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11 protocols using diabzi

1

STING overexpression in breast cancer cell lines

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HCC38, MCF7, and MDA-MB-231 cells were obtained from the American Type Culture Collection (ATCC). SKBR3 and MDA-MB-468 cells were purchased from the UCSF Cell Culture Facility. Cell lines were grown according to published guidelines62 (link) except for SKBR3 cells which were cultured using RPMI media supplemented with 10% fetal bovine serum (FBS) and 1% pen/strep. All cell lines tested negative for mycoplasma contamination. All drugs used in this study were purchased from Selleck Chemicals (Gemcitabine and diABZI). To exogenously overexpress TMEM173 or STING1, a STING1 ORF was cloned into the lentiviral pLX304-Blast-V5 vector as part of the CCSB-Broad Lentiviral Expression Library63 (link). The vector was transduced using a lentiviral system and cells were selected using 7.5 ug mL-1 blasticidin to establish stable HCC38 STING overexpressing cells.
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2

FTY-720, diABZI, and RU.521 Agonists and Inhibitors

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The following agonists and inhibitors were used: FTY-720 (Selleck, no. S5002), diABZI (Selleck, no. S8796), and RU.521 (Selleck, no. S6841).
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3

IFNAR Blockade and Type I IFN Therapy

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For IFNAR blockade, mice were treated once with 2 mg blocking antibodies diluted in 200 µl PBS 1 d before infection (Clone MAR1-5A3; BioXCell). Universal IFN-I (rIFN-αA/D, no. 11200; PBL Assay Science) was supplied frozen in PBS containing 0.1% BSA. Cross-species activity of rIFN-αA/D on mouse cells was confirmed by the manufacturer and a previous study (Uccellini and García-Sastre, 2018 (link)). 4 h after infection, 2 × 104 U rIFN-αA/D (low-dose; 106 U/kg) or 2 × 105 U rIFN-αA/D (high-dose; 107 U/kg) were diluted in 100 µl PBS and i.v. administered to mice. STING agonist diABZI (Compound 3; Selleckchem) was first reconstituted in DMSO at 50 mg/ml. 20 µg diABZI (1 mg/kg) was diluted in 100 µl PBS and i.v. administered to mice 4 h after infection. The dosage for systemic diABZI treatment was determined based on previous publications (Humphries et al., 2021 (link); Ramanjulu et al., 2018 (link)). The dosing solution was prepared fresh and confirmed to be clear at the time of administration.
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4

SARS-CoV-2 Signaling Pathway Analysis

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IFNβ and IFNλ1 were purchased from Biolegend. PAMPs were purchased from InvivoGen. diABZI, ruxolitinib and H-151 were purchased from Selleck Chemicals. The following antibodies were used for Western blotting or immunofluorescence: anti-RIG-I (Cell Signaling Technology, 3743S), anti-MDA5 (Cell Signaling Technology, 5321S), anti-MAVS (Cell Signaling Technology, 3993S), anti-cGAS (Cell Signaling Technology, 83623S), anti-STING (Cell Signaling Technology, 13647S), anti-STING (Proteintech, 19851-1-AP), anti-Phospho-STING (Ser366) (Cell Signaling Technology, 50907S), anti-TBK1 (Cell Signaling Technology, 3504S), anti-Phospho-TBK1 (Ser172) (Cell Signaling Technology, 5483S), anti-IRF3 (Cell Signaling Technology, 11904S), anti-Phospho-IRF3 (Ser396) (Cell Signaling Technology, 4947S), anti-NF-κB p65 (Cell Signaling Technology, 8242S), anti-Phospho-NF-κB p65 (Ser536) (Cell Signaling Technology, 3033S), anti-TRIM22 (Invitrogen, PA5-51964), anti-SARS-CoV-2 nucleocapsid (GeneTex, GTX135357), and anti-tubulin (Sigma, T6199). Anti-SARS-CoV-2 Spike antibody (CR3022) was from Absolute Antibody. HRP-conjugated secondary antibodies (anti-mouse or anti-rabbit) were purchased from Amersham. Alexa Fluor-conjugated secondary antibodies were purchased from Invitrogen.
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5

Investigating STING Pathway Activation

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Cells were treated with 2.5 μM diABZI (Selleckchem, S8796) and collected at the indicated time points. For cGAMP, 90mer and IVT4 stimulation, 0.1 μM cGAMP (Invivogen), 0.2 μg 90mer or 0.5 μg IVT4 was transfected using Lipofectamine 2000 (Invitrogen, 11668019) according to the manufacturer’s protocol, and cells were incubated for 3 h. The DNA sequences of 90mer is provided in Supplementary Table 1. Poly(I:C) (Invivogen) was added to the cell medium at a final concentration of 10 μg ml−1 for 24 h. After infection with the HSV-1 KOS strain (MOI of 10), infected cells were incubated for 6 h. Pretreatment with BX795 (MedChemExpress) was performed at 2 µM for 24 h and pretreatment with bafilomycin A1 (Baf A1; Sigma) was performed at 20 nM for 1 h. MEFs treated with 5 μg ml−1 or 40 μg ml−1 DMXAA (Invivogen) were collected 2 h or 3 h after stimulation. For STING inhibition by H-151, H-151 (2 µM) was added into cells every 24 h for three days before cells were examined by RT–qPCR.
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6

