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35 protocols using ruxolitinib

1

Poly(I:C) and Ruxolitinib Treatments

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For Poly (I:C) treatment, TOs or DOs were incubated with 10 µg/mL Poly (I:C) (Invivogen, tlrl-pic) diluted in organoid complete growth media for ~24 hr, then supernatant was collected for Luminex-based multianalyte profiling or RNA isolated as described for qRT-PCR or RNASeq. For ruxolitinib (Invivogen, tlrl-rux) treatment, TOs or DOs plated as previously described for HCMV infections were pre-treated with 20 µM ruxolitinib in appropriate complete growth media for 1 hr at 37oC, then were infected with GFP-tagged AD169r in the presence of ruxolitinib for 48 hr.
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2

Interferon Signaling in HaCaT Cells

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HaCaT cells plated at 3 × 104 cells/well were treated with varying concentrations of IFN-Lambda (IL-29 or IFN-λ1) or IFN Beta (IFN-β) (PBL Assay Sciences, Piscataway, NJ, USA) for 16 h. All dilutions were carried out in DMEM supplemented with 10% HI FBS.
HaCaT cells were plated at 4 × 104 cells/well in a 24-well plate and treated with DMSO as vehicle control or Ruxolitinib (Invivogen, San Diego, CA, USA) at a concentration of 1 μM for 16 h. Cells were infected for 1 h before washing and replacement with DMEM supplemented with 10% HI FBS and 1 μM Ruxolitinib or DMSO vehicle control. Alternatively, cells were infected and then treated with neutralizing antibodies against IL29 (Invivogen), IL28a or IFN-λ2 (Invivogen), and Human IFN-λ1 receptor (IFNLR; PBL Assay Science), or IFN-β (Millipore, Burlington, MA, USA) at the concentrations stated in the figure legends. Corresponding isotype antibodies were used as negative controls.
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3

Cytokine Profiling of Monocyte Subsets

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CD11b+-enriched cells (10,000–20,000 cells/well) from 27 samples were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum, 10,000 units/mL of pen/strep, 1% GlutaMAX (Thermo Fisher Scientific, Waltham, MA), and 5 ng/mL GM-CSF. Six different experimental conditions were tested per sample: (1) unstimulated cells; (2) stimulated with 10 μg/mL LPS; (3) 1 μM11 (link),54 (link) ruxolitinib (InvivoGen, San Diego, CA); (4) 1 μM tofacitinib (Invivogen); (5) 10 μg/mL LPS 1 mM ruxolitinib; and (6) 10 μg/mL LPS + 1 μM tofacitinib. After overnight incubation, supernatants were collected for cytokine quantification by Luminex using a Human High Sensitivity Cytokine customized premixed magnetic bead panel (R&D Systems, Minneapolis, MN) for the following: IL-1 β/IL-1F2, IL-6, IL-8/CXCL8, and TNF. The median fluorescence intensity data were analyzed using MILLIPLEX Analyst Software V.3.5 (MilliporeSigma), and concentrations were calculated in pg/mL in relation to an R&D standard.
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4

Macrophage Polarization Modulation

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Tissue culture plates were coated for 4 h with recombinant human DLL4 (rhDLL4) and DLL1 (rhDLL1) proteins purchased from R&D Systems (R&D Systems Europe Ltd., Abingdon, UK), diluted into PBS (5 μg/mL). Pharmacological inhibitors of γ-secretase (N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-Sphenylglycine t butyl ester; DAPT, Sigma Aldrich, Lyon, France) and of JAK1/JAK2 (Ruxolitinib, Invivogen, Toulouse, France) were used at 0.5 μg/mL and 0.1 μg/mL, respectively. For the inhibition of γ-secretase, macrophages were incubated with DAPT (0.5 μg/mL; Sigma Aldrich) for the 48 h during or for 24 h following M1 or M2 polarization. Similarly, inhibition of JAK/STAT signaling pathway was achieved by adding Ruxolitinib (0.1 μg/mL; Invivogen) during the polarization step. Macrophage Colony Stimulating Factor (M-CSF), IL-4 and IL-10 were from R&D Systems.
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5

Cytokine Profiling of Monocyte Subsets

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CD11b+-enriched cells (10,000–20,000 cells/well) from 27 samples were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum, 10,000 units/mL of pen/strep, 1% GlutaMAX (Thermo Fisher Scientific, Waltham, MA), and 5 ng/mL GM-CSF. Six different experimental conditions were tested per sample: (1) unstimulated cells; (2) stimulated with 10 μg/mL LPS; (3) 1 μM11 (link),54 (link) ruxolitinib (InvivoGen, San Diego, CA); (4) 1 μM tofacitinib (Invivogen); (5) 10 μg/mL LPS 1 mM ruxolitinib; and (6) 10 μg/mL LPS + 1 μM tofacitinib. After overnight incubation, supernatants were collected for cytokine quantification by Luminex using a Human High Sensitivity Cytokine customized premixed magnetic bead panel (R&D Systems, Minneapolis, MN) for the following: IL-1 β/IL-1F2, IL-6, IL-8/CXCL8, and TNF. The median fluorescence intensity data were analyzed using MILLIPLEX Analyst Software V.3.5 (MilliporeSigma), and concentrations were calculated in pg/mL in relation to an R&D standard.
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6

