Cell culture
One of the three human prostate cancer cell lines is PC3 (CRL-1435, ATCC), which was obtained from our department stock. Another cell line, LNCaP (CRL-1740, ATCC), was donated by Prof. Dr. Engin Ulukaya from Istinye University. The third cell line, RWPE-1, was donated by Dr. Yasemin Yozgat from Istanbul Medipol University. PC3 and LNCaP cell lines were cultured in RPMI 1640 with L-glutamine (RPMI-A, Capricorn) supplemented with 10% FBS (FB-1001/500, Biosera) and antibiotic-antimycotic (XC-A4110/20, Biosera) at 37°C and 5% CO2. The RWPE-1 cell line was cultured in keratinocyte serum-free media (17005042, Thermo Fisher Scientific) supplemented with human recombinant epidermal growth factor (EGF1-53) and bovine pituitary extract (BPE) (Keratinocyte-SFM Supplement 37000015, Thermo Fisher Scientific) without antibiotic-antimycotic at 37°C and 5% CO2.
2D cell culture
When cells reached 70-80% confluency in T25 flasks, they were trypsinized (5 minutes for PC3, 3 minutes for LNCaP) and collected in tubes after centrifugation at 1500 rpm for 5 minutes. Following cell counting, the cells were split into new wells for the 3D culture method and/or seeded in IBIDI 12-well slides for the continuing 2D culture process. Due to the slower metabolism, LNCaP cells were seeded at 1.2x104 cells/200 µl, RWPE-1 cells were seeded at 2x104 cells/200 µl, and PC3 cells were seeded at 1x104 cells/200 µl on slides in an appropriate culture medium.
3D cell culture
Each well of 96-well plates was covered with 100 µl of 3% warm agarose gel solution to obtain a ‘U’-shaped well bottom. PC3 cells were seeded at 1x104 cells/200 µl, and LNCaP cells were seeded at 3.5x104 cells/200 µl into each well. After seeding, the plates containing LNCaP cells were centrifuged for 3 minutes at 1200 rpm [28]. Spheroids grew to 350-400 µm diameters in 5 days by refreshing media to half volume every other day. Spheroids with different diameters were excluded from the experiments. Because of the slower metabolism of RWPE-1 cells, it is difficult to boost them to construct a spheroid structure. Any triggering manipulation brings a carcinogenic effect on these epithelial cells, which means changing their normal metabolism functions. On the other hand, the monolayer PBA viability analysis showed lower toxicity in RWPE-1 cells. Therefore, RWPE-1 cells were not included in the spheroid process and other analyses.
Chemotherapeutics treatment
The amount of PBA powder (P20009, Sigma‒Aldrich, Merck KGaA, Darmstadt, Germany) was determined by mass-molarity calculation, mixed with RPMI medium, and then sonicated for 10 minutes at 35°C. After the concentrations were determined according to viability assays, only the IC50 doses for each treatment duration were applied to the samples for further analysis.
Colchicine, which is known to inhibit tubulin polymerization, was included in the study as a positive control chemotherapeutic. Colchicine was purchased in powder form (C9754, Sigma‒Aldrich, Merck KGaA, Darmstadt, Germany) and dissolved in pure DMSO [29,30]. To avoid DMSO toxicity, the determined doses (0.05 μM-0.5 μM) were prepared by diluting the stock at a ratio of 1:1000 with appropriate media. Considering the possible toxicity of DMSO, viability analysis was also performed on cells treated with only 0.1% DMSO. As no toxicity was observed, a colchicine stock solution was formulated and utilized in the experiments. Experimental groups named according to the applied therapeutics, treatment time, and culture methods are listed in table 1.
Viability Analysis
The dose at which therapeutics kill half of the total cell population is known as the IC50 value of the therapeutic agent [31]. To determine the IC50 values of colchicine and PBA, MTT assays were conducted in 2D cultures, and CellTiter-GLO 3D viability analyses were performed in 3D cultures.
MTT analysis
Since the concentrations applied by Bradke et al. did not result in clear IC50 values in our experiments, the concentrations were revised and increased [32]. MTT [(3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] viability assay PBA (1 mM-20 mM) and colchicine (0.05 μM-0.5 μM) treatment were applied for 24 and 48 hours. After the treatment, the MTT assay was performed as described by Keskin et al. [33]. Absorbance measurements were recorded at 570 nm using a microplate reader. Each dose in the experimental set was performed in six replicates, and each experiment was repeated three times.
