Synthesis and characterization of PDA-ICG nanoprobe
PDA synthesis. The protocol to prepare PDA nanoparticles was adapted from Chen et al46. Trizma base (45 mg) was dissolved in 5 mL deionized water and then added to a solution of 15 mL DMSO and 45 mL deionized water, followed by 30-min magnetic stirring. Subsequently, dopamine (46 mg) was added to the reaction. The mixture was left overnight under stirring (500 rpm). Purification of nanoparticles was achieved by centrifugation at 4,000 xg (40C) for 15 min, followed by centrifugation of the obtained supernatant at 18,000 xg for 20 min. The resulting pellet was washed with deionized water thrice.
PDA-ICG synthesis. PDA-ICG was prepared by adding ICG (9 mg) to a 10-mL suspension of PDA nanoparticles in deionized water (0.125 mg/mL) with pH 3.0, adjusted by adding HCl. The mixture was sonicated for 10 min, following which was heated to 65oC and left to stir (500 rpm) for 4 h. The resulting particles were purified by centrifugation (like PDA synthesis) and washing with deionized water five times.
PDA-arginine synthesis. Arginine-functionalized PDA (PDA-arginine) was prepared through amide coupling between the carboxylic acid of arginine and primary amines of PDA. PDA (4 mg) was suspended in 30 mL of NH4OH solution. An aqueous 10-mL solution of L-arginine (20 mg), EDC (76 mg) and NHS (46 mg) was stirred for 30 min. The arginine solution was then added dropwise to the PDA nanoparticle suspension followed by vigorous stirring overnight. The final concentration of NH4OH was 10 mM. The resulting particles were purified by centrifugation (like PDA synthesis) and washing with deionized water five times.
PDA-peptide synthesis. Peptide-functionalized PDA (PDA-peptide) was prepared through Michael addition between the cysteine thiols and unsaturated carbon bonds of PDA. PDA (500 µg) was mixed with TAMRA-labelled peptide (500 µg) in 3 mL of 10 mM Tris buffer pH 8.5. Nanoparticles were obtained as pellets by centrifuging the mixture at 10,000 rpm for 10 min and washing with ethanol and deionized water consecutively.
ICG release. PDA-ICG (0.1 mg/mL) was firstly dissolved in phosphate buffer saline (PBS) at pH 7.4 and DMEM supplied with 10% FBS at 370C. ICG release in these media was then investigated by collecting the released ICG by centrifugation for different periods of time and then the absorbance was measured using UV-Vis spectroscopy.
Photostability. PDA-ICG and ICG, both suspended in deionized water, were separately added to a 96-well plate. Concentrations were adjusted to give an absorbance value of 1 A.U. Samples were then irradiated with a 740 nm laser (54 mW/cm2) and the absorbance spectra were recorded over time.
Colloidal and long-term stability. The colloidal stability of PDA-ICG was evaluated in deionized water, PBS pH = 5.5–8.5, cell growing media (DMEM and DMEM + 10% FBS). Suspensions of these media (1 mL) containing 0.1 mg/mL of PDA-ICG were incubated for 72 hours at 37oC. Following incubation, the hydrodynamic size, zeta potential and UV-Vis measurements of the suspensions were recorded. The same experiment was done for PDA-ICG suspended in ethanol and DMSO, except measurements were taken 5 min after suspension. For long term stability, a suspension of PDA-ICG (0.1 mg/mL) in 1-mL deionized water was kept for 150 days in a 4oC (protected from light).
Characterization. DLS and zeta potential measurements were performed using a Zetasizer Nano Range instrument (Malvern Analytical). SEM was performed using a TESCAN MIRA3 FEG-SEM. ImageJ software was used to calculate the diameter of 150–200 individual nanoparticles. UV-Vis spectra were recorded with an Agilent Cary 300 UV-Vis spectrophotometer. Fluorescence emission spectra were recorded using a Varian Cary Eclipse Fluorescence Spectrophotometer. Fourier transform infrared spectroscopy (FT-IR) spectra were recorded using a Bruker Tensor 27 FT-IR spectrometer with samples pressed into KBr pellets. CHN combustion was performed on a CE-440 Elemental Analyser from Exeter Analytical, Inc. (combustion temperature 9750C). ICP analysis was performed on an iCAP7400 Duo ICP spectrometer from Thermo Fisher Scientific.
