Cell culture and drug treatment
Human PCC lines PANC-1 and PATU-8988T were purchased from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 1% penicillin/streptomycin (Invitrogen). The cultured cells at a density of 1 × 106 were initially plated in a 10-cm dish for 24 h. After incubation for 24 h, the culture medium was replaced with serum-free medium. PANC-1 and PATU-8988T cells were treated with 0.2 and 0.5 mM puerarin (Fig. 1a, CAS#: 3681-99-0, Purity: ≥ 98% by HPLC, Yuanye Biotechnology, Shanghai, China) with or without MHY1485 (CAS#: 326914-06-1, MedChem Express, Monmouth Junction, NJ, USA).
Cell counting Kit-8 (CCK-8) assay
The CCK-8 assay kit (Dojindo, Shanghai, China) was used to detect the anti-tumor activity of puerarin in PANC-1 and PATU-8988T cells according to the manufacturer’s instructions. First, the cells were cultured in 6-cm dishes with fresh medium for 24 h. The cells in the logarithmic growth stage were inoculated into 96-well plates at a density of 5 × 103 cells/ml. Then, the cells were treated with different concentrations of puerarin for 24 h. After that, 10 µl of CCK-8 medium and 10 µl of CCK-8 were added and the plates were incubated for another 4 h. The absorbance was measured at a wavelength of 450 nm using a microplate reader. Statistical analyses were performed using Stata statistical software (StataCorp LP). Each experiment was repeated thrice and the average value was taken as the final result.
Flow cytometry analysis
The cells were serum-starved for 24 h and the medium was replaced with complete medium. PANC-1 and PATU-8988T cells were exposed to culture medium containing different concentrations of puerarin for 24 h, and cells in the standard control group were treated with dimethyl sulfoxide (DMSO, Sigma-Aldrich, St. Louis, MO, USA). After centrifugation to collect the cells, quantification of the apoptotic cells was performed using an Annexin V-FITC Apoptosis Detection Kit (Multisciences, Hangzhou, China) according to the manufacturer’s instructions. Cell apoptosis was assessed by flow cytometry (Ex = 488 nm; Em = 530 nm, BD FACSVerse™, BD Biosciences, San Jose, CA, USA), and the results were analyzed using FlowJo (TreeStar, Ashland, OR, USA).
Real-time cellular analysis (RTCA)
Cell proliferation was monitored by the xCELLigence RTCA MP System (ACEA Biosciences, San Diego, CA, USA) using 16-well E-Plates (ACEA Biosciences). The cells were seeded in triplicate at 5 × 103 cells/well in the plates. For the RTCA experiments, the cells were treated with puerarin after reaching steady growth (24 h). Impedance was measured every 15 min over 96 h and represented as the cell index by the RTCA-integrated software of the xCELLigence System. The cell index was normalized to 1 at the time point of drug administration. From this data, real-time cell growth curves were generated with GraphPad Prism 7 (GraphPad Software, La Jolla, CA, USA).
Transwell invasion assay
Transwell assays were performed using Transwell chambers (Costar, New York City, NY, USA) with Matrigel® (BD Biosciences). After treatment with various concentrations of puerarin for 24 h, cell suspensions were prepared using ethylenetetraacetic acid (EDTA) enzyme. The cells were resuspended in serum-free medium and transferred to the inner chamber (5×104 cells per chamber). Complete medium was added to the outer chamber, and the plate was incubated in a CO2 incubator (37 ℃) for observation for 12 h. After carefully removing the non-migrating cells at the membrane site with a cotton swab, the cells were fixed with formaldehyde and stained with 0.1% crystal violet (Sigma), and quantification was performed by counting five random fields under the microscope (Leica Microsystems, Wetzlar, Germany). Each experiment was repeated three times.
Colony formation assay
The cells were seeded into 6-well plates at 1 × 103 cells per well and treated with puerarin 24 h later. After 24 h, the media was replaced with fresh media and cultured for 14 days. The colonies were then fixed with 2% formaldehyde and stained with 0.5% crystal violet. The number of colonies with ≥ 50 cells was counted under a microscope.
Wound healing assay
PANC-1 or PATU-8988T cells were seeded in 6 well plates and maintained at 37 ℃ for 24 h. The cells were scratched using a crystal pipette tip to make a linear gap. Next, the detached cells were washed away with phosphate-buffered saline (PBS) and different concentrations of puerarin were added. The cells were allowed to fill the gap, and after 24 h, images of the areas were captured using a microscope (Leica Microsystems).
Immunocytochemical staining
Immunofluorescence staining was performed based on established protocols. PANC-1 and PATU-8988T cells with different treatments were grown on glass coverslips for 24 h. The cells were fixed with 4% formaldehyde and permeabilized with 0.1% Triton X-100 (Thermo Scientific, Waltham, MA, USA). Blocking was performed with 4% goat serum (Gibco, Thermo Fisher Scientific) in Dulbecco’s phosphate-buffered saline (DPBS; Invitrogen, Paisley, UK) for 1.5 h at 37 ℃, followed by incubation with the primary antibodies (Table S1): anti-Ki67 (1:200), anti-α-SMA (1:200), anti-E-cadherin (1:200), and anti-p-mTOR (1:200) at 4℃ overnight. Next, the membranes were incubated in the appropriate second antibodies for 1 h at room temperature. At least three independent experiments for immunofluorescence staining were conducted.
