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57 protocols using p tbk1

1

Immunoblotting for Antiviral Signaling Proteins

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Immunoblotting was performed as described in our previous study. The antibodies used in this study were as follows: ALKBH5, FTO, RIG-I and HNRNPC purchased from Abcam (Cambridge, MA, UK); MAVS, IKKε, p-IKKε, TBK1, p-TBK1, IRF3, and p-TBK1 purchased from Cell Signaling Technology (Danvers, MA, USA); GAPDH and α-tubulin purchased from Proteintech Inc. (Proteintech, Rocky Hill, NJ, USA). The TBK1/IRF3-specific inhibitor Bay-985 was purchased from Selleck (Houston, TX, USA).
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2

Western Blot Analysis of STING Pathway

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Equal amounts of proteins were resolved on sodium dodecyl sulfate (SDS)-Polyacrylamide gels and transferred to polyvinylidene fluoride (PVDF) membranes (Millipore). After blocking with 5% Blocking Reagent, membranes were incubated with various primary antibodies (and appropriate secondary antibodies). The image was resolved using an enhanced chemiluminescence system ECL (Thermo Scientific) and detected by autoradiography (Kodak). Antibodies: rabbit anti STING polyclonal antibody was developed in our laboratory as described previously in Ishikawa et al, 2008 (link); other antibodies were obtained from following sources: β-actin (Sigma Aldrich), p-IRF3 (Cell Signaling), IRF3 (Santa Cruz Biotechnology), p-p65 (Cell Signaling), p65 (Cell Signaling), p-TBK1 (Cell Signaling), TBK1 (Abcam), cGAS (Cell Signaling).
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3

Antibody Immunoblotting for Cellular Signaling

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We used the following antibodies and dilutions for this study: ubiquitin (catalogue (cat.) no. 3936S, Cell Signaling Technology; 1:20:00), ISG15 (cat. no. HPA004627, Sigma Aldrich/Merck; 1:1,000), GAPDH (cat. no. 2118, Cell Signaling Technology; 1:2,000), GFP trap beads (cat no. gta-100, ChromoTek), GFP (cat. no. sc-9996, Santa Cruz Biotechnology; 1:2,000), IRF3 (cat. no. 4302, Cell Signaling Technology; 1:2,000), phospho-IRF3(Ser396) (cat. no. 4947, Cell Signaling Technology; 1:1,000), IκBα (cat. no. 4812, Cell Signaling Technology; 1:2,000), phospho-IκBα(Ser32/36) (cat. no. 9246, Cell Signaling Technology; 1:1,000), TBK1 (cat. no. 3013, Cell Signaling Technology; 1:2,000), pTBK1 (cat. no. 3300-1 Epitomics; 1:1,000), NF-κB p65 (cat. no. 8008, Santa Cruz Biotechnology; 1:2,000), lamin B1 (cat. no. sc-373918, Santa Cruz Biotechnology; 1:2,000).
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4

Immunoblotting Analyses of Innate Immune Signaling

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We used the following antibodies and dilutions for this study: ISG15 (cat. no. HPA004627, Sigma Aldrich/Merck; 1:1000), GAPDH (cat. no. 2118, Cell Signaling Technology; 1:2000), GFP trap beads (cat no. gta-100, ChromoTek), GFP (cat. no. sc-9996, Santa Cruz Biotechnology; 1:2000), IRF3 (cat. no. 4302, Cell Signaling Technology; 1:2000), phospho-IRF3(Ser396) (cat. no. 4947, Cell Signaling Technology; 1:1000), TBK1 (cat. no. 3013, Cell Signaling Technology; 1:2000), pTBK1 (cat. no. 3300–1 Epitomics; 1:1000), NF-κB p65 (cat. no. 8008, Santa Cruz Biotechnology; 1:2000)
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5

STING Signaling Pathway Analysis

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Cells were lysed with radioimmunoprecipitation assay (RIPA) buffer supplemented with a protease inhibitor (Cat. 25765800, Sigma Aldrich) and a phosphatase inhibitor (Cat. P5726, Sigma Aldrich). After denaturing the samples at 95°C for 5 minutes, 30μg of each protein sample was separated using SDS-PAGE and transferred onto nitrocellulose membranes (Cat. 1620112, Bio-Rad, Hercules, CA). Next, the membranes were blocked with 5% BSA for 1 hour, and then incubated with primary antibodies against STING (Cat. 13647S, Cell Signaling), IRF3 (Cat. 4302S, Cell Signaling), p-IRF3 (Cat. 4947S, Cell Signaling), TBK1 (Cat. 3013S, Cell Signaling), p-TBK1 (Cat. 5483S, Cell Signaling), β-actin (Cat. 3700S, Cell Signaling), and Vinculin (Cat. 13901S, Cell Signaling) overnight at 4°C. The following day, the membranes were washed with PBST and incubated with anti-mouse (Cat. NXA931, GE Healthcare, Chicago, IL) or anti-rabbit (Cat. NA934V, GE Healthcare) secondary antibody for 2 hours before developing with ECL substrates (Cat. 170506, BioRad). The gel images were captured using Chem-DocXRS image acquisition machine (Bio-Rad).
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6

