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9 protocols using ifn λ2

1

Detailed Procedures for Cell Experimentation

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All cell lines were short tandem repeat–authenticated cell lines purchased directly from ATCC, expanded, and stock vials frozen down within two passages of receipt. Cells were grown in 10% FBS/RPMI, renewed from fresh stocks after 1 month in culture, and were confirmed negative for Mycoplasma monthly. Reagents for cell culture and lipid-based transfection were from Thermo Fisher Scientific. Reagents for nucleofection were from Lonza. Nucleic acid purification kits were from Qiagen. RNA sequencing (RNA-seq) library prep kits were from New England Biolabs. Oligonucleotides, Cas9 protein, guide cRNAs, and trans-activating CRISPR RNA (tracrRNAs) were from IDT, single-guide RNAs were from Synthego. Selective antibiotics were from Invivogen. IFNα (universal type I IFN) and IFNβ was from PBL Assay Science, IFNγ was from Sigma, and IFNλ2 was from R&D Systems. The drug library used for the screen (the “FDA-approved drug library” catalog L-1300) contained 1,443 different inhibitors and was from Selleckchem. Individual drugs were either from Selleckchem or MedChemExpress. Nocodazole was from Sigma.
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2

Interferon Stimulation Assay

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Murine IFN-α, IFN-β, IFN-γ, IFN-λ2, and IFN-λ3, as well as human IFN-α and IFN-β were purchased from R&D Systems. For IFN-I treatment, cells were given 10 units/mL of IFN-α and IFN-β unless otherwise noted. Cells were treated with 10 ng/mL of IFN-II (IFN-γ) or IFN-III (IFN-λ2 and IFN-λ3). For JAK inhibition, cells were treated with 50 nM tofacitinib (Cayman Chemical) at the time of stimulation.
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3

IFN-I and IFN-λ2 Induction in A375 Cells

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In 24-well plates, 3 × 105 A375 cells were plated per well. The following day, Universal IFN-I (R&D Systems, #11200–1) or IFN-λ2 (R&D Systems, #8417-IL-025/CF) was added at 100 U/mL or 100 ng/mL, respectively, and incubated at 37°C, 5% CO2. After 6-h incubation, cells were harvested and subjected to RNA extraction and qPCR analysis as described above.
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4

Cell Culture and Cytokine Treatment

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Huh7, HepG2, U87, U373, A549, 293T, BHK-21, B16, BNL, and NIH3T3 cells were maintained in high glucose DMEM supplemented with 10% heat-inactivated FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 1× MEM nonessential amino acids, and 10 mM HEPES (Invitrogen). Jurkat cells were cultured in complete RPMI 1640 medium. Cryopreserved PHHs from HIV, HBV, and HCV-free donors were purchased from BD Biosciences. Fresh PHHs were also obtained from the Cellular and Molecular Physiology core facility of the Yale Liver Center. Primary human astrocytes and HCMV-GFP were kindly provided by Dr. Anthony van den Pol (Yale University). Primary human T lymphocytes were originally obtained from the New York Blood Bank, and the CD4+ population was purified and kindly provided by Dr. Walther Mothes (Yale University). CD4+ T cells were cultured in complete RPMI 1640 medium supplemented with 100 U/ml IL-2 and 100 ng/ml IL-7 and stimulated with 10 µg/ml PHA every 72 h. Cells were treated with recombinant human IFN-α2a, IFN-β, human IFN-λ1, IFN-λ2, IFN-λ3 (R&D Systems), murine IFN-λ2 (PeproTech), or universal type I IFN (hIFN-αA/D) (PBL Interferon Source). DNMT inhibitor 5azadC and HDAC inhibitors SAHA, TSA, sodium butyrate, MS-275, apicidin, tubacin, and nicotinamide were purchased from Selleckchem.
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5

Cytokine Detection in Human Samples

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ELISAs for analysis of human IL-8, IFN-β, IFN-λ1, and IFN-λ2 (all from R&D Systems) were performed according to the manufacturer’s protocol.
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6

Intranasal Cytokine and LPS Modulation

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Naive mice were intranasally administered recombinant mouse IL-13 (15 µg/35 µL; Biolegend), IL-5 (15 µg/35 µL; Biolegend) or a low or high dose (0.12 µg/50 µL and 10 µg/50 µL ,respectively) of lipopolysaccharide (LPS) (Escherichia coli, 0111:B4; Sigma-Aldrich), with samples collected 24 h later. HDM-sensitised and challenged Tlr7−/− mice, which also received live RV1B, were intranasally administered either recombinant mouse IFNα2 (10 000 IU/50 µL; eBioscience), IFNβ1 (10 000 IU/50 µL; Biolegend), IFNλ2 (1 µg/50 µL; R&D Systems)14 (link) or a vehicle control (phosphate buffered saline) on day 18 (2 h following RV1B infection). Mice were sacrificed 24 h postinfection and samples collected.
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7

Interferon treatment of cells

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Cells were seeded in 12-well plates and treated for 8 hours in biological quadruplicates with IFNα (0.5 ng/ml, R&D Systems), IFNβ (0.5 ng/ml, GenScript), IFNγ (1 ng/ml, R&D Systems), IFN-λ1 (5 ng/ml, R&D Systems), IFN-λ2 (60 ng/ml, R&D Systems), and custom IFN-λ3 (20 ng/ml) and IFN-λ4 (50 ng/ml) (25 (link)), with no treatment used as a negative control.
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8

HCVcc Infection and IFN Treatment Protocol

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The JFH-1 strain (genotype 2a) of HCVcc was produced and quantified as previously described 21 (link). Huh-7.5 cells (provided by Apath, LLC, Brooklyn, NY) were infected with HCVcc at 0.01 to 0.1 multiplicity-of-infection (MOI), depending on the experiment. Transfection with HCV protein-encoding plasmids was performed as previously described 22 (link). To study IFN-induced MHC class I expression, HCV-infected cells were treated with 3 ng/mL IFN-β (PeproTech, Rocky Hill, NJ), 10 ng/mL IFN-γ (PeptroTech), 100 ng/mL IFN-λ1 (R&D Systems, Minneapolis, MN) or 100 ng/mL IFN-λ2 (R&D Systems) for 24 h. Cell culture media and HCV RNA transfection are described in the Supplementary Materials and Methods section.
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9

Cytokine-Modulated Dendritic Cell Activation

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cDC1s were treated with 10 ng/mL IL-10 (PeproTech), 10 ng/mL IFN-β (R&D Systems, Minneapolis, MN USA), 10 ng/mL IFN-γ (PeproTech), 10 ng/mL IFN-λ2 (R&D Systems), 3 μg/mL anti–IFN-λ (R&D Systems), or 20 μg/mL poly I:C (Millipore Sigma), as indicated in the Figure legends.
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