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20 protocols using ssrna40 lyovec

1

Cell Culture and Stimulation Assay

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Cells were cultured in RPMI supplemented with 10% [v/v] heat inactivated FBS (R102) (both Sigma-Aldrich). Human rIL-2 was obtained from the National Institute of Health AIDS Research & Reference Reagent Program. The following reagents and stimuli were used in tissue culture: LPS from Escherichia coli, CL097 Imidazoquinoline, HKLM3 and ssRNA40/LyoVec (all InvivoGen, San Diego, CA, USA), Dynabeads® Human T-Activator CD3/CD28 beads (LifeTechnologies, Grand Island, NY, USA), Brefeldin A (Sigma-Aldrich) and GolgiStop (BD). Cell proliferation was assessed by addition of CellTrace Violet BMQC dye (LifeTechnologies).
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2

Targeting EGFR with Cetuximab and TLRs

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Antibody targeting EGFR (Cetuximab) was purchased from Merck Serono. Gardiquimod, R848 (Resiquimod), ssRNA40/LyoVec and ORN06/LyoVec were purchased from InvivoGen. The 257–264 OVA peptide (SIINFEKL) was provided by Dr. S. Amigorena (Institut Curie, Paris, France). TLR3/dsRNA Complex Inhibitor was purchased from Calbiochem.
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3

Flow Cytometric Analysis of Dendritic Cells

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The mAbs anti-HIV-1 p24-FITC (clone KC57), anti-Vα24-FITC (clone C15), and anti-Vβ11-PE (clone C21) were from Beckman Coulter, anti-CD1d-PE (clone CD1d42), anti-CD3 AF700 (clone UCHT1), anti-CD4 BV605 (clone RTA-T4), anti-CD11c-allophycocyanin (clone B-ly6), anti-CD11c PE-Cy5 (clone B-ly6), anti-CD45 PerCP (clone 2D1), anti-CD56 AF700 (clone B159), anti-CCR5 APC-Cy7 (clone 2D7/CCR5), anti-DC-SIGN v450 (clone DCN46) and anti-HLA-DR APC (clone L243) were from BD Biosciences (San Jose, CA, USA), anti-CD4 BV711 (clone OKT4) and anti-CD8 BV570 (clone RPA-T8) were from BioLegend (San Diego CA), anti-CD14 PE-Texas red was from Invitrogen, and anti-CD19 PE-Texas red (clone SJ25-C1) was from Abcam (Cambridge, UK). Data were acquired on a BD LSRFortessa instrument (BD Biosciences) and analyzed using FlowJo Version 9.7.5 software (TreeStar, Ashland, OR, USA). In some experiments, DCs were treated with 5 µg/ml Imiquimod (InvivoGen, Toulouse, France), 5 µg/ml Poly(I:C) (InvivoGen), 1 µg/ml ssRNA40LyoVec (Invivogen), 50 µM N-(n-Butyl)-deoxygalactojirimsin (NB-DGJ) (Toronto Research Chemicals, Toronto, Canada), 10 µM Chloroquine (InvivoGen), or with 5.6 µM TLR7 oligonucleotide antagonist IRS954: 5′-TGCTCCTGGAGGGGTTGT-3′ or the control oligo 5’-TCCTGCAGGTTAAGT-3 (Integrated DNA Technologies) (41 (link)).
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4

Activation of Human PBMCs by TLR Ligands

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The following TLR ligands (InvivoGen, each 1 µg/mL) were added into wells of 24-well plate containing 1-2 x 106 PBMCs: Poly(I:C) HMW (TLR3), LPS-EK Ultrapure (lipopolysaccharide, TLR4), Imiquimod (IMQ) (R837, TLR7), Resiquimod (R848, TLR7/8), TL8-506 (TLR8), ssRNA40/LyoVec (TLR8) and CpG-ODN (TLR9). The concentration of 1 µg/mL is within the range of manufacturer recommendation and induced maximum cytokine response (not shown) (10 (link), 12 (link)). Golgi plug (1 µl/mL, BD Biosciences) was added to block the cytokines release and cell culture continued for 18h. For some experiments, PBMCs were stimulated with agonists alone or in combination with recombinant human HBsAg subtype adw (10 µg/mL, Fitzgerld) (15 (link)) and PepMix HBV (LEP) Ultra (2 µg/mL, JPT) and cultured for 5 days at 37°C incubator. In experiments for transcription factor induction, cells were re-stimulated with Phorbol-12-myristat-13-acetate (PMA, 50ng/mL) and Ionomycin (Ion, 1 µg/mL) on day 4.
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5

