Patient samples and data collection
The study was approved by the Institutional Review Board of the Gyeongsang national university hospital. Tissue samples were obtained from patients with stage I–IV gastric cancer who had been diagnosed at Gyeongsang national university hospital between 2001 and 2010. For immunohistochemical (IHC) studies, tissue microarrays were incubated overnight at 4°C with anti-Sirt6 antibodies (Abcam, Cambridge, UK). Sirt6 gene expression and clinical data was obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/), specifically datasets GSE29272, and The Cancer Genome Atlas (TCGA) dataset. These data were used to compare Sirt6 gene expression between normal gastric tissue and gastric cancer samples, and the association between Sirt6 expression and survival rates was evaluated.
Cell lines and chemicals
The gastric cancer cell line SNU-638 and human primary stomach epithelial cells (HPSECs) were obtained from the Korean Cell Line Bank (Seoul, Korea) and Cell Biologics, Inc. (Chicago, IL, USA). Cells were cultured in RPMI1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (GenDEPOT) and 1% penicillin/streptomycin (Thermo Fisher Scientific); HPSECs were cultured at 37°C with 5% CO2 in a humidified incubator using Epithelial Cell Medium /w Kit (H6621). The chemicals used in this study were nutlin-3 (MDM2 inhibitor, Sigma-Aldrich (St. Louis, MO, USA).,) and MG-132 (Calbiochem, EMD Millipore Corp. Billerica, MA USA).
Western blot analysis
Total proteins were extracted from SNU-638 cells and HPSECs using radioimmunoprecipitation assay lysis buffer (Thermo Fisher Scientific) supplemented with a protease inhibitor cocktail (GenDEPOT). Cells were sonicated for 2 min and centrifuged at 14,000 g for 10 min at 4°C to remove insoluble cell debris. Protein concentration was determined using the BCA protein assay kit (Pierce, Rockford, IL, USA). Total protein lysates (30 µg) were separated by SDS-PAGE and transferred to PVDF membranes (Millipore, Bedford, MA, USA). After blocking with 5% BSA, membranes were incubated with primary antibodies against Sirt1, α-tubulin, lamin a/c (Santa Cruz, CA, USA, MDM2 (Cell Signaling Technology, Inc.), and Sirt6 (Abcam). The blots were then incubated with horseradish peroxidase-conjugated anti-rabbit IgG or anti-mouse IgG (Thermo Fisher Scientific). Signals were visualized using the Clarity Western blot ECL Substrate (Bio-Rad, Hercules, CA, USA). and imaged using the ChemiDoc Touch Imaging System (Bio-Rad).
Flow cytometric DNA analysis
Collected cells were washed twice with cold PBS, fixed with 70% ethanol for 1 h at 4°C, treated with 1 mg/ml RNase A (Sigma-Aldrich, St. Louis, MO, USA), and then stained with 50 µg/ml PI (Sigma-Aldrich). Data were acquired on a Cytomics FC500 Flow Cytometer equipped with two laser sources (Beckman-Coulter). Results were analyzed using CXP Software (Beckman-Coulter).
ROS measurement
Intracellular generation of ROS was measured using 2’,7’-dichlorodihydrofluorescene diacetate (DCF-DA; Molecular Probes, Eugene, OR, USA). Cells were stained with 5 µM DCF-DA in serum-free medium for 15 min and removed from the plate with trypLE-Express (Gibco). Fluorescence intensity was measured on a Cytomics FC500 flow cytometry (Beckman-Coulter) with an excitation wavelength of 480 nm and an emission wavelength of 525 nm. Data were analyzed using CXP Software (Beckman-Coulter).
IHC analysis of Sirt6 and evaluation of IHC reactions
Formalin-fixed, paraffin-embedded tissue samples from nude mice injected with SNU-638 cells were subjected to IHC. Tissue blocks were cut into 5 µm slices, which were de-paraffinized and rehydrated. The slides were incubated in 3% hydrogen peroxide for 10 min to block endogenous peroxidase activity, and then heated for 20 min in 10 mM citrate buffer (pH 6.0) in a microwave oven (700 W). The sections were incubated overnight at 4°C with anti-Sirt6 antibodies (Abcam).
ICC-Immunofluorescence (IF) for Sirt1 and Sirt6 double staining
HPSECs and SNU-638 cells were seeded on coverslips and treated with Ad-Lac Z or Ad-Sirt6 for 72 h. The cells were fixed using paraformaldehyde (3.7%) for 15 min at RT, washed with 1 × PBS + 0.1 M glycine, and permeabilized with 1 × PBS + 0.2% Triton-X. Cells were then blocked with 1% BSA for 30 min at RT and stained with primary antibodies (Ad-Sirt1, Ad-Sirt6; Abcam) and the corresponding secondary antibodies. Nuclei were stained with DAPI. Stained cells were analyzed using a laser scanning confocal microscope (Olympus).