Evaluation of JAK2 V617F Mutant Cell Lines

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SET2 cells were kindly provided by Prof. Dr. Fabíola Attié de Castro (School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil). HEL was obtained from ATCC (Philadelphia, PA, USA). SET2 and HEL cells harboring JAK2V617F mutation were tested and authenticated by Short Tandem Repeat (STR) matching analysis using the PowerPlex® 16 HS system (Promega, Madison, WI, USA) and the ABI 3500 Sequence Detector System (Life Technologies, Foster City, CA, USA). Cell culture conditions were performed in accordance with the recommendations of ATCC and DSMZ. All cell lines were mycoplasma-free. Ruxolitinib was obtained from InvivoGen (San Diego, CA, USA). Reversine was obtained from TargetMol (Target Molecule Corp., Boston, MA, USA). Aurora-A Inhibitor I (SML0882), AZD1152-HQPA (SML0268), NMS-P715 (475949) and SP600125 (S5567) were obtained from Sigma-Aldrich (St. Louis, MO, USA).
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7

Virulent, Recombinant, and Attenuated DPV Strains

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The virulent strain of DPV, CHv, was isolated and characterized by our lab (32 (link)). The recombinant virulent strain of DPV, BAC-CHv-EGFP (CHv-GFP), was constructed by our research center (33 (link)). The attenuated vaccine strain of DPV, CHa, was retrieved from storage at our research center. The Duck Tambusu virus (DTMUV) was stored at our research center. Each DPV and DTMUV strain was propagated on DEFs. The Rabbit anti-human MAP2 and -human GFAP polyclonal antibody and the goat anti-human β-actin monoclonal antibody were purchased from Abclonal (Wuhan, China). Mouse anti-duck CD80 (Gene ID:101796029) and CD86 (Gene ID:101794331) antibodies were generated by our research center. Ruxolitinib, poly(dA:dT), and poly(I:C) were purchased from Invivogen (Hong Kong, China).
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8

Evaluating Epigenetic Modulators in Cell Assays

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(+)-JQ-1 (Cat no. SML1524-5MG) was purchased from Sigma. ABBV-075 (Cat no. S8400) (ClinicalTrails.gov Identifier: NCT02391480), OTX015 (Cat no. S7360) (ClinicalTrails.gov Identifier: OTX015&draw=2&rank=5">NCT02698176), ARV-825 (Cat no. S8297) and ML385 (Cat no. S8790) were purchased from Selleckchem. Dimethyl sulfoxide (DMSO) (Item no. 10127403) was purchased from Thermo Fisher Scientific. 4-octyl itaconate (4-OI) was purchased from MedChemExpress (Cat. no. HY-112675). Dimethyl fumarate (DMF) was purchased from Sigma (Cat. No. 227056). Ruxolitinib was purchased from InvivoGen (Cat. No. tlrl-rux). IFN-α2a (Roferon) was obtained from Roche.
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9

SARS-CoV-2 Infection Inhibition by Ruxolitinib

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Calu3 cells were infected as described above with 0.01 MOI of SARS-CoV-2 wt or SARS-CoV-2 mut. After 1 h at 37°C, the cells were washed as detailed above and treated with 4μM Ruxolitinib (InvivoGen). Fresh Ruxolitinib was added at 24hpi.
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10

Inhibition of GPCMV Replication by IFN-I

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On day 0, GPL cells were pre-treated with 100 IU/ml or 1000 IU/ml universal human IFN-I (PBL Assay Science). The next day, IFN pre-treated and control untreated cells were infected separately with either WT GPCMV or vIET mutant virus (0.1 MOI) and incubated at 37°C with 5% CO2. After 72 hrs, supernatants and monolayers were harvested and titrated in duplicate on GPL cells as previously described. IFN-I IU/ml were confirmed by VSV growth experiments in the presence or absence of different concentrations of IFN-I on GPL cells prior to reported studies (data not shown). GPL cells were pre-treated with 10 μM of the JAK1/JAK2 inhibitor ruxolitinib (Invivogen) for 1–6 hrs. Depending on the experimental condition, some cells were treated with 100 IU/ml of universal human IFN-I (PBL Assay Science). Cells were subsequently infected with vIET (0.1 MOI) for 1 hr. Cells were washed and fresh F-12 medium supplemented with 10% FCS plus 10 μM ruxolitinib were added then incubated at 37°C with 5% CO2 for 4 days. Cells and supernatant were harvested and virus titrated on GPL cells.
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