Western Blot Analysis of Signaling Pathways

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Cells were lysed in complete radioimmunoprecipitation assay buffer with added 1× protease and Phosphatase Inhibitor Cocktail (Life Technologies). The lysate was centrifuged at 4 °C, 13,000 rpm for 20 min, and total cytoplasmic supernatant fraction was stored at −80 °C until future use. For mouse ear, whole immunoblot tissue was homogenized in 1× complete radioimmunoprecipitation assay buffer. Total protein was quantified for each treatment with Bio-Rad Protein Assay (Bio-Rad). About 10 μg of total protein was loaded onto a 4 to 20% Mini-PROTEAN TGX gel (Bio-Rad), transferred to a polyvinylidene difluoride membrane, and probed with primary antibodies. The following primary antibodies from Cell Signaling were used: p-TBK1 (5483; 1:1000 dilution), TBK1 (38066; 1:1000 dilution), p-IRF7 (5184; 1:1000 dilution), IRF7 (4920; 1:1000 dilution), p-Akt (4060; 1:1500 dilution), Akt (4685; 1:1500 dilution), p-p38 (4511; 1:1500 dilution), p38 (8690; 1:1000 dilution), phosphorylated extracellular signal–regulated protein kinase 1/2 (4370; 1:2000 dilution), and extracellular signal–regulated protein kinase 1/2 (4695; 1:2000 dilution). IRDye-conjugated anti-rabbit and antimouse secondary antibodies (IRDye800CW; Licor; 1:10,000 dilution) were used. The images were acquired on an Odyssey CLx Imaging System (Licor).
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7

Immunoblotting Protocol for ER Stress Proteins

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Cell lysis was performed in RIPA buffer (Boston Bio Products) supplemented with Halt protease and phosphatase inhibitor cocktail (ThermoFisher Scientific). SDS-PAGE was performed on NuPage Bis-Tris gels (ThermoFisher Scientific) using MOPS or MES running buffer. Gels were dry transferred onto 0.45 μm nitrocellulose membranes using the iBlot® Dry Blotting System (ThermoFisher Scientific).
The following Abs were purchased from Cell Signaling Technology: EIF2A (#5324), p-EIF2A (#3398), ATF4 (#11815), CHOP (2895), CALR (#12238), cGAS (#15102), TBK1 (#3504), pTBK1 (#5483), pIRF3 (#29047), STING (#13647). GAPDH (#2118) and B-ACTIN (#4970) were used as loading controls.
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8

Comprehensive Western Blot Analysis

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Western blotting was performed as previously described27 (link) using primary antibodies against LANA (Abcam), K-bZIP (Santa Cruz), β-actin (Santa Cruz), XPO1 (Sigma), p62 (Cell Signaling), pTBK1 (Cell Signaling), TBK1 (Novus Biologicals), pIRF3 (Novus), IRF3 (Novus), STING (Novus), and LC3B (Sigma). ORF65 and RTA antibodies were previously described5 (link),28 (link).
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9

Bone Marrow-Derived Dendritic Cell Generation and Cytokine Analysis

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For the generation of bone marrow-derived dendritic cell (BMDCs), the bone marrow cells (5 million cells in each 15 cm cell culture dish) were isolated from WT or STINGGt/Gt mice and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), in the presence of 30 ng/ml GM-CSF (BioLegend), for 10-12 days.
For cytokine assays, BMDCs or B16-F10 melanoma cells were infected with various viruses at an MOI of 10 for 1 hour, or mock-infected. The inoculum was removed, and the cells were washed with PBS two times and incubated with a fresh medium. Supernatants were collected at various times postinfection. Cytokine levels were measured by using ELISA kits for murine IFN-α/β (PBL Biomedical Laboratories), IL-6, CCL5, CXCL10, or GM-CSF (R & D Systems).
For western blot analysis, BMDCs or B16-F10 cells were infected with the indicated viruses at an MOI of 10, and cell lysates were collected at different time points after virus infection. Polypeptides were separated by 15% SDS-PAGE, and western blot analysis was performed to determine the expression of mGM-CSF, using an anti-mGM-CSF antibody (Thermo Fisher), or to investigate the activation status of different components of the cGAS/STING pathway using antibodies against TBK-1, p-TBK-1, IRF-3, p-IRF-3, STING, p-STING, and cGAS (Cell Signaling Technology). GAPDH (Cell Signaling Technology) was used as a loading control.
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10

Western Blot Analysis of Signaling Proteins

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Protein lysates were prepared as previously described and resolved on 10% SDS–polyacrylamide gels (3 (link), 4 (link)). Following dry transfer, polyvinylidene difluoride membranes were blocked for 1 hour in intercept blocking buffer (LI-COR Biosciences, #927-70001) and incubated overnight in primary antibodies at 4°C. The next day, blots were incubated with fluorescent-conjugated secondary antibodies (LI-COR Biosciences, #926-32221 and #926-32210) for 1 hour. Signals were detected using the Odyssey Infrared Imaging System (LI-COR Biosciences). Actin was used as a loading control.
Primary antibodies for Western blot include pHCK (Abcam, #61055), HCK (Santa Cruz Biotechnology, # N-30), pLYN (Cell Signaling Technology, #2731), LYN (Cell Signaling Technology, #2732), pSRC (Cell Signaling Technology, #2101), SRC (Cell Signaling Technology, #2109), IκBα (Cell Signaling Technology, #9242), pTBK1 (Cell Signaling Technology, #5483), TBK1 (Cell Signaling Technology, #3504), pp65 (Cell Signaling Technology, #3033), p65 (Cell Signaling Technology, #8242), and Actin (Sigma-Aldrich, #A228 for mouse and Cell Signaling Technology, #3700 for human samples).
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