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127 protocols using 2 3 cgamp

1

RNA-Seq Analysis of Polyp Responses to cGAMP

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For the RNA-Seq experiment on polyps (Fig. 1 and SI Appendix, Fig. S1), ∼4-wk-old polyps were treated in duplicate in a bath of 500 μM c-di-AMP, c-di-GMP, 2′3′-cGAMP, or 3′3′-cGAMP (all InvivoGen) in 1/3× sea water for 24 h. For remaining cGAMP treatment experiments, 50 to 100 48-h-old embryos were treated with 100 μM 2′3′-cGAMP (InvivoGen) in 1/3× sea water for 4 h.
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2

Characterizing 2'3'-cGAMP Signaling Pathway

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2′3′-cGAMP was purchased from Invivogen. 2′3′-cGAMP (5 µg/ml) (Invivogen, tlrl-nacga23-02) was added to the cells complexed with LyoVec (Invivogen, Lyec-12) in order to aid internalization. ISD (Interferon stimulatory DNA)/LyoVec (Invitrogen, tlrl-isdc, 1 µg) was also used. Membrane lipid strips were obtained from Echelon. The following inhibitors were used: Fura-2 AM, Ca2+ selective fluorescent indicator (Abcam, ab120873), BX795 (TBK-1 inhibitor, Invivogen, tlrl-bx7, 1 µM), RU.521 (cGAS inhibitor, Invivogen, inh-ru521, 500 nM). GSK2998533 (100 nM) & GSK2683449 (100 nM) were provided by GlaxoSmithKline (GSK). PIK93 was also used (Sigma Aldrich, 1 µM)
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3

Stimulation and Transfection of Immune Cells

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Cells were seeded at 1–1.5 × 105 cells per ml 24 h before transfection, and stimulated with 1 μg ml−1 HT DNA (HT DNA, Sigma), a double-stranded 70mer oligonucleotide derived from VACV (5′-CCATCAGAAAGAGGTTTAATATTTTTGTGAGACCATCGAAGAGAGAAAGAGATAAAACTTTTTTACGACT-3′)10 (link), Y-G3 DNA (5′-GGGGAACTCCAGCAGGACCATTGGGG-3′) or Y-C3 DNA (5′-CCCGAACTCCAGCAGGACCATTGCCC-3′)24 (link). DNA oligonucleotides were synthesized by Biofins Genomics, Germany. In vitro transcribed RNA containing a 5′-triphosphate was generated using the MEGAScript T7 transcription kit (Thermo Fisher) with pcDNA3.1: EGFP as template. 50 ng ml−1 of in vitro transcribed RNA and 100 ng ml−1 poly(I:C) (Sigma) were used, unless indicated otherwise. 2′3′ cGAMP (Invivogen) or cyclic di-AMP (Invivogen) were transfected at 20 and 100 μg ml−1, respectively. All transfections were carried out with 1 μl Lipofectamine 2000 (Life Technologies) per ml medium.
Transfection by digitonin permabilization was carried out in a buffer containing 50 mM HEPES (pH 7), 100 mM KCl, 3 mM MgCl2, 0.1 mM DTT, 85 mM saccharose, 1 mM ATP, 0.1 mM GTP and 0.2% (v/v) BSA. 25 μg ml−1 HT DNA (Sigma). 15 μM 2′3′ cGAMP or 2′3′ cGAM(PS)2 (both Invivogen) was transfected using 5 μg ml−1 digitonin in permeabilization buffer for 10 min at 37 °C before replacing the permabilization buffer with DMEM containing 10% (v/v) FCS.
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4

DNA Damage Induction and ATM Inhibition

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The ATM inhibitor AZD1390 (ATMi; Selleck Chemicals) was used at 10 nM for 1–9 days with replenishment of the inhibitor every 2 days. To induce ATM activation, cells were treated with 1 μM camptothecin (CPT; Cayman Chemical Company) for 1 h. The STING agonist diABZi (Selleck Chemicals) was used at 1 μM. To induce DNA damage, cells were treated with 250 nM etoposide (ETO; Cayman Chemical Company), 30 nM mitomycin C (MMC; Santa Cruz), or 150 nM aphidicolin (APH; Merck) for 6 days. To induce apoptosis, cells were treated with 1 μM staurosporine for 6 h. Treatment times are indicated in figure captions. For compounds dissolved in DMSO, DMSO concentration was equivalent between conditions and <0.1% (v/v).
For 2′,3′-cGAMP stimulation, cells were washed in PBS then incubated for 3 min at 37ºC in digitonin permeabilization buffer (50 mM HEPES pH 7.0, 100 mM KCl, 3 mM MgCl2, 0.1 mM DTT, 85 mM sucrose, 0.2% (w/v) BSA, 1 mM ATP, 0.1 mM GTP, 4 μM digitonin) with or without 7 μM 2′,3′-cGAMP (Invivogen). Cells were further washed in PBS and incubated in culture medium until collection. Incubation times post-treatment are indicated in figure legends.
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5