CellTiter-Glo® 3D analysis
The CellTiter-Glo assay is a luminescent analysis that measures cellular viability based on the amount of ATP present in cells. PC3 and LNCaP cells were used for 3D cultures, and the assay offers enhanced lytic capacity for use in microtissues. The half-life of the resulting luminescent signal is at least 3 hours, making CellTiter-Glo a preferred choice for viability analysis in 3D cultures [34].
Following the manufacturer's recommendations, CellTiter-Glo reagent was stored at -20°C and thawed slowly at +4°C one day prior to use. Spheroids were brought to room temperature 30 minutes before application. To ensure a 1:1 ratio of reagent to media, spheroids were transferred into 96-well mat white plates in 100 μL of existing media, and then 100 μL of reagent was added to each well. Afterward, samples were pipetted 8 times by using a multipipette. The plate was kept in a dark box on a shaker for 25 minutes at room temperature. The luminescent signal was recorded using a microplate reader following a total of 30 minutes of incubation. The experimental set comprised 6 replicates of each dose, and each experiment was repeated 3 times.
Colony formation assay
To examine the tumorigenic behavior of cancer cells after antimitotic chemotherapy, colony formation analysis was performed [35]. For the colony formation assay, 500 cells were seeded per well in a 6-well plate, and colonies were grown for a total of 10 days with media changes every two days. To prevent the formation of colonies beyond 10 days, PBA and colchicine treatments were applied at the IC50 doses on days 8 and 9, respectively, according to the treatment duration (24 hours or 48 hours). On the 10th day of the colony formation analysis, samples were fixed with 4% paraformaldehyde (PFA) and stained with 2% crystal violet (ab246816) for 5 minutes. After washing with distilled water to remove excess dye, images of the samples were photographed by a mobile camera. Colonies were counted using ImageJ software. The number of colonies of the treated samples was compared with that of the untreated groups for every treatment duration. Each treatment group was seeded in triplicate, and each experiment was repeated 3 times.
Migration Analysis (Scratch Assay)
The scratch assay is a method used to investigate cancer cells' metastatic behavior in 2D culture (143). Migration ability is defined as the ability of cells to acquire mobility and migrate toward the empty space created between them [36]. For the migration model, cells were seeded into 6-well plates (PC3: 500,000 cells, LNCaP: 700,000 cells), and the media was refreshed every two days. On the 5th day, when the cells reached 70-80% confluency, a straight line was created in the center of the plate using a pipette tip. Wells were washed with Ca+2- and Mg+2-containing PBS to remove any debris. To record the closure of the scratch, images were taken at 0 h, 24 h and 48 h intervals depending on the treatment duration. At the end of the incubation period, the migration rate was calculated as the ratio of the remaining area (Tf) to the initial area (T0). Three replicates were performed for each sample in each experimental set. The experiment sets were repeated three times.
Cell Proliferation Assay (Ki-67 Test)
2D and 3D culture samples were prepared as a single cell suspension. 2D cultured cells were briefly harvested and fixed with 4% PFA at +4oC for 30 mins. Spheroids obtained from 3D cultures were initially treated with 0.2% trypsin and then sonicated to obtain single cell suspension. Single cells fixed with 4% PFA along with 2D cultured cells.
All samples then permeabilized with Perm buffer according to the manufacturer (TrueNuclear Transcription Factor Buffer Set, BioLegend). Cells were incubated with primary antibody at RT for 15 mins, then washed and stained with fluorochrome-conjugated secondary antibody at RT for 15 mins. Cells were then washed and resuspended in FACS buffer.
Acquisition on Symphony A1 (BD Bioscience, USA) is held and FlowJo (BD Bioscience, USA) software is used for analysis.
