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14 protocols using heat inactivated fetal bovine serum

1

Generation of mouse bone marrow-derived dendritic cells

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Bone marrow cells were isolated from the tibia of C57BL/6
mice and
cultured in Dulbecco’s modified Eagle’s medium (Lonza,
Basel, Switzerland) supplemented with 10% heat-inactivated fetal bovine
serum (Lonza), 2 mM l-glutamine (Lonza), 100 U/mL penicillin
(Lonza), 100 μg/mL streptomycin (Lonza), and 20 ng/mL granulocyte-macrophage
colony-stimulating factor (ImmunoTools, Friesoythe, Germany) for 7
days at 37 °C and 5% CO2. The purity of the BMDCs
was evaluated with PE-labeled anti-mouse CD11c (Biolegend, San Diego,
CA, U.S.A.) by flow cytometry with >90% shown to be CD11c positive.
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2

Cytoskeletal Dynamics in Cancer Cell Lines

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A549 (lung carcinoma) cell line was purchased from National Centre for Cell Sciences, Pune. Human colon carcinoma HCT116 (p53+/+/p53−/−) and lung Carcinoma cell line H1299 (p53−/−) were purchased from ATCC, USA. The cell lines were cultured in DMEM or RPMI, supplemented with 10% heat-inactivated fetal bovine serum (Lonza, USA), L-glutamine (2 mM), sodium pyruvate (100 μg/ml), non-essential amino acids (100 μM), streptomycin (100 μg/ml), and penicillin (50 U/ml; Himedia, India). Primary antibodies used are p53 (DO-1; Santa Cruz, USA), α-GFP (Cell signaling, USA), α-Tubulin (Thermo Scientific, USA), GAPDH and Histone-3 (Biobharati Lifescience, India). Precision plus protein dual color standards (Bio-Rad) was used to detect the molecular weight of proteins in SDS-PAGE. Cyt-D, Lat-B, and Jas purchased from Calbiochem, USA was used at 5 μM, 1 μM, and 50 nM concentration respectively followed by Dox (1 μM, Sigma, USA) for 45 minutes. We made working stocks of all drugs (dimethyl sulfoxide for Cyt-D, Lat-B, and Jas; sterile H2O for Dox).
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3

Isolation of Lamina Propria Mononuclear Cells

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TI-LPMC were freshly isolated as described previously.24 (link), 25 (link) Briefly, after collection of biopsies from routine colonoscopy volunteers, tissues were treated with HBSS (without CaCl2, MgCl2, MgSO4; Gibco, Carlsbad, CA) and EDTA (1 mM; Ambion, Grand Island, NY) to remove intraepithelial cells. LPMC were then isolated following enzymatic digestion of the biopsies with Collagenase D (100 μg/mL; Roche, Indianapolis, IN) and DNase I (10 μg/mL; Affymetrix, Cleveland, OH) and homogenization using the Bullet Blender homogenizer (Next Advance Inc, Averill, NY). Cells were then washed and resuspended in complete medium (RPMI 1640 [Gibco Invitrogen, Carlsbad, CA] supplemented with 10% heat-inactivated fetal bovine serum [BioWhittaker, Walkersville, MD], 2 mM l-glutamine [HyClone, Logan, UT], 2.5 mM sodium pyruvate [Gibco], and 10 mM HEPES [Gibco], 100 U/mL penicillin [Sigma-Aldrich, St. Louis, MO], 100 μg/mL streptomycin [Sigma-Aldrich], and 50 μg/mL gentamicin [Gibco]) and counted using Kova Glastic Slides (Hycor Biomedical, Garden Grove, CA). Cells were either stained immediately for immune-phenotyping by flow cytometry or stimulated overnight with S Typhi–infected targets before staining (see later).
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4

Evaluating Human Androgen-Refractory Prostate Cancer Cell Lines

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Human androgen-refractory PCa ARCaPE and ARCaPM and LNCaP, LNCaPNeo and LNCaPRANKL PCa (15 (link)–17 (link)) were used. PCa cells and 293T cells were cultured in T-medium (GibcoBRL) supplemented with 5% heat inactivated fetal bovine serum (Bio-Whittaker) as previously mentioned (18 (link)). All cells were tested for mycoplasma every three months and were negative. The embryonic stem cells and iPSCs derived small RNA preparations were provided by Drs. Sareen and Svendsen. Derivation of these cells is included in the Supplementary materials and methods and figure legends.
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5

Cultivation of HL-1 Cardiac Muscle Cells

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HL-1 cells, a cardiac muscle cell line derived from the AT-1 mouse atrial myocyte tumor lineage, were a gift from William C. Claycomb, and maintained according to described protocols [18 (link)]. The cells were grown in Ex-Cell 320 medium (JRH Biosciences, Lenexa, KS) with 10% heat-inactivated fetal bovine serum (BioWhittaker), 10 mg/ml insulin (Life Technologies, Grand Island, NY), 50 mg/ml endothelial cell growth supplement (Upstate Biotechnology, Lake Placid, NY), 1 mM retinoic acid (Sigma), 10 mM norepinephrine (Sigma), 100 units/ml penicillin, 100 mg/ml streptomycin (Life Technologies), and an additional 13 nonessential amino acids (Life Technologies). The cells were grown at 37°C in an atmosphere of 5% CO2 and 95% air at a relative humidity of approximately 95%.
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6

