3.1. Drugs and Reagents
Gamabufotalin, sourced from TargetMol, is derived from bufotenine and dissolved in dimethyl sulfoxide (DMSO) as the solvent to prepare a 10 mM stock solution stored at -20°C; after serial dilution to the experimental GA concentrations (0 - 100 nM), the final concentration of DMSO in the cell culture medium was 0.01% (v/v), which was verified to have no cytotoxicity on the tested cells in preliminary experiments. Phosphate-buffered saline (PBS), dimethyl sulfoxide (DMSO), and neutral formalin were all procured from Solarbio Technology Ltd.
3.2. Cell Culture
SW480, HCT-116, NCM460, and 293T human colon cancer cell lines were procured from the American Type Culture Collection (ATCC). DMEM medium (06-1055-57-1ACS, BI, Israel) was used to cultivate the cells, supplemented with 10% fetal bovine serum (FBS, A3160801, Hyclone, USA) and 1% penicillin-streptomycin (P/S, UB89609, GBICO, USA). The cultures were kept in a 37°C incubator with an atmosphere of 5% CO2.
3.3. Cell Viability Assay
Once the 96-well plates had been seeded with cells at a density of 25% and the density had risen to around 40%, they were then exposed to GA (0 - 100 nM) for 48 hours of treatment. Subsequently, following the instructions provided by the CCK-8 kit (CK04, Japan), the relative cell activities of SW480, HCT116, HT-29, NCM460, and 293T after GA treatment were evaluated. All the experiments were repeated at least three times independently.
3.4. Cell Morphology Assay
SW480 cells were plated in 12-well plates at a 25% confluency. After they attached, their starting shape was recorded (T0). They were then treated with varying concentrations of GA (0 - 100 nM) for 48 hours, and changes in cell appearance throughout the experiment were photographed using an inverted microscope (Nikon, Japan).
3.5. Cell Migration Experiments
In accordance with the manufacturer's instructions, the insert (80469, IBIDI, Germany) was affixed to the bottom of a 12-well plate. Subsequently, SW480 cells were seeded into the same plate. The insert was removed once the cells reached approximately 80% confluence. A scratch measuring 500 µm in width was then created. Gamabufotalin (0 - 100 nM) was added for treatment and incubated for a duration of 48 hours. The width of the cell scratch was observed and documented using a microscope (Nikon, Japan). Three independent experiments were conducted, and in each experiment, three separate culture wells were used.
3.6. Cell Membrane Staining Assay
SW480 cells at a density of 30% were seeded in 12-well plates and incubated with GA (0 - 100 nM) for 24 hours before being washed with PBS and fixed with 4% paraformaldehyde for 15 min. Subsequently, after three washes with PBS, the cells were stained with a double dye solution of Hoechst 33342 (diluted at 1:1000, C1022, Beyotime, China) and Dio (diluted at 1:1000, C1038, Beyotime, China) for a duration of 20 minutes. Images were subsequently taken using a Nikon, Japan fluorescence inverted microscope.
3.7. Clone Formation Experiments
Twelve-well plates were used to seed SW480 cells at an initial confluency of 30%, which were then incubated at 37°C in a 5% carbon dioxide environment. Once colony formation was observed, varying concentrations of GA were introduced, and the cultures were maintained for a duration of nine days, with medium changes occurring every three days. After drug treatment, 4% paraformaldehyde was used to fix the cells at room temperature for fifteen minutes, followed by staining with KGA229 (KeyGEN BioTECH, China) crystal violet staining solution for five to ten minutes. The colonies were then documented under an inverted microscope (Nikon, Japan).
3.8. Live/Dead Cell Detection
Twelve-well plates were utilized to cultivate SW480 cells, which were then subjected to a range of GA concentrations (0 - 100 nM) at an estimated cell density of 40% for 36 hours. Cell viability was evaluated using the Calcein AM Cell Viability Assay Kit (C2013FT, Beyotime, China), followed by microscopic examination of the stained cells (Nikon, Japan).
