Cell lines and reagents
Human GC cell lines (NCI-N87, SGC7901, MGC-803, and MKN45) were purchased from the Cell Bank of Chinese Academy of Sciences (Shanghai, China). Human HER2-positive GC SNU216 cells were a generous gift from Professor Ruihua Xu, of Sun Yat-sen University Cancer Center (Guangzhou, China). NCI-N87-AR is a pyrotinib-resistant cell line obtained by continuous exposure of NCI-N87 cells to pyrotinib. All cells were cultured in RPMI-1640 (Hyclone, Provo, UT) containing 10% fetal bovine serum (FBS; Gibco, MD, USA) in an incubator with 5% CO2 and proper humidity, at 37 ℃. Pyrotinib (SHR1258) and apatinib (YN968D1) were obtained from Hengrui Medicine Co., Ltd (Lianyungang, China). Reagents were dissolved in dimethyl sulfoxide (DMSO) and stored at − 20 ℃. Recombinant human SCF was purchased from MedChemExpress LLC. (New Jersey, USA) and maintained at − 20 ℃ until further use.
Cell viability assay
Cells (4000–8000 cells/100μL per well) were seeded in 96-well plates and incubated at 37 °C overnight. After 72 h of treatments, the Cell Counting Kit (CCK)-8 reagent (Promotor, Wuhan, China) was added at a concentration of 10%, and the absorbance of the samples was measured at 450 nm using a microplate reader (BioTek, VT, USA). The experiment was performed in triplicate and data were representative of three separate experiments.
Colony formation assay
Cells were cultured in 6-well plates at a density of 800–1000 cells/well. The culture medium was renewed to normal after 72 h of different treatments and incubated for 2 weeks. The colonies were fixed and stained with 0.1% Crystal Violet, and colony (> 50 cells/colony) counts of the samples were then compared to that of the control group. The experiments were performed in triplicate and data were representative of three separate experiments.
Transwell assay
Cells (5 × 104) suspended in 200 µL serum-free medium were transferred into the upper chamber of a 24-well insert containing a membrane with an 8-μm pore size (Corning, New York, USA), and 500 μL medium containing 20% FBS was added to the bottom chamber. After incubation for 72 h, the cells that crossed the membrane were fixed and stained with 0.1% Crystal Violet for 30 min. For each sample, 10 fields of view were counted and the average was calculated (100 ×). The final data were obtained from three independent experiments.
Cell apoptosis analysis by flow cytometry
5 × 105 cells were obtained, washed twice with PBS, and re-suspended in 200 μL of 1 × binding buffer (BD Biosciences, NJ, USA), stained with 5 µL of FITC Annexin V, and incubated in the dark for 15 min, at 37 ℃. 5 µL of propidium iodide (PI) and 300 μL of 1 × binding buffer were then added 5 min prior to testing in the dark, at room temperature. Samples were measured by flow cytometry on an LSRFortessa cell analyzer (BD Biosciences), and the results were analyzed using FlowJo software (v.10.0; TreeStar, CA, USA). The final data were obtained from three independent experiments (Table 1).
Table 1 Synergism analysis in NCI-N87 xenograft models RNA extraction and quantitative real-time PCR (qRT-PCR)
Total RNA was extracted using RNAiso Plus (Takara, Dalian, China), and reverse-transcribed to cDNA with the RevertAid first-strand cDNA synthesis kit (Thermo Fisher) according to a standard protocol. Real-Time qPCR was performed using the 7900HT Fast real-time PCR system (Thermo Fisher). GAPDH and β-actin were used as control and the 2−ΔΔCt method was used to quantify the relative mRNA expression of the genes. The sequences of primers are enlisted in the Supplementary Table 2. The experiments were performed in triplicate and the data were obtained from three separate experiments.