Photoacoustic measurements. Photoacoustic measurements were performed using a commercial photoacoustic tomography system (inVision256-TF; iThera Medical GmbH). Briefly, the system uses a tunable (660–1300 nm) optical parametric oscillator pumped by a nanosecond pulsed Nd:YAG laser operating at 10 Hz repetition rate for signal excitation. As the detector, a transducer array (5 MHz center frequency, 60% bandwidth, toroidal focusing) was used. Tissue mimicking phantoms were used to closely mimic the optical and acoustic properties of biological tissues. ICG, PDA-ICG and PDA were encapsulated separately inside thin walled optically transparent tubes located at 1 cm depth along the center of the phantom, which was placed inside the imaging chamber of the photoacoustic system. Photoacoustic signals were acquired at 710, 780, 810 and 850 nm excitation wavelengths. Mean pixel intensity (MPI) values were then obtained from a region of interest drawn within the thin-walled plastic straw (tubes) and then averaged from five different scan positions. Photoacoustic signal generation efficiency was obtained by normalizing the absorbance of ICG and PDA-ICG to 1 A.U. to give fair comparison since the generated photoacoustic signal depends on the amount of light absorbed by materials. The absorbance of PDA was matched to the PDA absorbance that gave 1 A.U. in PDA-ICG.
In vitro evaluation of PDA-ICG nanoprobe
Cell lines and growth conditions. Human melanoma (SK-MEL-103) and human lung adenocarcinoma (A549) cell lines were purchased from American Type Culture Collection (ATCC). All cell lines were grown in a complete growth medium (DMEM supplemented with 10% fetal bovine serum (FBS)). These cells were cultured in a humidified incubator at 37oC with 5% CO2. Experiments were formed using cells at passage number between 5 and 18.
Cytotoxicity studies. Cellular toxicity of PDA-ICG on the viability of drug-treated (senescent) and vehicle-treated (non-senescent) SK-MEL-103 and A549 cells was evaluated using a standard MTS assay. Cells (2000 cells/well) were seeded into clear 96-well plates in 100 µL complete growth medium and cultured for 24 h at 37oC. Following which, the cells were treated with varying concentrations of PDA-ICG (0.001–500 µg/mL) suspended in complete growth media containing 0.4% PBS. MTS assay was performed according to the manufacturer’s instruction. After further 72 h incubation, 20 µL of CelTiter 96® One Solution was added into each well and incubated for 2 h at 37oC. Subsequently, the absorbance of each well was measured at 490 nm using a Spark plate reader (TECAN). Control measurements, to account for potential sample interferences with MTS reagent, included negative control (cells only with DMEM), cells with DMEM containing 0.4% PBS, cell-free DMEM + 10% FBS (blank) and cell-free nanoprobe dilution in culture media. All experiments were conducted in biological triplicates. Cell viability was calculated as a percentage according to the following equation:
$$\:Cell\:viability=\frac{Absorbance\:of\:treated\:cells-Absorbance\:of\:blank}{Absorbance\:of\:control-Absorbance\:of\:blank}\:x\:100\%$$
Senescence induction. For chemotherapy-induced senescence, cisplatin was reconstituted in sterile PBS while palbociclib was prepared in DMSO. A549 cells were treated with 15 µM cisplatin for 10 days. SK-MEL-103 cells were treated with 5 µM Palbociclib for 10 days. These cells were used for experiments immediately after drug removal.
β-galactosidase staining. After 10 days under drug treatment, cells were washed thoroughly with pre-warmed PBS and then fixed and stained for senescence-associated β-galactosidase activity using the Senescence β-galactosidase Staining Kit (Cell Signaling) as per manufacturer’s instructions. After staining, cells were washed with PBS and then imaged using an Olympus Compact Brightfield Modular Microscope (Life Technologies). Total number of senescence-associated-β-galactosidase positive cells (blue colored) was counted to determine the proportion of senescent cells after drug treatments.