3.9. Measurement of DNA Synthesis Rate by EdU Method
SW480 cells were seeded in 12-well plates at a density of 30% until the density reached about 50%, and then the cells were treated with GA (0 - 100 nM) for 24 hours. The rate of DNA synthesis in SW480 cells treated with GA (0 - 100 nM) was assessed using the EdU-594 cell proliferation assay reagent (C0078S, Beyotime, China). Staining results were documented under a microscope (Nikon, Japan) and subsequently quantified using ImageJ software. All assays were performed with the use of three biological replicates and three technical replicates within each group.
3.10. Cell Cycle Assay
SW480 cells treated with GA (0 - 100 nM) for 24 hours were harvested by centrifugation. After 70% cold ethanol was added, the samples were incubated overnight at 4°C. Centrifugation at 300 xg then caused the supernatant to be discarded, and the cells were resuspended in a solution of propidium iodide (PI) (KGA214, KeGEN BioTECH, China), 0.2% Triton X-100 (P0096, Beyotime, China), RNase (ST579, Beyotime, China), and PBS. Subsequently, further analysis was conducted using a flow cytometer (Beckman Coulter, CytoFLEX, USA). The experiment was performed with three independent biological replicates.
3.11. Detection of ROS by H2DCFDA
At 37°C, SW480 cells treated with GA were incubated in a carbon dioxide incubator for 30 minutes with H2DCFDA. To evaluate the alterations in ROS levels induced by the cell-permeable ROS probe H2DCFDA (HY-D0940, USA), Beckman flow cytometry (Cytomics FC500, USA) was employed to measure intracellular ROS levels. To determine whether ROS contributed to the observed inhibition of cell activity, SW480 cells were pretreated with the antioxidant N-acetylcysteine (NAC) (ST1546, Beyotime, China) for one hour and subsequently exposed to 50μM NAC for an additional 48 hours. Finally, cell viability was evaluated using the CCK-8 assay kit.
3.12. Mitochondrial Membrane Potential Staining Experiment
After treating SW480 cells with different concentrations of GA for 24 hours, the JC-1 mitochondrial membrane potential reagent mixture was prepared according to the instructions of the JC-1 reagent kit. The cells were incubated in the dark for 25 minutes, then washed with PBS. Afterwards, Hoechst 33342 (C1022, Beyotime, China) was added to stain the cell nuclei for 10 minutes. The procedure was carried out using a fluorescence microscope (Nikon, Japan). The experiment was performed with three independent biological replicates.
3.13. Apoptosis Detection
SW480 cells treated with GA were digested using EDTA-free trypsin (T1350, Solarbio, China). After digestion, the cells were incubated in the dark for 20 minutes, having been mixed with Annexin V-FITC (C1062M, Beyotime, China) and PI (KGA214, KeyGEN BioTECH, China). The apoptosis rate was subsequently assessed and recorded via flow cytometry (Beckman, Cytolfex, USA). The experiment was repeated independently three times, with each biological replicate consisting of three technical replicates.
3.14. Immunofluorescence Staining
After 24 hours of GA treatment, SW480 cells were fixed in 4% paraformaldehyde (PFA) for 15 minutes. Subsequently, permeabilization was applied with 0.3% Triton X-100 for an additional 15 minutes, followed by blocking with 3% BSA for 30 minutes. The Ki67 antibody (1:3000, ab15580, Abcam, UK) was incubated overnight at 4°C. Finally, the cells were exposed to Coralite 488-labeled pure goat anti-rabbit IgG (H+L) (SA00013-2, Proteintech, China) for a period of 1.5 hours. After staining the cytoskeleton with Red594 F-actin tracker (C2205S; Beyotime, China) and incubating with H33342 for an extra 10 minutes, the cells were then washed with PBS and viewed under a fluorescence inverted microscope (Nikon, Japan).