Western blot analysis
After treating the cells for 24 h, the cells in each group were collected and the total cellular protein was extracted. After separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), the proteins were transferred onto polyvinylidene fluoride (PVDF) membranes. The membranes were blocked with 5% non-fat milk for 1 h at room temperature and incubated overnight at 4 ℃ with the primary antibodies (Table S1). The membranes were washed three times in Tris-buffered saline with 0.1% Tween 20 (TBST) the following day and incubated with the second antibody (anti-rabbit IgG) at room temperature for 1 h. After the membranes were rinsed, the protein expression levels were detected by enhanced chemiluminescence (ECL) and visualized by autoradiography. GAPDH was used as the internal reference protein.
Glucose metabolism assay
The intact cellular oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) were measured using a Seahorse XF96 Extracellular Flux Analyzer (Seahorse Bioscience, North Billerica, MA, USA). Briefly, 1 ×104 PANC-1 and PATU-8988T cells were seeded into 96-well cell plates and incubated overnight at 37 ℃ at 5% CO2. Both cells were pretreated with or without different concentrations of puerarin for 24 h. Simultaneously, the calibration plates were incubated overnight at 37 ℃ in a non-CO2 incubator, then the cell medium was replaced with assay medium. Once the probe calibration was completed, the cell plate replaced the probe plate. The analyzer plotted the OCR value, followed by the injection of the compounds sequentially as follows: oligomycin (an inhibitor of ATP synthase; 2.5 µM), carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP, an uncoupler of OXPHOS; 2 µM), rotenone (an inhibitor of complex I; 0.25 µM), and anti-mildew A (an inhibitor of complex III; 0.25 µM) (n = 8). The ECAR was evaluated after the continuous injection of glucose (10 mM), oligomycin (1 µM), and 2-Deoxy-D-glucose (2-DG, 50 mM) (n = 8). After completing the test, the BCA Protein Assay Kit was used to determine the protein concentrations to normalize the OCR and the ECAR according to the manufacturer’s instructions.
Nude mouse tumorigenicity
Male BALB/c nude mice (6–8 weeks old) were obtained from the Wenzhou Medical University Experimental Animal Center (Wenzhou, China). All mice were housed under controlled conditions (temperature, 21–23 ℃; 12 h light/dark cycle; 55% humidity). PANC-1 cells (3 × 106) in 0.2 ml PBS were subcutaneously injected into the right thighs of 10 nude mice, which were randomly divided into two groups (n = 5 in each group). Mice in the experimental group received puerarin by intragastric gavage every three days for one month. The control group received DMSO injections for one month. Tumor formation in the nude mice was monitored for 30 days, with the length and width measured every three days. The tumor size was calculated according to the standard formula: tumor volumes (cm3) = (the longest diameter) × (the shortest diameter)2 × 0.5. The mice were deeply anesthetized with sodium pentobarbital and euthanized by cervical dislocation.
This animal study was approved by the Institutional Animal Care and Use Committee of Wenzhou Medical University, China. The animal experiments were conducted according to all regulatory and institutional guidelines for animal welfare (National Institutes of Health Publications, NIH Publications No. 80 − 23) [11].
Histopathological analysis
Tumor specimens from the animals were paraffin-embedded and cut into 4-µm-thick sections. Standard hematoxylin and eosin staining (HE, Yuanye Biotechnology) was performed on 4-µm sections from the paraffin-embedded tumor samples. Immunohistochemical (IHC) analysis was conducted under a microscope according to a previous method [11]. In brief, 4-µm-thick sections were dewaxed with xylene and rehydrated in a graded ethanol series. The sections were incubated in 0.1% sodium citrate buffer (pH 6.0) for antigen retrieval, and endogenous peroxidase activity was blocked with 3% hydrogen peroxide (Beyotime, China). IHC staining was performed using the following primary antibodies: anti-Ki67 (1:200), anti-c-Myc (1:200), anti-α-SMA (1:200), anti-E-cadherin (1:200), anti-cleaved caspase-8 (1:100), anti-cytochrome C (1:100), and anti-HIF-1α (1:200). The integrated optical density (IOD) was measured using Image-Pro Plus software (version 6.0, Media Cybernetics, Silver Spring, MD, USA). All samples were semi-quantitatively or quantitatively assessed by two independent investigators in a blinded manner.
Molecular docking
Molecular docking was performed as previously described [12], Puerarin and mTOR were rigidly docked, and the docking results were analyzed by PyMOL software. The puerarin molecule was downloaded from Pubchem, and the molecular energy was optimized through Chem 3D Ultra Software (8.0.3 version, Cambridge-Soft, MA, USA). The crystal structure of mTOR was downloaded from the Protein Structure Database (Protein Data Bank, PDB) (http://www.rcsb.org/pdb/), and the protein was processed by Autodock (MGLTools-1.5.6) to remove water molecules and hydrogenate and to add volume.
Database analysis
The correlation between AKT and mTOR expression and the activity of KRAS, TP53, CDKN2A, and SMAD4 was evaluated in the GEPIA 2 database website (http://gepia2.cancer-pku.cn/#analysis).
Statistical analysis
The data are expressed as the mean ± standard deviation for the in vitro and in vivo experiments. All statistical analyses were performed using GraphPad Prism statistical analysis software (version 8.0, GraphPad Software, Inc., LaJolla, CA, USA). Statistical comparisons were made with a two-sided t-test. One-way analysis of variance (ANOVA) with Bonferroni’s post-hoc test was used when more than two groups were present. Statistical significance was indicated by a P-value of < 0.05.