Investigating Immune Cell Signaling Pathways

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The following inhibitors were used: cytochalasin D (Sigma‐Aldrich) 5 μg/mL; bafilomycin A1 (Sigma‐Aldrich) 10 nM; IKK inhibitor VII (Merck‐Millipore, Darmstadt, Germany) 5 μM; (5Z)‐7‐oxozeaenol (Tocris, Bristol, UK) 0.75 μM. The effect of inhibitors on THP1 cell viability is shown in Supplementary Fig. 4. The following TLR agonists were used at 1 μg/mL unless otherwise indicated: Pam3CSK4, HKLM, Poly(I:C), LPS E. coli K12, flagellin Salmonella Typhimurium, FSL‐1, Imiquimod, ssRNA40/Lyovec, and ODN2006 (all InvivoGen, San Diego, CA, USA). The following cytokines were used: M‐CSF (R&D Systems) 50 ng/mL; IFN‐γ (Miltenyi Biotec) 1000 U/mL; interferon‐α2a (Miltenyi Biotec) 1000 U/mL. The following blocking antibodies were used: anti‐MR1 (clone 26.5; TH) 10 μg/mL; anti‐IL‐12p40/70 (eBioscience, Hatfield, UK) 5 μg/mL; anti‐IL‐18 (MBL International, Woburn, MA, USA) 5 μg/mL.
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6

Measuring TLR Activation in HEK-Blue Cells

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HEK-Blue human TLR reporter cells were purchased from Invivogen (San Diego, CA). All reporter lines were cultured according to the manufacturer’s instructions. Briefly, cells were cultured in Dulbecco’s modified Eagle medium with 10% FBS, penicillin–streptomycin, and 100 μg/mL normocin. The selection antibiotics zeocin (100 μg/mL) and blasticidin (10–30 μg/mL) were added for two passages after the cells were thawed. Then, the cells were cultured for two additional passages before experimental use. For the reporter cell assay, cells were plated in 96-well flat-bottomed plates at 40 000–80 000 cells per well. NANPs were added, and cells were incubated at 37 °C for 24 h. Supernatants were collected and assayed using QUANTI-Blue (Invivogen, San Diego, CA) and recombinant SEAP as a standard. Specific TLR agonists were used as follows: 1 μg/mL poly(I:C) (TLR3), 5 μg/mL Imiquimod (TLR7), 5 μg/mL ssRNA40/LyoVec (TLR8), and 100 μg/mL ODN 2216 (TLR9) (all from Invivogen, San Diego, CA).
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7

NF-κB Signaling Assay with TLR Ligands

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In total, 50,000 cells/well were plated in a tissue-culture treated 96-well plate (Costar, No. 3596) in unsupplemented DMEM. Cells were then treated with 100 μM R848 (InvivoGen, No. tlrl-r848), 5 μg/mL ssRNA40/LyoVec (InvivoGen, No. tlrl-lrna40), and/or 5 μg/mL ORN06/LyoVec (InvivoGen, No. tlrl-orn6) and the indicated concentrations of the compounds. Cells were incubated overnight at 37 °C in a humidified atmosphere of 5% CO2 and assayed for NF-κB signaling. Cell media was assayed with Quanti-Blue (InvivoGen, No. rep-qbs3) per the manufacturer’s recommendations. Specificity test in HEK-Blue hTLRs cells for CU-CPD107 using TLR-specific ligands to selectively activate the corresponding TLRs: 100 ng/mL of Pam3CSK4, 100 ng/mL of Pam2CSK4, 5 μg/mL of polyriboinosinic: polyribocytidylic acid [poly(I:C)], 20 ng/mL of LPS (lipopolysaccharide), 50 ng/mL of Flagellin, 2.9 µM of R848, 22.8 µM of R848, and 0.5 μM of ODN2006 were used to selectively activate hTLR1/2, hTLR2/6, hTLR3, hTLR4, hTLR5, hTLR7, hTLR8, and hTLR9 cells, respectively. The SEAP reporter is constructed as a IFN-β promoter fused to five NF-κB and AP-1-binding sites. SEAP was quantified by measuring absorbance at 620 nm. Data were normalized with ligand + DMSO as 100% activity and untreated cells as 0. Each data point represents the average and standard deviation of at least three biological replicates.
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8