Murine Norovirus Protein Detection

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DMXAA, H151 and 2ʹ3ʹ-cGAMP were purchased from InvivoGen. JAK inhibitor 1 (SC-204021) was purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). N-Acetyl-L-cysteine was purchased from Sigma-Aldrich. Rabbit polyclonal antisera to MNV NS1/2 was kindly provided by Prof. Vernon K. Ward (School of Biomedical Sciences, University of Otago, New Zealand).47 (link) Rabbit polyclonal antisera to MNV NS7 was kindly provided by Prof. Ian Goodfellow (Department of Pathology, University of Cambridge, UK).48 (link) Antibodies against STAT1 (#9172), pSTAT1 (Ser727, #9177), RIG-I (D14G6, #3743), MDA5 (D74E4, #5321), cGAS (D3O8O, #31659), STING (D2P2F, #13647), Myc-tag (71D10, #2278) and Myc-Tag (9B11, #2276) were purchased from Cell Signaling Technology. Rabbit anti-GBP2 (11854-1-AP) and anti-GBP5 (13220-1-AP) antibodies were purchased from Proteintech. Mouse anti-Flag (F1804, Sigma-Aldrich) and anti-β-actin (#sc-47778, Santa Cruz Biotechnology) antibodies were used. Anti-rabbit and anti-mouse IRDye-conjugated secondary antibodies (Li-Cor Bioscience, Lincoln, USA) were used.
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6

Ionizing Radiation and Pharmacological DNA Damage

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DNA damage was induced by ionizing radiation (IR) with the indicated Gray (Gy) in the figure legends using a Faxitron CellRad irradiator (130 kV, 5 mA, 0.5 mm Al) or by treatment of cells with PBD SG-3199 (40 pM for FaDu cells and 400 pM for THP-1 cells)3 (link) obtained from internal stock. Ceralasertib 20 (link) (1 µM) or AZD0156 22 (link) (10 nM) were obtained from internal stocks, recombinant human IFNβ (300 U/ml, R&D) and the JAK1/2 inhibitor INCB018424 ruxolitinib (1 µM, Chemietek) were obtained commercially. The cGAS agonist dsDNA HT-DNA (25 µg/ml, Sigma) and the STING agonist 2ʹ3ʹ-cGAMP (25 µg/ml, Invivogen) were transfected into tumor cells using 2 µl Lipofectamine™ 2000 (ThermoFisher Scientific) according to manufacturer’s instructions.
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7

Innate Immune Response Profiling

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Patient and control PBMCs were thawed and seeded in RPMI supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin (cRPMI) at a density of 5 × 105 cells/well for infection experiments and 1 × 106 cells/well for stimulation with 2′3′-cGAMP and dsDNA and incubated overnight at 37 °C and 5% CO2. Cells were infected with 50 HAU of Sendai virus (SeV) (Cantell strain, Charles River), 3 MOI of HSV1 (KOS Strain), or 0.2 MOI of cell-free (CF) VZV debris (rOKa strain) or CF debris mock). Following 24 h of infection, supernatants were harvested for mesoscale, and cells were lysed for RNA isolation. In addition, PBMCs were stimulated with 100 µg/mL of 2′3′-cGAMP (InvivoGen) or 2 µg/mL of transfected ht (herring testes) dsDNA for 3 h following cell lysis for Western blotting or stimulated with 50 µg/mL high molecular weight poly(I:C) (InvivoGen, USA) or 5 µg/mL CpG ODN2395 (InvivoGen, USA) for 6 h before being lysed for downstream RT-qPCR analysis.
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8

ER Stress and Immune Signaling Pathways

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Herring testis DNA was used as dsDNA for immune stimulations (Sigma). 2’3’-cGAMP and DMXAA were used for STING agonists (Invivogen). PolyI:C was transfected as a MAVS-pathway agonist (Invivogen). Lipofectamine 2000 was used as transfection reagent for intracellular stimulations (Thermo Fisher).
Antibodies: ATF4 (CST D4B8), ATF6 (CST D4Z8V), BIP (CST C50B12), CHOP (CST L63F7), phospho-EIF2α (CST D968), HMGB1 (Abcam 18256), IRAK1 (CST D5167), IRE1α (CST 14C10), phospho-IRE1α (Thermo Fisher PA1-16927), IRF3 (CST D83B9), phospho-IRF3 (CST 4D4G), MAVS (CST 4983), STING (CST D2P2F), TOLLIP (Abcam ab187198), goat anti-rabbit IgG (Biorad 1706515), goat anti-mouse IgG (Biorad 1706516).
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9

Type I IFN Pathway Activation in THP1-Dual Cells

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THP1-Dual™ cells (InvivoGen) are derived from the human THP1 monocyte cell line by stable integration of secreted inducible reporter construct to monitor type I IFN pathway activation. THP1-Dual™ cells were pre-incubated for 24 h with scalar concentrations of 2′3′-cGAMP (0.5–1.25–2.5–5–10–20 μg/mL, InvivoGen), and then challenged for 1 h with LPS (0.5 μg/mL, Sigma-Aldrich).
Type I IFN pathway activation was measured according to the manufacturer’s instructions.
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10

Generating Murine Dendritic Cells

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Bone marrow (BM) cells were isolated by flushing the long bones with PBS. BM-derived GM-CSF DC cultures were grown in 24 well plates as previously described57 (link) in RPMI 1640 supplemented with 40 pg/ml recombinant GM-CSF (BioLegend) and 5% FBS, plus 100 μg/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 10 mM HEPES, 1 nM sodium pyruvate, 1× MEM nonessential amino acids, and 2.5 μM β-mercaptoethanol (all Sigma). After 5 days of culture, BMDCs were harvested and replated with MOI (multiplicity of infection) =10 of Citrobacter rodentium (DBS100, ATCC) or incubated with 5 μg/ml of the 2’3’-cGAMP (cyclic [G(2’,5’)pA(3’,5’)p]) (Invivogen). For infection, bacteria were grown to exponential phase in lysogeny broth (LB) medium, then washed and resuspended in PBS.
Two hours post-treatment, culture medium was removed and cells resuspended in 1 ml of TRIzol Reagent (Life Technologies).
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