Tissue microarray and bioinformatics analysis
The lung cancer tissue microarray was purchased from Outdo (Shanghai, China), containing 92 LUAD tissues and paired para-carcinoma tissues. Both intensity and positive percentage of immunohistochemistry (IHC) were used to examine MUC3A expression: the IHC H-score (values 0-400) = the scores for intensity of positive staining (negative = 0, weak = 1, moderate =2, or strong = 3) × the percentage of positive-stained cells × 100. A total of 156 cases of Hou Lung lung cancer data from Oncomine was used to analyze the expression of MUC3A in various lung cancer histological types and normal tissue. A TCGA based database http://gepia.cancer-pku.cn. To analysis, the Pearson correlation of two genes. A total of 156 cases of MUC3A expression in the normal and various lung cancer tissues was analyzed in the online database Oncomine. R language package to analyze the Pearson correlation of MUC3A and RELA log2 expression.
Cells
The NCI-H1975 and NCI-H1299 cell lines were purchased from the Type Culture Collection (Chinese Academy of Sciences, Shanghai, China) with the short tandem repeat sequencing authentication (Cellcook Biotech, Guangzhou, China, Figure S1-2). Both cell lines were cultured in RPMI-1640 medium (HyClone, USA) with 10% fetal bovine serum (HyClone), 100 units/ml penicillin and 100 µg/ml streptomycin (HyClone) at 37 °C with 5% CO2.
Cell viability assay
The cells were seeded in 96-well plates (7,000 cells/well) and cultured for 5 days. After adding 10 μl CCK8 (Dojindo, Japan) to each well and incubating at 37 °C for 2 h, the absorbance at 450 nm was measured by the Rayto-6000 system (Rayto, China), and normalized to that of RPMI-1640 medium as control.
Colony formation assay
For cell proliferation, we seeded 50 cells to each well of 12-well plates for 7 days, then fixed with 4% paraformaldehyde (PFA) and stained with crystal violet. For radiation sensitivity, 100, 200, 400, 1,000, 2,000 and 10,000 cells were seeded in 6-well plates. The cells were then irradiated at 0, 1, 2, 4, 6, 8, and 10 Gray (Gy) with the Small Animal Radiation Research Platform (SARRP, 204 kV, PXI X-RAD 225Cx, CT, USA) from a photon beam. After 15 days, the colonies were fixed with 4% PFA for 15 min and stained with crystal violet. The cells were photographed, and the numbers of colonies were counted. A “multitarget-single hitting” model was applied to fit the survival curve.
Cell cycle assay
After starving for six h, the cells were harvested, fixed with cold ethanol overnight, and then incubated with propidium iodide and RNAse (BD, USA) in the dark for 15 min. The stained cells were assessed by flow cytometry (FACS AriaIII, BD, USA) and analyzed by FlowJo vX.0.7 software.
Cell apoptosis assay
The cells cultured on 24-mm coverslips were fixed by 4% PFA at room temperature for 30 min. After incubating with 0.1% Triton X-100 for 2 min, the TUNEL assay was performed according to the manufacturer’s instruction (Roche, Germany). The nuclei were labeled with DAPI at 2 μg/ml, and the immunofluorescence staining was analyzed by a fluorescence microscope (Olympus IX 73 DP80, Japan).
Modified Boyden chamber migration and invasion assay
The cells were seeded into the upper chambers of 12-well plates (1.5 × 105 cells/well) and cultured for 24 h. For invasion assay, the transwell membranes were precoated with Matrigel (1:40 dilution, Corning, USA) at 37 °C. After 24h, the cells were fixed with 4% PFA and stained with 0.1% crystal violet. The invaded and migrated cells were counted at five random fields per chamber under a phase-contrast microscope (DC 300F, Leica, Germany).
Immunoblotting analysis
The cells were lysed in RIPA buffer containing protease inhibitor and phosphatase inhibitor (Sigma-Aldrich, USA) on ice for 30 min. The cell lysates were centrifuged at 12,000 g for 15 min, and the supernatants were collected. The protein concentration was determined by Bradford protein assay (Bio-Rad, USA). The total proteins were separated using 7.5-12.5% SDS-PAGE (Bio-Rad) and transferred to a PVDF membrane (Millipore, USA). TBST with 5% milk was used to block non-specific binding sites. The dilution of antibodies for WB has been list in Table S1-2. The immunoreactive proteins were detected by enhanced chemiluminescence.
Immunofluorescence staining
The NSCLC cells were seeded on 24-mm coverslips, fixed with 4% PFA for 30 min, penetrated with 0.1% Triton X-100 and blocked with 5% BSA at room temperature for 1 h. After incubated with primary antibody at 4 °C overnight, the cells were incubated with Cy3-labelled or FITC-labelled secondary antibodies at room temperature for 1 h. The nuclei were labeled with DAPI (2 μg/ml). The immunofluorescence staining was examined using a fluorescence microscope (IX 73 DP80, Olympus, Japan) or a laser confocal microscope (C2, Nikon, Japan). The mean density was applied to semi-qualified by Image-Pro Plus 6.0.
