner and do not cooperate. The
calculated K<sub>M</sub> for QCASP3.2 is consistent with previously published values (Nicholson
et al. 1995), indicating that neither the cyanine 5.0 nor the quenching group affect the
recognition of DEVD by recombinant caspase-3. It also reflects a high affinity between
the enzyme and QCASP3.2. The catalytic turnover k<sub>cat</sub> is below previous data obtained
with other substrates containing the DEVD sequence. It should be pointed out that the
data available are very heterogeneous. For instance, a 16-fold difference has been
reported for the same substrate Ac-DEVD-amc, suggesting a predominant role of the
experimental conditions in the determination of the k<sub>cat</sub> value (Garcia-Calvo et al. 1999;
Moretti et al. 2002). In order to have a validated comparison, we independently
determined this value in a parallel experiment with Ac-DEVD-amc (k<sub>cat</sub> = 0.75 s<sup>-1</sup>) and
QCASP3.2 (k<sub>cat</sub> = 0.30 s<sup>-1</sup>). The k<sub>cat</sub>/K<sub>M</sub>ratio is consistent with values reported for other
protease substrates designed for in vivo imaging, indicating that QCASP3.2 could be a
suitable probe for in vivo experiments (Zhang et al. 2009). Moreover, as the rate of the
reaction is directly proportional to the concentration of recombinant caspase-3,
QCASP3.2 represents a tool to quantify the amount of active enzyme.

QCASP3.2 Cleavage in Neurons is Specific of Caspase-3
Activity

Caspase activation is an early event in the apoptotic process, which can be detected
before cell death occurs (Davoli et al. 2002; Lakhani et al. 2006). In the present study,
cultured CGC were used as a model for the determination of caspase activity in neurons
(Vaudry et al. 2000, 2003), to test and characterize QCASP3.2. The occurrence of basal
caspase-3 activity in lysates from CGC is consistent with the fact that in these culture conditions, cells slowly die by apoptosis within 3 or 4 days (Gonzalez et al. 1997). Other proteases such as calpain (Ortega and Moran 2011) or caspase-1 (Tanaka et al. 1998) are also activated when CGC enter apoptosis. Inhibitors directed against several proteases ensured that QCASP3.2 cleavage in cerebellar neurons was specifically due to the presence of active caspase-3. Indeed, antipain and leupeptin had no effect on QCASP3.2 cleavage which demonstrated that cathepsin, plasmin, trypsin, papain and calpain do not recognize the substrate. Z-VAD-FMK, a broad spectrum caspase inhibitor, significantly reduced the $V_i$ which indicates the involvement of this family of proteases. The potent caspase-1 inhibitor, Ac-YVAD-CHO, could only decrease the velocity of the reaction at a concentration of $10^{-5}$ M whereas it inhibits caspase-1 activity with a $K_i$ in the nanomolar range (Thornberry et al. 1994). In the present experiments, the most potent inhibitor of QCASP3.2 cleavage was Ac-DEVD-CHO which exhibited a $K_i$ of 0.53 nM, a value close to that previously obtained with recombinant caspase-3 (Chen et al. 2006; Fang et al. 2006).

## Effects of PACAP and $H_2O_2$ on Caspase-3 Activity and QCASP3.2 Cleavage

Oxidative compounds are known to induce apoptotic cell death via the mitochondrial pathway and caspase-3 activation. At low concentrations, the effect of $H_2O_2$ on cell survival mirrored the dose-dependent increase of caspase-3 activity. At higher concentrations (80 µM and above) there was no correlation between caspase activation and cell death, probably because in these conditions, most cells die by necrosis (Aito et al. 2004). The neuropeptide PACAP can prevent apoptosis of CGC induced by reactive oxygen species by reducing caspase-3 activity (Vaudry et al. 2002). The robust neuroprotective effect of PACAP was also confirmed in vivo using various animal models of stroke (Ohtaki et al. 2006; Dejda et al. 2011; Lazarovici et al. 2012). In neuronal lysate and living CGC, QCASP3.2 was able to detect the deleterious effect of $H_2O_2$ and the protective activity of PACAP, indicating that this probe is adapted to determine caspase-3 enzymatic activity in cellular lysate as well as within cultured neurons. Caspase-3 can be released in the late stage of apoptosis from cultured cells and retained a proteolytic activity (Hentze et al. 2001). As culture supernatants were not potent inducer of QCASP3.2 cleavage, it strongly suggests that QCASP3.2 can enter into the cells where it gets cleaved by endogenous enzymes.

## QCASP3.2 Allows Visualization of Caspase-3 Activation

Confocal microscopic observation of cultured CGC revealed cells with well-developed extensions forming a network, and isolated, round and shrunk cells. This is in accordance with the fact that these cells are cultured in survival conditions leading to their natural progressive degeneration (Gonzalez et al. 1997). Incubation with QCASP3.2 demonstrated that its activation occurred specifically inside neurons with round morphology and allowed the discrimination of two kinds of apoptotic cells: viable neurons containing active caspase-3 that are just entering apoptosis and dying cells that are in a late stage of apoptosis. The concomitant observation of different stages of
apoptosis highlights the fact that cultured cells are heterogeneous and undergo cell death
at different rates (Smolewski et al. 2002).

To translate the findings in vivo, a rodent stroke model was used. To monitor caspase-3 activity, the intravenous injection of QCASP3.2 was realized 24 h after the insult when caspase-3 was found to be activated, which is consistent with previous reports (Zhu et al. 2004). A fluorescent signal was detected in cell bodies of the ischemic hemisphere. Interstitial fluorescence was also observed which could result, in part, from active caspase-3 released from dead cells (Hentze et al. 2001).

In conclusion, we have developed a Cy 5.0-labelled probe, QCASP3.2, to detect caspase-3 activity in living neurons. This probe is recognized with a high affinity and a high specificity by its target and appears to be well suited to monitor the effects of antiapoptotic drugs on caspase-3 activity. Experiments conducted with mice revealed that QCASP3.2 can be activated in animals after stroke. One of the advantages of this probe is that it can be used for a wide spectrum of experiments ranging from cell lysate analysis to in vivo investigations. Moreover, the wavelength of the fluorescent signal generated by QCASP3.2, in the near-infrared domain, enables in-depth travel of the light through tissues and should thus allow the monitoring of the signal in living animals with an optical imager.

## Acknowledgments

The authors thank Drs. M. Bénard and L. Galas from the Cell Imaging Platform of Normandy (PRIMACEN) for excellent technical assistance in microscopy experiments and Dr. N. Thorel for her contribution to cytometry experiments.