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8 protocols using nutridoma cs

1

Short Tandem Repeat Authenticated HL-60 Cell Differentiation

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Short tandem repeat authenticated HL-60 cells Saha et al. (2023) (link) were maintained in R10 media at 5% CO2 and 37°C and at a concentration of 0.2–1 million/mL by passaging them every 2–3 days. 5 days prior to experiments, HL-60s were differentiated into a neutrophil-like state by taking an aliquot of cells in their culturing medium and supplementing with an equal volume of Nutridoma-CS (Roche #11363743001) and DMSO diluted in RPMI such that that the final concentrations were 0.2 million/mL HL-60 cells, 2% (v/v) Nutridoma-CS, 1.3% (v/v) DMSO, 5% (v/v) FBS in RPMI. After 5 days at 37°C/5% CO2, we observed robust expression of terminal differentiation markers like FPR1 as reported previously Rincón et al. (2018) (link).
Lenti-X HEK-293Ts (Takara) were used for lentivirus production and maintained at below 80% confluency in DMEM supplemented with 10% (v/v) heat-inactivated fetal bovine serum. These cells were also maintained at 5% CO2 and 37°C. All cell lines were routinely monitored for mycoplasma contamination using standard mycoplasma monitoring kits (Lonza).
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2

Differentiation of mESCs to Endothelial and Smooth Muscle Cells

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A3 mESC were plated at 10,000 cells/cm2 on 50 ng/mL fibronectin-coated plates (BD Biosciences) and cultured in Stage 1 Differentiation Medium.24 (link) After 3 days, the cells were replated at 10,000 cells/cm2 on 50 ng/mL fibronectin-coated plates and cultured in Stage 2 Differentiation Medium containing 70% alpha-MEM (Mediatech) and 30% DMEM (Invitrogen) plus 2x Nutridoma CS (Roche), 1x penicillin-streptomycin (Invitrogen), 1x nonessential amino acids (Invitrogen), 2 mM L-glutamine (Invitrogen), and 0.05 mM 2-mercaptoethanol (Calbiochem), 10 ng/mL basic Fibroblast Growth Factor (Sigma), and 10 ng/mL VEGF (R&D Systems). On days 5, 7, 10, 12, and 14 of total differentiation, the differentiating cells were removed using Cell Dissociation Buffer (Invitrogen) for 30–60 minutes and analyzed for Tie-2 GFP or α-SMA RFP expression on an Aria III Flow Cytometer (BD). Data analyses were performed using FlowJo software (Tree Star Inc.). FITC- and PE-labeled compensation beads were used for compensation of potentially double positive cells. Unstained and undifferentiated A3 mESC were used as a negative control and gated to <5% of the negative control. Fluorescent populations of cells were analyzed for statistical significance using one-way analysis of variance and a post hoc Tukey’s HSD test using the R programming language.
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3

Producing anti-flavivirus monoclonal antibodies

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Hybridomas secreting anti-flavivirus monoclonal antibodies were generated from the most responsive JEV VLP-vaccinated mice (JEV FRµNT50 > 120) following the standard protocol111 with minor modifications112 (link). Briefly, JEV VLP-vaccinated mice were boosted intraperitoneally with either 4 µg of purified JEV VLP or mD2VLP emulsified in Freund’s incomplete adjuvant (Sigma-Aldrich, St. Louis, MO, USA) for three consecutive days. Two days after the last boost, the splenocytes were harvested and then individually fused with NSI/1-Ag4-1 myeloma cells using 50% polyethylene glycol (PEG) (PEG Hybri-Max™, Sigma-Aldrich, St. Louis, MO, USA). Fused cells were resuspended in RPMI supplemented with 20% FBS, hypoxanthine-aminopterin-thymidine medium, and hybridoma growth factor (Nutridoma™-CS, Roche Diagnostics, Indianapolis, IN, USA). Two weeks post-fusion, supernatants from the selected polyclonal colonies were individually screened for secretion of mAbs by IgG ELISA as described above using JEV, DENV-2, and ZIKV VLPs, and detected with an HRP-conjugated goat anti-mouse IgG. The positive clones (P/N values of ≥2) were subcloned by limiting dilution to isolate monoclonal cells and then further screened for VLP ELISA binding and flavivirus neutralization activities using unpurified supernatants.
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4

Monocyte-Derived Dendritic Cell Differentiation

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PBMCs (5 × 106; 1 mL) were incubated for 2 h at 37°C in 5% CO2 to allow monocytes to adhere in 24-well plates. Non-adherent cells were washed out and the adhered monocytes were used throughout the experiments. NETs-enriched supernatants treated or not with DNase, or filtered were added and cultures maintained at 37°C in 5% CO2. After 18 h, GM-CSF and IL-4 (50 ng/mL each; Peprotech) were added and the cultures maintained for 5 days at 37°C in 5% CO2. Cells were then harvested, stained for CD1a (PE; BD), CD14 (FITC; BD), CD68 (FITC; BD), CD32 (PE-Cy7; BD), CD163 (APC; BD), and CD80 (APC-Cy; BD), and analyzed on a MACSQuant flow cytometer (Miltenyi Biotec). Cells were acquired based on forward and side scatter and data analyzed with FlowJo Software 10.0.8. All experiments with monocytes were done in medium supplemented with Nutridoma-CS (1×; Roche Applied Science). In some experiments, monocytes were pretreated with cytochalasin D (CytD) (10 µg/mL; Sigma) or the diluent DMSO for 30 min before the addition of NETs.
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5