Co-immunoprecipitation
The NSCLC cells were lysed in RIPA buffer containing protease inhibitor and phosphatase inhibitor (Sigma-Aldrich, USA) on ice for 30 min. The cell lysates were centrifuged at 12,000 g for 15 min to collect the supernatant. Co-immunoprecipitation was performed as the protocol of BeaverBeads™ Protein A/G Immunoprecipitation Kit (Beaverbio, Suzhou, China).
Autophagy investigation
Mcherry-GFP-LC3 II adenovirus infection
3×105 cells were seeded in 6-well plate; once the cells stuck to the wells, Mcherry-GFP-LC3 II (Beyotime Ltd, Beijing, China) adenovirus was infected into cells. The cells were treated with 4 Gy X-ray 24 h after infection. Fluorescence microscope (Olympus IX 73 DP80, Japan) was used to observe the fluorescence 12 h after irradiation. After infection of cells with Ad-mCherry-GFP-LC3B adenovirus, mCherry-GFP-LC3B was presented in the cytoplasm with diffuse yellow fluorescence (a combination of mCherry and GFP) in the absence of autophagy. In the case of autophagy, mCherry-GFP-LC3B accumulated on the autophagic membrane in the form of yellow spots (LC3B dot or punctae) under fluorescence microscopy; when the autophagosome was fused to lysosomes, as a consequence of GFP fluorescence quenching under acidic environment, it appeared as red spots.
Transmission electron microscopy (TEM)
Four hours after irradiation, the cells were washed three times with PBS and then collected by cell scraper, centrifuged at 2000 r/min for 5 min, discarded the supernatants. The cell pellets were fixed with 2.5% glutaraldehyde for 1h, then post-fixed with 1% osmium tetroxide buffer for 1 h. Subsequently, an ascending series of alcohol were performed for dehydration before embedding samples in Araldite. Ultrathin sections were observed by TEM (HT7700, Hitachi, Japan, 100kV).
Tissue assay
The microarrays including 92 pairs of lung adenocarcinoma and corresponding non-tumor tissues are purchased from BioChip (Shanghai, China), the samples come from National Human Genetic Resources Sharing Service Platform (2005DKA21300), all the dots on the chip were detected by IHC with survival information and included in univariate and multivariate survival analyses (Table S3). H-score applied to semi-qualify the IHC results; the representative images of 4 different staining intensities were shown in Figure 1A.
Animals
Six-week-old female BALB-C/NULL mice (Vital River Laboratory Animal Technology Co., Ltd, Beijing, China) were housed in a specific pathogen-free, temperature, and humidity-controlled environment with food and water in their cages. All animal experiments were performed according to the Wuhan University Animal Care Facility and the National Institutes of Health Guidelines.
In vivo assay
Approximately 5 × 106 H1975-GFP cells were harvested, resuspended in 100 μl PBS, and injected subcutaneously into the right flank of each mouse. Treatment was commenced when the tumor size reached approximately 100 mm3. The mice were randomized into four groups and treated as follows: control, MUC3A KD group, control with radiation group (20 Gy/2 f, Small Animal Irradiation Research Platform SARRP, PXI X-RAD 225Cx, CT, USA), and MUC3A KD with radiation group. The size of the subcutaneous tumors and weight of the mice were recorded every day. Before the mice were radiated, we applied X-ray fluoroscopy to confirm the completed loci in the irradiated field. An animal in vivo imaging system was used to evaluate the size of the tumor at Day 7 and 14 after radiotherapy. Tumor volume (V) was calculated according to the formula: π/6 × length × width2. The mice were sacrificed when the following points were reached: 1, tumor size reached 1,500 mm3; 2, the tumor influenced breathing, eating, walking, and any other physiologic functions; 3, the tumor surface appeared to have anabiosis.
The tissues from the tumor-bearing mice were fixed in 4% PFA at four ℃ overnight and embedded into paraffin (Paraplast, Sigma-Aldrich) using tissue processor (Thermo Fisher Scientific, Loughborough, UK). Paraffin sections (5 µm) were cut with a rotation microtome (Thermo Fisher Scientific, Bremen, Germany). The images were collected by Versa 8 (Leica, Germany). IHC was followed by the protocol described. The integrated optical density (IOD) of the immunohistochemistry (IHC) section was calculated by Image-Pro Plus 6.0.
Statistical analyses
Each experiment was performed in triplicates and data presented in the representation of 3 individual experiments. A two-tailed Student’s t-test and one-way analysis of variance (ANOVA) were used to evaluate the statistical significance of different groups. Statistical analyses were performed with SPSS 16.0. P < 0.05 were considered as statistical significance.