Immunofluorescence Analysis
For 2D culture samples, all cell lines were seeded onto 12-well chambers (81201, IBIDI GmbH, Germany) and allowed to adhere to the surface overnight. The next day, PBA and colchicine were applied at the determined IC50 doses for 24 and 48 hours. After removing the media from the wells, the samples were fixed with 4% PFA at room temperature for 20 minutes. Wells were washed three times with PBS. Permeabilization was achieved with 0.5% Triton-X solution at room temperature for 10 minutes. Then, the samples were washed three times with PBS. The samples were treated with blocking solution (0.3% Triton-X, 5% goat serum) at room temperature for 1 hour. The primary antibodies anti-JNK1+JNK2+JNK3 (1:200, sc-7345, Santa Cruz Biotechnology, USA), anti-p38 (1:100, 9212, Cell Signaling Technology, USA), and anti-ERK1/ERK2 (1:200, sc-135900, Santa Cruz Biotechnology, USA) were prepared in dilution buffer. After removing the blocking solution, plates were incubated in a humid box at +4°C overnight. After washing with PBS, the plates were incubated with anti-JNK1+JNK2+JNK3 and anti-ERK1/ERK2 (goat anti-mouse 568, 1:1000, Ab175473, Abcam, UK) and anti-p38 (goat anti-rabbit 488, 1:1000, Ab150077, Abcam, UK) secondary antibodies at room temperature in the dark for 1 hour. Nuclei were stained with (4′,6-diamidino-2-phenylindole) DAPI for counterstaining. After removing the IBIDI chambers from the glass slides, the samples were gently closed with Floromount, and images were obtained using a Zeiss LSM 800 microscope (Zeiss, Germany). The whole 3D immunofluorescence protocol was performed in eppendorf tubes with a liquid volume of 100 μl for each step similar to 2D protocol. For permeabilization, samples were treated with a 0.5% Triton-X solution at room temperature for 10 minutes. Thereafter, the primary and secondary antibody incubation times increased. For imaging, the spheroids were transferred to 12-well IBIDI chambers with 30 μL of media. Images were obtained using a Zeiss LSM 800 (Zeiss, Germany) microscope without removing the chamber. Intensity measurements were performed using ImageJ software. The intensity data of 2D culture samples were measured on three different areas with a 10X objective for each group. The intensity data were obtained by dividing the intensity of one cell by the area of every cell in the selected era. For 3D samples, the spheroids were imaged using the Z-stack method on a confocal microscope. After combining all the layers for analysis, the total protein intensity of the spheroid was measured. The intensity value was divided by the measurement area to obtain data specific to the sample. Subsequently, for 2D and 3D intensity analysis, the results were normalized based on the intensity value of the negative control sample.
Transmission Electron Microscopy
Colchicine- and PBA-treated 2D cells were detached from the plate using trypsin and mixed with 5% FBS containing medium to inhibit trypsinization. After centrifugation at 1200 rpm for 5 minutes, the resulting cell pellet was fixed with 2.5% glutaraldehyde. The 3D culture samples were transferred within 30 µL media to eppendorf tubes containing 2.5% glutaraldehyde for fixation. The fixed 2D and 3D samples were then embedded in 1.5% agar and incubated for further processing.
The agar-embedded samples were then washed with a buffer solution, postfixed with 1% osmium tetroxide for an hour, and dehydrated in an ascending series of acetone (30%, 60%, 90%, and 100%) for 30 minutes each. The Epoxy-Embedding Kit (Sigma 45359) protocol was used. The molded samples were left at 60°C for 24 hours to polymerize the epon. Semithin sections of 1 µm were obtained using an ultramicrotome (Leica Ultracut R) from the blocks. The sections were stained with 1% toluidine blue, and the area of interest was determined by light microscopy. The blocks were then trimmed accordingly, and ultrathin sections of 60 nm were obtained and placed on 200 mesh copper grids. Sections with a thickness of 1 μm were obtained from the epoxy blocks, and areas, where 60 nm sections would be taken, were identified and photographed after staining with toluidine blue. Untreated 2D culture model samples were obtained by trypsinization and centrifugation to form pellets, resulting in the cells being scattered and losing their original morphologies due to the disconnection of cell‒cell and cell-surface adhesions. Since individual cells were visible in the 2D samples, it was easy to distinguish whether the cells in the image had a normal or apoptotic appearance. The sections were examined and photographed using a Zeiss Gemini SEM 500.
Statistical Analysis
The absorbance values obtained from the microplate reader in the viability analysis were normalized using the GraphPad Prism program, and the IC50 values were obtained by taking the logarithm of the treated concentrations. For the colony formation analysis, the counted colonies were analyzed statistically using one-way ANOVA, Tukey's posttest, and Dunnett's posttest. In the migration analysis, following the closure ratio calculated via Excel the data were analyzed statistically using one-way ANOVA and Tukey's posttest. For the immunofluorescence analysis, the data were analyzed using one-way ANOVA and Dunnett's posttest in GraphPad Prism software, comparing with the control group and with each other experimental group. The statistical significance value was evaluated as p≤ 0.05.