RNA extraction, cDNA synthesis and quantitative real-time PCR. RNA from cells was extracted using the RNeasy Mini Kit (Qiagen) and resuspended in RNase-free water. Complementary DNA (cDNA) was synthesized from the extracted RNA with the High-Capacity RNA-to-cDNA Kit (Thermo Fisher Scientific) using a total of 500 ng RNA per reaction. The levels of senescence-associated genes (LMNB1, GLB1, CDKN1A) were measured by RT-qPCR of the synthesized cDNA performed on a Quantstudio 1 Real-Time PCR instrument (Applied Biosystems) using Luna Universal qPCR Master Mix (New England Biolabs) according to the manufacturer’s instructions. Relative quantification was performed using the 2−ΔΔCt method. A list of primers used to amplify senescence-associated genes are detailed in Table S2.
Western blot. To extract proteins from cells, cells were lysed using RIPA buffer (Sigma) supplemented with phosphatase inhibitors (PhosSTOP™ EASYpak Phosphatase Inhibitors Cocktail, Roche) and protease inhibitors (cOmplete™ Protease Inhibitor Cocktail, Roche). Proteins were then quantified, separated by SDS-PAGE and transferred to polyvinylidene difluoride (PVDF) membranes (Millipore) following standard protocols. Membranes were then blotted with primary antibodies against β-actin, p21, and pRb. Following overnight incubation at 4oC, membranes were rinsed and incubated with secondary HRP-conjugated AffiniPure antibodies for 1 hour at room temperature. Subsequently, the membranes were incubated with Enhanced Chemiluminescence Detection solution (Amersham) and then imaged with a ChemiDoc imager (Bio-Rad) at automatic exposure times. Details on the antibodies used are available on Table S4 and Table S5.
Confocal imaging. Cells were seeded into a glass bottom dish (MatTek Life Science, US) (150,000 cells/well for non-senescent (control) cancer cells, 200,000 cells/well for senescent cells) and incubated at 37oC for 24 h, following which the cells were treated with different concentrations of PDA-ICG for another 24 h at 37oC. After 3 washed with PBS the cells were stained with CellMask™ Green (Thermo Fisher) plasma membrane stain, nucleus stain Hoechst 33342 (Thermo Fisher) and lysosome stain LysoTracker Red (Thermo Fisher) according to the manufacturer’s instructions. Cells were then washed gently with PBS three times, following which the cells were imaged using Axio Observer Z1 LSM 800 (Zeiss) confocal microscope. Image acquisition and processing were performed using Zen software (Zeiss).
Flow cytometry. Cells seeded at a 2 x 105 cells/well density in a 6-well plate were cultured for 24 h. Subsequently, the cells were treated with 10 and 50 µg/mL PDA-ICG prepared in the culture media and incubated for 24 h. After being incubated with PDA-ICG, cells were washed with PBS three times to remove the residual nanoprobes both in culture media and on the cell surfaces. Cells were then detached with 0.25 mL TrypLE (Thermo Fisher) and centrifuged for 5 min at 300 xg, 4oC. The cell pellets were then resuspended in 1 mL of FACS buffer (PBS with 4% FBS), into which 0.1 µg/mL DAPI dye was added. Cells were kept on ice (4oC) until flow cytometry experiments. Flow cytometry was performed on a Canto II flow cytometer (BD Biosciences) using 355, 488 and 640 lasers. As many as 10,000 events were acquired for each sample. Data analysis was performed using FlowJo software (version 10.2). In short, the population of live cells was gated in a plot of FSC versus DAPI channel, then cell debris and doublets were excluded from the live single-cell population by gating the plot of FSC versus SSC. Finally, a histogram from the 640/730 nm channel, which corresponded to the fluorescence emission from PDA-ICG, for the live, single-cell population was obtained and analyzed. This population of cells was deemed to internalize the nanoprobe.
Statistical analysis. Experiments in this study were independently repeated at least in triplicates and all data were presented as mean ± standard deviation. The GraphPad Prism 10 software (GraphPad Software, USA) was used to perform all statistical analysis; student -test or 2Way ANOVA depending on the dataset. Significance levels are defined as the following: not significant (ns) for p > 0.05, * for p ≤ 0.05, ** for p ≤ 0.01, *** for p < 0.001, and **** for p < 0.0001.