Immunoprecipitation (IP) assay
The interaction between proteins was examined by immunoprecipitation (IP) assays. Cell lysates were first incubated with Dynabeads with Sirt6 (1:50) antibody for 3 h at 4°C. The immunocomplexes were washed three times with 1× wash buffer, extracted with elution buffer, and analyzed by western blotting using antibodies against Sirt1 and Sirt6.
Preparation of adenovirus
Adenovirus encoding Sirt6 (Ad-Sirt6) was created using the ViraPower adenovirus expression system (Invitrogen by Thermo Fisher Scientific, USA). Briefly, cDNA encoding Sirt6 was subcloned into the pENTR vector. After sequence verification, the Sirt6 cDNA was transferred to the pAd/CMV/V5-DEST vector using the Gateway system with LR Clonase (Invitrogen). The verified clone (Ad-Sirt6) was linearized using PacI (New England Biolab), and then transfected into 293A cells using Lipofectamine 3000 (Invitrogen; Thermo Fisher Scientific, Inc.). Virus was prepared and amplified with the ViraPower adenoviral expression system (Invitrogen), and viral titers were determined by plaque-forming assay after serial dilution. Aliquots of viral suspension were used to infect SNU-638 cell lines. Recombinant replication-defective adenovirus encoding green fluorescent protein (Ad-GFP) or β-galactosidase (Ad-LacZ) was used as a control.
Short hairpin RNA (shRNA)-mediated silencing of Sirt6 and MDM2
For shRNA-mediated depletion of Sirt6 and MDM2, glycerol stocks of bacteria containing Sirt6- or MDM2-targeting shRNA plasmid DNA (MISSION shRNA), as well as a non-targeting control plasmid DNA (SHC002) were purchased from Sigma-Aldrich. Lentiviral particles were used to deliver and express shRNAs to knock down human Sirt6 and MDM2, and a scrambled shRNA was used as a control. Lentiviral particles were generated by co-transfection of a targeting set of shRNA plasmids (Sirt6 and MDM2) or non-targeting control shRNA plasmid along with MISSION Lentiviral Packaging Mix (SHP001; Sigma-Aldrich) into 293FT cells (Thermo Fisher Scientific) using Lipofectamine 3000 (Life Technologies, Germany). Cell culture supernatants containing lentiviral particles were collected at 24 and 48 h post-transfection, filtered, and used to infect SNU-638 cells. The efficiency of Sirt6 and MDM2 knockdown was evaluated by western blotting of whole-cell extracts.
Preparation of nuclear and cytosolic extracts
Nuclear and cytoplasmic cell fractions were prepared using the NE-PER Reagent (Pierce). Briefly, cells were harvested in trypsin-EDTA (MediaTek) and spun at 500 g for 3 min. Cell pellets were resuspended in Cytoplasmic Extraction Reagents (CERI and CERII), vortexed at high speed for 15 seconds, and centrifuged at 16,000 g for 5 min at 4°C. Cytoplasmic protein was recovered from the supernatant. The pellet was resuspended in Nuclear Extraction buffer (NER) by intermittent high speed vortexing over 40 min, and the sample was centrifuged at 16,000 g for 10 min at 4°C. Nuclear protein was recovered from the supernatant. The protein concentration of the nuclear and cytoplasmic fractions was determined using the BCA assay. Cytosolic and nuclear proteins or whole-cell lysates were separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) in a 10% polyacrylamide gel and transferred to a nitrocellulose membrane (Millipore, Bedford, MA, USA). Membranes were incubated with primary antibodies against lamin A/C (Santa Cruz Biotechnology, Dallas, TX, USA) and α-tubulin (Sigma, St. Louis, MO, USA), followed by incubation with horseradish peroxidase-conjugated anti-rabbit IgG or anti-mouse IgG (Cell Signaling Technology, Beverly, MA, USA). Antibody binding was detected using an enhanced chemiluminescence detection reagent (Pierce). Images were acquired with the ChemiDoc Touch Imaging System (Bio-Rad).
In vivo xenograft mouse model
All animal experiments were approved by the Institutional Animal Care and Use Committee of Gyeongsang National University and conducted according to the National Research Council Guidelines. A cell suspension (5 × 106 cells/mouse) of SNU-638 was injected subcutaneously into 6-week-old male nude mice (athymic nude mice; KOATECH corporation, Harlan, Indianapolis, IN, USA). Nine days after inoculation of the cells, animals with xenograft tumors measuring 0.6–0.7 cm in diameter were subjected to intratumoral injections of Ad-GFP or Ad-Sirt6. Tumor diameters were measured with digital calipers on days 5, 10, 15, and 20, and tumor volume was determined using the modified ellipsoidal formula (tumor volume = 1⁄2[length × width2]).
Statistics
All statistical analysis was performed with SPSS software, version 20.0 (IBM, Armonk, NY, USA) and GraphPad Prism (version 8.0; GraphPad Software, San Diego, CA, USA). Chi-squared analysis was used to assess the relationship between Sirt6 expression and clinicopathological parameters. Student’s t-test was used to analyze the differences between groups and among groups, respectively. All tests used a p-value < 0.05 as the cut-off for statistical significance.