RNA sequencing and data analysis
RNA (1 μg) with an RNA Integrity number above 6.5 was used for following library preparation. Libraries with different indices were multiplexed and loaded onto an Illumina HiSeq instrument (Illumina, CA, USA) according to manufacturer’s instructions. The sequences were processed and analyzed by GENEWIZ (NJ, USA). A P value < 0.05 was used as the cut-off criterion.
Protein extraction and western blot analysis
Total protein was extracted with a radioimmunoprecipitation assay (RIPA) buffer (Beyotime, Shanghai, China) supplemented with phenylmethylsulphonyl fluoride (PMSF) and phosphatase inhibitors (Servicebio, Wuhan, China). Protein quantification was then performed using the BCA reagent (Beyotime), following the manufacturer's instructions. The extracted proteins were loaded into 10% SDS-PAGE for separation, and transferred to a 0.45 μm polyvinylidene fluoride (PVDF) membrane (Millipore, Massachusetts, USA). Primary antibodies were added, and the membrane was incubated at 4 ℃ overnight. Subsequently, the membrane was incubated with secondary antibodies (Promotor) at room temperature for 1 h. Post incubation, the SuperSignal West Pico Chemiluminescent Substrate (Thermo Fisher) was added. The immuno-reactive bands obtained were analyzed using the G: BOX Chemi X system (Syngene, Cambridge, UK). The primary antibodies used are enlisted in the Supplementary Table 3.
Xenograft models
Female nude mice (4–6-weeks old; BALB/c nu-nu) were purchased from the Hunan SJA Laboratory Animal Co., Ltd. (Changsha, China), and raised in a specific pathogen-free laboratory. Cells (5 × 106 cells/100 μL) were injected subcutaneously into the left posterior side of each mouse, and mice were randomized into different groups (n = 6) when the tumors reached about ~ 100 mm3. The size of the tumor and the weight of the nude mice were measured every 3 days, and the tumor volume was calculated as follows: [(short diameter)2 × (long diameter)]/2. Mice were sacrificed after 21 days. Tumor samples were collected, photographed, and stained. The fixed dose ratio of apatinib/pyrotinib was determined from the median effective dose (ED50) of the two monotherapies to prevent bias. The combination index (CI) was calculated to determine the combined effect, with CI < 1, CI > 1, and 1 used to defined synergism, antagonism, and additivity, respectively. To determine the statistical relevance of CI < 1 [i.e., ln(CI) < 0], the variance of ln(CI) was calculated according to a previous described method [16]. All institutional and national guidelines for the care and use of laboratory animals were followed.
Immunohistochemistry (IHC)
Immunohistochemistry was performed following the manufacturer’s instructions. In brief, tissue samples from xenograft models (n = 6 per group) were formalin-fixed overnight at 25 ℃, prior to embedding in paraffin. All tissue sections were obtained as slices from the paraffin blocks and the slices were incubated with primary antibodies against SCF (1:200, ab52603, Abcam, Cambridge, UK), Ki67 (1:200, #9027, Cell Signaling Technology, MA, USA), and CD31(1:2000, #3528, Cell Signaling Technology, MA, USA). The TdT-mediated dUTP nick-end labeling (TUNEL) assays were performed using a TUNEL in situ cell death detection kit (Sigma-Aldrich, MO, USA), according to manufacturer’s instructions. The results were then evaluated by two professional pathologists independently. The assays were performed by Biossci Biotechnology Co., Ltd. (Wuhan, China).
Statistics
Chart generation and statistical calculations were performed using the GraphPad Prism software (v8.0; CA, USA), and SPSS (v19.0; NY, USA) was used for statistical analysis. All descriptive statistics were presented as the mean ± standard deviation (SD). Statistical comparisons between two experimental groups were performed using Student's t test. If multiple groups were compared, the one-way analysis of variance (ANOVA) was performed first. The least significant difference t test was applied if the overall difference was statistically significant. The main objective of statistical analysis in isobologram studies was to generate an upper confidence limit for the CI to determine whether the observed synergy was statistically relevant (CI < 1). A P < 0.05 was considered statistically significant for all tests.