Bone Marrow Macrophage Stimulation Assay

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BMDMs were seeded into 12-well plates (Corning, 3513) at a density of 1 million cells per well and incubated overnight before stimulations or treatments with the following reagents where indicated: GSK8612 (Selleckchem, S8872); H151 (Selleckchem, S6652); Nec-1s (Selleckchem, S8641); poly(I:C) (for extracellular stimulation, InvivoGen, tlrl-picw); poly(I:C) (for transfection, InvivoGen, tlrl-pic); diABZI (Selleckchem, S8796); c-di-GMP (InvivoGen, tlrl-nacdg); IFNβ (PBL Assay, 12400-1); anti-IFNAR1 (MAR1-5A3, Invitrogen, 16-5945-85);, LPS (Sigma, L2630); or z-VAD-FMK (Cayman, 14463). Transfection was performed using Xfect transfection reagent (Takara, 631318) according to the manufacturer’s instructions. Fetal liver derived macrophages (FLDMs) were differentiated from fetal liver cells collected at embryonic day E14.5 and cultured with the same protocol as BMDMs.
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7

Signaling Pathway Modulation in Cell Lines

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G150 (cat. no. HY‐128583; MedChemExpress, NJ, USA); H‐151 (cat. no. S6652, Selleck, Houston, TX, USA); TBK1/IKKε‐IN‐2 (cat. no. S0425, Selleck); Stattic (cat. no. S7024; Selleck); diABZI (cat. no. S8796; Selleck); G140 (cat. no. HY‐133916; MedChemExpress); RU.521 (cat. no. S6841; Selleck); TG003 (cat. no. S7320; Selleck), DOX (cat. no. S1208, Selleck); etoposide (cat. no. HY‐13629, MedChemExpress).
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8

Bone Marrow Macrophage Stimulation Assay

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BMDMs were seeded into 12-well plates (Corning, 3513) at a density of 1 million cells per well and incubated overnight before stimulations or treatments with the following reagents where indicated: GSK8612 (Selleckchem, S8872); H151 (Selleckchem, S6652); Nec-1s (Selleckchem, S8641); poly(I:C) (for extracellular stimulation, InvivoGen, tlrl-picw); poly(I:C) (for transfection, InvivoGen, tlrl-pic); diABZI (Selleckchem, S8796); c-di-GMP (InvivoGen, tlrl-nacdg); IFNβ (PBL Assay, 12400-1); anti-IFNAR1 (MAR1-5A3, Invitrogen, 16-5945-85);, LPS (Sigma, L2630); or z-VAD-FMK (Cayman, 14463). Transfection was performed using Xfect transfection reagent (Takara, 631318) according to the manufacturer’s instructions. Fetal liver derived macrophages (FLDMs) were differentiated from fetal liver cells collected at embryonic day E14.5 and cultured with the same protocol as BMDMs.
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9

Cell Culture and Transfection Protocol

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L929 and HEK293T cells were purchased from ATCC (American Type Culture Collection) and BJ cells was a kindly gift from Dr. Daxing Gao of University of Science and Technology of China (USTC), and all the above cells were maintained in DMEM (Gibco) with 10 % fetal bovine serum (FBS, Hyclone) and 100 units/ml penicillin (Gibco) plus 100 μg/ml streptomycin (Gibco). Plasmids were purified with endotoxin-free purification kits (CoWin Biosciences, CW2105) and transfected into cells with Lipofectamine 3000 (Invitrogen) according to the user manual. For small molecule inhibitors: DMXAA (Tocris Bioscience, #5601), EACC (MedChemExpress, HY-129111), diABZI (Selleck, S8796), AP20187 (Takara, #635058), Baf A1 (Selleck, S1413), cGAMP (Sigma, SML1229).
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10

STING Agonists Delivery in Cell Lines

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BJ, U2OS, and 293T cells were from ATCC and were authenticated through short tandem repeat (STR) profiling. All relevant authentication data are publicly available from ATCC. These cell lines differ in their growth rates and morphologies. All cell lines in this study were free of contaminations from other cell lines or mycoplasma. Cells were maintained with mycoplasma reagent and potential contaminations are regularly monitored through polymerase chain reaction (PCR) detection. All cells were cultured at 37 °C with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 8% fetal bovine serum (FBS) and penicillin/streptomycin. Cyclic [G(2’,5’)pA(3’,5’)p] or cGAMP (#CT-CGMAP, ChemieTek) was dissolved in water and stored at −20 °C. The other two STING agonists diABZI (#S8796, Selleck) and C53 (#37354, Cayman) were dissolved in DMSO and stored in aliquots at −80 °C. Monensin (#16488, Cayman) was dissolved in ethanol and stored at −20 °C. cGAMP was delivered to cells using a mild digitonin buffer (50 mM HEPES pH 7.0, 100 mM KCl, 3 mM MgCl2, 0.1 mM DTT, 85 mM sucrose, 0.2% BSA, 1 mM ATP, 8 μg/mL digitonin) (Woodward et al, 2010 (link)). Cells were treated with the buffer containing 1 μM cGAMP for 5-10 min and then changed back to the original culture media. All other chemicals were directly added to the cell culture media.
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