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85 protocols using p irf3

1

Immunoblotting Techniques for Cellular Signaling

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Antibodies against Myc-tag, G3BP1, RIG-I, p-P65, P65, p-IRF3, IRF3, p-IκBα, and IκBα were obtained from Cell Signaling Technology; anti-Flag, anti-HA, and anti-β-actin were from Sigma; horseradish peroxidase (HRP)-conjugated anti-mouse IgG and anti-rabbit IgG were from Thermo; HRP-conjugated anti-goat IgG was from Zhong Shan Jin Qiao; MG132 and 3-MA were from Sigma; RNF125 and K48-Ub were from Abcam; Ub was from Santa Cruz Biotechnology; 5´ppp-dsRNA was from InvivoGen; EZ-link Psoralen-PEG3-Biotin and Streptavidin agarose resin were from Thermo Fisher. SeV and VSV-GFP were described previously26 (link),27 (link). The cultivation of human embryonic kidney (HEK) 293 T cells have been described previously28 (link).
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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

Protein Extraction and Western Blot Analysis

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Total proteins were extracted from tissues and cells with precooled SDS lysis buffer containing protease inhibitor phenylmethanesulfonyl fluoride (PMSF) (Beyotime Biotech, Haimen, China). BCA Protein Assay Kit (Beyotime Biotech) was used to determine protein concentration. Lysates were separated in resolving gel and transferred to polyvinylidene difluoride (PVDF) membrane (Millipore, USA). After blocking with 5% skimmed milk for 2 h, the membrane was incubated with the primary antibodies overnight at 4°C. The superfluous primary antibody was washed away with TBST followed by the incubation of goat anti-rabbit IgG-HRP secondary antibody (Beyotime Biotech) for 2 h at room temperature. The chemiluminescence detection was finally carried out with the ChemiDocTM XRS imager (Bio-Rad, USA).
Antibodies against cGAS (ab252416), PD-L1 (ab213480) were purchased from Abcam (Cambridge, UK). Antibodies against p-IRF3 (#4947), p-TBK1 (#5483), IRF-3 (#11904S), TBK1 (#38066), LC3 (#4599), p62 (#5114), Cleaved Caspase-3 (#9664), were purchased from Cell Signaling Technology (Boston, USA). Antibodies against STING (19851-1-AP), Lamin A/C (10298-1-AP) was purchased from Proteintech (Wuhan, China). Antibodies against Tubulin (AF0001) was purchased from Beyotime Biotech.
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4

Antibody Detection Protocol

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Antibodies against actin (Santa Cruz Biotech), Hsp90α (Santa Cruz Biotech), p-IRF3 (Cell Signaling), p-STAT1 (Santa Cruz Biotech), PARP-1 (Santa Cruz Biotech) and NP (H16-L10-4R5, ATCC) were purchased from the respective commercial sources. 525A, 526A, 527A and 528A were dissolved in DMSO and DMSO was used as a mock treatment.
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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

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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7

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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8

Intestinal Ischemia-Reperfusion Injury in Mice

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Lungs and small intestines were harvested from mice 4 hours after intestinal I/R, flash-frozen in liquid nitrogen, stored at −80°C, and crushed over dry ice to a fine powder, then homogenized in RIPA buffer (1X TBS [pH 7.5], 50mM EDTA, 50mM EGTA, Triton-X1000[1%], 2mM Na Orthovanadates [pH 7.6], 0.2mM PMSF) containing a protease inhibitor and phosphatase inhibitor using high-frequency sonication. Samples were then centrifuged at 12,000 ×g for 14 minutes at 4°C and supernatant was collected for further analysis. Protein concentration was determined by detergent compatible (DC) protein assay (Bio-Rad, Hercules, CA). Equal amounts of tissue homogenates were fractionated on SDS-PAGE (Invitrogen, Waltham, MA) and transferred to nitrocellulose membrane. The membranes were blocked by incubation with 0.1% casein in 0.2× PBS and incubated at 4°C overnight with the following primary antibodies: IRF3 (Cell Signaling Technology, Danvers, MA; catalog 4302S), pIRF3 (Cell Signaling Technology, Danvers, MA; catalog 4947S), and β-actin antibody (Sigma-Aldrich, St. Louis, MO; catalog A5441) in 0.2× PBS with 0.1% casein and 0.1% Tween 20. After washing, the blots were subsequently incubated with the corresponding fluorescent secondary antibody (LI-COR, Lincoln, NE). Bands were detected using the Odyssey FC Dual-Mode Imaging system 2800 (LI-COR, Lincoln, NE).
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9

Western Blot for STING Signaling

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Equal amounts of proteins were resolved on SDS-polyacrylamide gels and then transferred to polyvinylidene fluoride 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 polyclonal antibody against STING was developed in our laboratory as described previously (Ishikawa et al.6 (link)); other antibodies were obtained from following sources: HA (Sigma Aldrich, at 1:10,000 dilution), β-actin (Sigma Aldrich, at 1:10,000 dilution), p-IRF3 (Cell Signaling, at 1:1,000 dilution), p-p65 (Cell Signaling at 1:1,000 dilution), p65 (Cell Signaling at 1:1,000 dilution), IRF3 (Santa Cruz Biotechnology, at 1:1,000 dilution), Histone H3 (Abcam at 1:1,000 dilution) and MyD88 (Abcam, at 1:500 dilution).
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10

Tanreqing Injection Modulates Inflammatory Response

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Tanreqing injection (TRQ, 33 mg/ml) was provided by Shanghai Kaibao Pharmaceutical Company, China, Lot. No. 2003210. LPS (Escherichia coli 055: B5, L2880) was purchased from Sigma-Aldrich (St. Louis, MO, United States). Fetal bovine serum (FBS) was obtained from Invitrogen Gibco (Grand Island, NY). Penicillin and streptomycin, Dulbecco’s modified Eagle’s medium (DMEM), 0.25% trypsin, and phosphate buffer saline (PBS) were purchased from Meilunbio (Dalian, China). Antibodies against cGAS, P-STING, STING, P-TBK, TBK, P-IRF3, IRF3, NF-κB p65, P-P65, and P-IκBα were obtained from Cell Signaling Technology (Beverly, MA, United States). All the immunosorbent assay (ELISA) used in this study were acquired from Multiscience (Zhejiang, China), Elabscience (Wuhan, China), and Neobioscience Technology Company (Shenzhen, China). The MPO, LDH, MDA, GSH, and SOD assay kits were purchased from Nanjing Jiancheng Biology Institution (Nanjing, China). DNeasy Blood & Tissue Kit was purchased from Qiagen (Hilden, Germany). TB Green Premix Ex Taq II was acquired from TaKaRa (Beijing, China).
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