Innate Immune Stimulants Evaluation

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Poly(I:C) High Molecular Weight (HMW), Poly(A:U) HMW, Poly(I:C) HMW LyoVec, pppRNA LyoVec, LPS, 2'3'cGAMP, CL264, ODN2006, TL8-506, ssRNA40 LyoVec, and Bafilomycin A1 were purchased from InvivoGen. Human TNFα was purchased from PeproTech (NJ, USA). Universal IFNα was purchased from PBL Assay Science (NJ, USA). Z-FA-FMK was purchased from Sigma-Aldrich (MO, USA). Z-VAD-FMK was purchased from R&D Systems (MN, USA). RNAse III was purchased from Thermo Fischer. Human serums were purchased from NeoBiotech (France).
Synthesis of dsRNAs was performed by different manufacturers: IDT (IA, USA), Horizon Discovery (UK), or NittoAVECIA (CA, USA). A 45 grams batch of TL-532 was synthesized by NittoAVECIA under non-GMP standards. Lyophilized powders were resuspended using apyrogenic, nuclease-free, sterile NaCl 0.9% (InvivoGen). All dsRNAs were used without transfection reagents unless otherwise stated. NaCl 0.9% was used as the Mock condition for all experiments unless stated differently in the text.
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9

Radiolabeled Transporter Substrates Assay

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Elacridar, Ko143, dipyridamole, and 6-S-[(4-Nitrophenyl)methyl]-6-thioinosine (NBMPR) were purchased from Tocris (Minneapolis, MN). Verapamil was purchased from Sigma-Aldrich (St. Louis, MO). All compounds were dissolved in DMSO and stored at −20°C until use. CL097, ssRNA40/LyoVec and ssRNA41/LyoVec, and imiquimod were purchased from InvivoGen (San Diego, CA). The anti-MDR1/ABCB1 monoclonal antibody (D3H1Q) was obtained from Cell Signaling Technology (Danvers, MA). The anti-BCRP antibody (clone BXP-21) was obtained from Millipore Sigma (Burlington, MA). ENT1 (clone F-12) and ENT2 (clone A-8) monoclonal antibodies were from Santa Cruz Biotechnology (Santa Cruz, CA). [3H]-Entecavir (6.4 Ci/mmol) and [adenine-2,8-3H]-Tenofovir (17.1 Ci/mmol) were acquired from Moravek Biochemicals, Inc. (Brea, CA). [N-methyl-3H]-Sofosbuvir (80 Ci/mmol) was purchased from American Radiolabeled Chemicals (St. Louis, MO). Corning Gentest ABC transporter membranes were purchased from Corning (Corning, Woburn, MA).
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10

TLR8-Mediated Modulation of T Follicular Helper Cells

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To examine TLR8-mediated differentiation of TFH cells, CD14+ monocytes and naïve CD4+ T cells were isolated from autologous human PBMCs of CHB patients (n=4) by negative selection (Miltenyi Biotec). The following co-culture experiments were adopted from previously published methods (12 (link)). First, purified CD14+ monocytes (1 x 106 cells/mL) were left untreated or treated with TLR8-specific agonists ssRNA40/Lyovec (1 µg/mL, InvivoGen) or TL8-506 (1 µg/mL, InvivoGen) for 1.5 h. Isolated autologous naïve CD4+ T cells were directly added into the culture at a ratio of 2:1 (monocyte:CD4+) along with SEB (1 µg/mL, Toxins Technology). After 6 days, cells were either processed for TFH cell sorting for further downstream study or re-stimulated overnight (O/N) with PMA (phorbol-12-myristat-13-acetate, 50 ng/mL, Sigma) and ionomycin (Ion 1 µg/mL, Sigma) as positive control to effectively activate TFH cells. After 3-4h, Golgi plug (1 µl/mL, Invitrogen) was added and culture continued for additional 18h to investigate TFH cell proliferation and differentiation related markers by flow cytometry. The culture supernatants were recovered and tested for IL-12p40, IL-18 and IL-21 cytokine quantifications by Luminex multiplex immunoassay.
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