Maintaining Human DLBCL Cell Lines

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Human DLBCL cell lines were maintained in RPMI-1640 (Lonza; DHL-4, DHL-6, TOLEDO, U2932, K422, RIVA, PFEIFFER) or Iscove’s Modified Dulbecco’s Medium (Lonza; Ly-1, Ly-3, Ly-4, Ly-7, Ly-18, Ly-19, HBL-1), each supplemented with 100 U/mL penicillin, 100 U/mL streptomycin (Lonza), 10% or 20% heat-inactivated fetal bovine serum (Biowest), L-glutamine (2mM, Lonza) and HEPES (10Mm, Lonza). Cell GCB- and ABC designations were determined previously (18 (link)). Cells were grown in a humidified atmosphere at 37°C with 5% CO2. AD-O51.4 was synthesized and provided by Adamed S.A. TRAIL was purchased from R&D. Dynasore, venetoclax, SAHA and panobinostat were purchased from Selleckchem. Methyl-β-cyclodextrin (MβCD) and filipin were purchased from Sigma Aldrich. Caspase 3 inhibitor (Z-DEVD-FMK), caspase 8 inhibitor (Z-IETD-FMK), caspase 9 inhibitor (Ac-LEHD-CMK) and pan-caspase inhibitor (Z-VAD-FMK) were purchased from Merck-Millipore and used at 20 μM (caspase 8 and 9 inhibitors and pan-caspase inhibitor) or 50 μM (caspase 3 inhibitor) final concentration.
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7

LCMV Cl13 infection in A549 cells

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A549 cells (ATCC) were cultured in Dulbecco's modified Eagle's medium (DMEM) (Lonza, Walkersville, MD, USA) supplemented with 2 mM l-glutamine, 50 U ml−1 penicillin, and 50 mg ml−1 streptomycin (Gibco, Grand Island, NY, USA), plus 10% heat-inactivated fetal bovine serum (Lonza). The cells were maintained in 175-cm2 flasks at a density of 0.5 × 106 to 1 × 106 cells ml−1 in a total volume of 30 ml. A total of 1 × 106 A549 cells were left untreated or pretreated for 1 h with 20 or 100 ng ml−1 human recombinant IL-27 (Biolegend). The cells were subsequently infected with LCMV Cl13 at a multiplicity of infection (MOI) of 0.05 or 0.5. After 1 day, the cells were washed with PBS and collected in lysis buffer (Qiagen) for RNA analysis.
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8

Culturing Leishmania donovani Promastigotes

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Promastigotes of the L. donovani Karthoum strain (MHOM/SD/43/124) were kindly provided by A. Toraño and M. Domínguez (Department of Immunology, Centro Nacional de Microbiología, Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Majadahonda, Spain). Three cultures were set at an initial cell density of 2 × 106/ml in RPMI 1640 supplemented with L-glutamine (Life Technologies, Carlsbad, CA), 10% heat-inactivated fetal bovine serum (Lonza, Basel, Switzerland), and 100 μg/ml streptomycin—100 IU/ml penicillin (Life Technologies), and incubated at 27 °C. Cell density was estimated with a Neubauer chamber and total protein extracts from 108 promastigotes per culture were prepared daily after harvesting them at 2000 g for 10 min.
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9

Isolation and Stimulation of pDCs

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The CAL-1 human pDC cell line was grown in complete RPMI 1640 medium (Lonza, Walkersville, MD) supplemented with 2 mM L-Glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 1 × MEM NEAA (all from Gibco, Grand Island, NY) to which 10% heat inactivated fetal bovine serum (Lonza) was added. Cells were cultured at 37°C in a CO2 in air incubator. Prior to stimulation, the CAL-1 cells were serum starved for 16 h in complete RPMI supplemented with 0.1% FBS and then treated with 1 μM “K” ODN for the indicated times as previously described [10 (link)].
Mononuclear cell enriched human buffy coats were obtained by leukopheresis (DTM, NIH, Bethesda, MD) using an IRB approved protocol. Following Ficoll Hypaque (Sigma, St. Louis, MO) and Percoll gradient (Pharmacia, Uppsala, Sweden) centrifugation of the buffy coat, pDCs were MACS sorted using a BDCA two purification kit per manufacturer’s instructions (Miltenyi Biotechm Auburn, CA). The pDCs isolated by this procedure were 93–95% pure and their viability was >95%. A total of 5 × 105 freshly isolated pDC/well were cultured in 48-well plates in complete media and then stimulated with 1 μM “K” ODN for the times indicated.
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10

Syngeneic Colorectal Carcinoma Model

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The CT-26 colon carcinoma cell line established from a chemically-induced colorectal adenocarcinoma in BALB/c mice was purchased from ATCC (CRL-2638). CT-26 cells were cultured in RPMI 1640 medium supplemented with glutamine (Sigma-Aldrich, USA), 10 % heat-inactivated fetal bovine serum (Lonza, Switzerland), and antibiotics: Streptomycin 100 lg/ml, Penicillin 100 U/ml (Polfa, Poland). Cells were maintained under a humidified atmosphere with 5 % CO 2 at 37 °C. Before injecting the syngeneic mice, CT-26 cells were suspended in phosphate buffered saline solution (PBS). Female BALB/c mice, aged 8 weeks, were obtained from the Department of Genetics at the Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology (Warsaw, Poland). Mice were maintained on standard laboratory chow and under pathogen-free conditions.
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