3.15. Xenograft in Nude Mice
The BALB/c-nude mice utilized in this study were procured from Jinan Pengyue Laboratory Animal Technology Co., LTD. For the experiment, a total of 10 female mice, each weighing approximately 20 g, aged 6 weeks, were chosen. Female BALB/c-nude mice were injected subcutaneously with CRC SW480 cells. Upon reaching 100 mm³ of tumor volume, the mice were randomly divided into two groups (each containing five nude mice). The GA treatment group received an injection of 0.058 mg/kg every three days, while the control group was given DMSO at the same volume and frequency. Mice were euthanized by carbon dioxide inhalation after 10 injections; their CRC xenografts were then harvested, weighed, and photographed.
3.16. H&E Staining
Using a rotary paraffin microtome (LEICA RM2235), 4.0 um thick tissue samples were sliced from pre-prepared paraffin sections. Subsequently, the sections were stained with a G1120 staining kit (Chabi, China) and then imaged using a pathological section scanner (3DHISTECH, Hungary).
3.17. Immunohistochemical Staining
After antigen retrieval, the tissue sections were subjected to boiling with a modified sodium citrate repair solution (072420210224, Bayes, China) for treatment. Following this step, the cells were blocked using goat serum (17H18B09, Bost, China) for 30 minutes before incubation with the primary antibody Ki67(ab15580, Abcam, USA) at a dilution of 1:350 in 1% BSA. Staining was performed using a DAB kit (17I07A22; Bost, China), and the results were documented accordingly. Finally, dehydration was carried out, and the slides were mounted. Scanning observations were conducted using a panoramic stage (3DHISTECH, Hungary).
3.18. Western Blotting
Protein extraction was performed using GA-treated SW480 cells, and the reagent used was RIPA lysis buffer (P0013B, Beyotime, China). Electrophoresis of the protein extracts on SDS polyacrylamide gels was conducted, and they were then transferred to PVDF membranes for immunoblotting. The primary antibodies used in this study were TP53I3/PIG3 (1:1000,14828-1-AP, Proteintech, China), β-Actin (1:2000, GB11001, Servicebio, Wuhan, China), and Cleaved caspase-3 (1:500; WL0217; Wanlei, China). Following incubation with the primary antibodies, HRP-labeled secondary antibodies were utilized to detect the immune response signals. The secondary antibody used was HRP-conjugated sheep anti-rabbit IgG (1:3000; AS014; AB-clonal; Wuhan, China), which was then developed with an ECL hypersensitive detection reagent (P0018AS; Beijing, China).
3.19. Molecular Docking
The interaction proteins of GA in CRC cells were investigated using the Protein Data Bank (PDB). The database code for the MDM2 protein is 4hbm. Molecular docking simulations were performed using AutoDock software. For subsequent docking procedures, three rotatable bonds of GA were activated, and a grid box was configured with dimensions of 40 × 40 × 40ų. To account for the flexibility of the protein, a soft docking feature was employed. The results from the protein-ligand docking were evaluated based on binding affinity (kcal/mol). All structural images were generated using PyMOL software (version 2.0, Schrodinger, LLC).
3.20. Proteomics
To evaluate the effects of GA on protein expression levels, protein extraction was performed on three control samples (CTL1, CTL2, CTL3) and three samples treated with 25 nM GA for a duration of 24 hours (GAT1, GAT2, GAT3). The proteomic analysis utilized the SDT method and was conducted in Shanghai, China. Each sample consisted of a total cell count of 1.5 × 107 cells. Subsequent proteomic analyses and data conversion tasks were carried out by a specialized protein technology company based in Shanghai, China.
3.21. Transcriptome Analysis
For transcriptome sequencing, three GA-treated samples and three control samples were lysed using Trizol reagent, respectively. Library construction, mRNA sequencing, and bioinformatics analysis were performed at Biomarker (Beijing, China).
3.22. Statistics
Statistical analyses were performed using GraphPad Prism software. Normality and homogeneity of variance were examined prior to statistical testing. All the experiments were conducted with three repetitions. For comparisons between two independent groups, an unpaired Student’s t-test was used. For comparisons among three or more groups, one-way ANOVA was applied. A P-value < 0.05 was considered statistically significant.