Granulosa Cell Hormonal Stimulation

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GC were cultured in DMEM/F12 medium supplemented with 10 % FCS and antibiotics for 72 h to regain a more native reaction pattern before hormonal stimulation [24 (link)]. After three days in culture, GC were either untreated (control) or treated for 48 h with 30 ng/ml of r-FSH (Puregon®, Schering Plough, Courbevoie, France) or 30 ng/ml of hCG (Ovitrelle ®, Merck Serono, Lyon, France), individually or in combination. One μl of Androstenedione (Sigma, Poole, UK) was added to the culture medium to provide specific substrate to GC, for oestrogen synthesis. Therefore, 17 β-estradiol quantification by immuno-chemiluminescence using a commercially kit (ADVIA® Centaur, Bayer Diagnostics, Tarrytown, NY, USA) allowed to check GC viability (Additional file 3: Figure S1). From day 3, FCS was replaced in culture medium by Nutridoma-CS (Roche Applied Science, Germany) in order to avoid lipoproteins contamination. After 5 days of culture, culture medium and GC samples were retrieved and stored at –80 °C. Each culture’s experiment was performed in triplicate and 10 times.
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6

Differentiation of Mouse ESCs into VPCs

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Mouse ESC-R1 were first sorted for Flk-1+ expression using an Aria III Fluorescence Activated Cell Sorter (FACS; BD Biosciences). The scaled-up early stage induction of Flk-1+ mESC-A3 was found to be consistently above 90% and did not require sorting. The Flk-1+ VPC were plated on 50 ng/ml collagen-type IV (BD Biosciences) or 50ng/ml fibronectin (BD Biosciences) at either: 5,000, 10,000, or 20,000 cells/cm2. The stage 2 medium consisted of: 70% alpha-MEM (Mediatech) and 30% DMEM (Invitrogen), 2Χ Nutridoma CS (Roche), 1Χ ps, 1Χ NEAA, 2 mM L-glutamine, and 0.05 mM 2-mercaptoethanol. The supplemental amounts of bFGF (Sigma) examined included: 0 ng/ml, 10 ng/ml, 25 ng/ml, or 50 ng/ml; while amounts of VEGF examined were: 0 ng/ml, 10 ng/ml, 50 ng/ml, or 100 ng/ml. Partial media changes occurred every other day. After 7 days, cells were harvested for analysis.
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7

Detailed Flow Cytometry Protocol

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DMSO, ATRA, CA, dbcAMP, PMA, fMLF and NBT were purchased from Sigma; Nutridoma-CS from Roche, Trypan Blue solution from Corning, G-CSF from Applied Biological Materials (abm), FLPEP (catalog # F1314); Sytox Blue (catalog #S11348), TO-PRO3 Ready Flow dead cell stain (catalog #R37170), and NucRed Dead 647 (catalog #R37113) from Life Technologies; and Anti-CD11b-APC (Clone ICRF44, catalog # 301309), isotype control mouse IgG1κ (Clone MOPC-21, catalog # 400107) and Fc Receptor Blocking Solution (catalog # 422302) from Biolegend.
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8

Monoclonal Antibody Production Against PAX3-FOXO1

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mAbs were prepared as previously described [10 (link), 11 (link)]. Briefly, female Balb/c mice (6–8 weeks old) were injected i. p. with 100 μg of KLH conjugated with peptide PF corresponding to the PAX3-FOXO1 translocation region aa 100-117 (TIGNGLSPQNSIRHNLSL) in Freund’s adjuvant (Sigma) followed by additional i.p. injections of 100 μg of purified KLH peptide in Freund’s adjuvant at two weeks intervals. Two weeks after the third injection, one mouse received i.p. and i.v. boosts of purified KLH peptide in PBS for 3 consecutive days. A day after the final boost, the spleen of the mouse was removed and fused with the myeloma cell line P3x63Ag8.653 as previously described using 50% PEG with 5% DMSO. Fused cells were resuspended in HY media supplemented with 20% FBS, HAT, and 1× Nutridoma-CS (Roche) and seeded into 96-well plates. Hybridoma colonies were screened by ELISA for secretion of mAbs that bound to ovalbumin coupled peptide. Hybridomas secreting mAbs of interest were subcloned twice by limiting dilution and final hybridoma clones were isotyped using a murine antibody isotyping kit (Roche).
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