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9 protocols using sodium pyruvate

1

Hypoxia-induced mTOR Signaling Pathway

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HT (purity ≥98%) was obtained from Extrasynthese, France. Dulbecco’s modified Eagle’s medium (DMEM) and sodium pyruvate were from Capricorn Scientific, Germany, foetal bovine serum (FBS) was from Sigma, USA, and Trypan Blue Solution, 0.4% from Thermo Fisher, USA. Primary antibodies mTOR (2972 S), p-mTOR (2971 S), S6 (2217 S) and p-S6 (2211 S) were purchased from Cell signaling Technology, USA; HIF-1α (A300–286A) from Bethyl, USA; PARP-1 (C-2-10) from Calbiochem, Germany; anti-poly(ADP-ribose) (α-PAR) (4355-MC) from Trevigen, USA; α-Tubulin antibody (T5168) from Sigma, USA and FIH-1 (sc-26219) from Santa Cruz, USA. Apoptosis was quantified using the FITC Annexin V Apoptosis Detection Kit with PI (ANXVKF, Immunostep, Spain). RNA was isolated using the RNeasyPlus Mini kit (Qiagen, Germany). cDNA Synthesis Kit for RT-qPCR and iTaq UniverSYBR for Real-time PCR were from Bio-Rad, USA. Primers were synthesized by Biomedal S.L. (Spain). ARNT siRNA (s1613 and s1615), scramble siRNA (sc-37007) and the transfection reagent jetPRIME were from Ambion, Santa Cruz and Polyplus Transfection, USA, respectively. HIF-1α siRNA was from Sigma (forward 5′-CUGAUGACCAGCAACUUGA-3′, reverse 5′-UCAAGUUGCUGGUCAUCAG-3′).
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2

Culturing and Characterizing Human Glioblastoma Cells

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The human glioblastoma cell line U251 was obtained from the European Collection of Animal Cell Cultures (Salisbury, UK). The cells were incubated at 37°C, in a humidified atmosphere with 5% CO2, in the RPMI cell culture medium (Gibco, Life Technologies, MA, USA) supplemented with 5% fetal calf serum (FCS), 2 mM L-glutamine, 10 mM sodium pyruvate, and penicillin/streptomycin (all from Capricorn Scientific, Ebsdorfergrund, Germany). Cells were prepared for experiments using the conventional trypsinization procedure with trypsin/EDTA and seeded in 96-well flat-bottom plates (1 × 104 cells/well) for the cell viability¯ assessment, 6-well plates (2.5 × 105 cells/well) for flow cytometric analysis, or 60 mm Petri dishes (1 × 106 cells) for the electron microscopy, immunoblot, and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR).
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3

Neutrophil Enrichment from Murine Bone Marrow

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Following the manufacturer’s protocol, neutrophils were negatively enriched using the EasySep Mouse Neutrophil Enrichment Kit (StemCell Technologies) from the bone marrow of adult wt mice. The cells were resuspended in PBS supplemented with 2 % FCS and 1 mM EDTA and cultured in RPMI medium supplemented with 100 U ml−1penicillin, 100 µg ml−1streptomycin, 10 % FCS, 1 mM sodium pyruvate (Capricorn Scientific) and 4 mM glutaMAX (Thermo Fisher Scientific).
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4

Agarose-based Culture and Slicing Media

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Low-melting agarose was obtained from Sigma-Aldrich Chemie GmbH (Steinheim, Germany). The culture medium consisted of minimal essential medium (pH 7.2) composed of CaCl2, MgSO4, KCl, NaCl, NaH2PO4, glucose, NaHCO3 (all from Sigma-Aldrich), HEPES (Carl Roth GmbH + Co. KG, Karlsruhe, Germany), sodium pyruvate, glutamine (both from Capricorn Scientific GmbH, Ebsdorfergrund, Germany), amino acids and vitamins (both from Sigma-Aldrich) and was supplemented with penicillin and streptomycin (Sigma-Aldrich) (Additional file 1: Table S1) as described before [27 (link)]. The slicing medium consisted of the same components except for sodium pyruvate, glutamine, amino acids, vitamins, penicillin and streptomycin. Besides, a culture medium with the addition of 10% heat-inactivated and sterile-filtered FBS (Thermo Fisher Scientific, Life Technologies Europe BV, Bleiswijk, Netherlands, Gibco 10,270) was used for viability tests.
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5

Culturing Breast Cancer Cell Lines

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MDA-MB-231 and MCF-7 cells were grown as adherent monolayers in low glucose (1.0 g/L) or high glucose (5 g/L) Dulbecco's Modified Eagle's Medium (DMEM) with stable L-glutamine (2 mM) and sodium pyruvate (from CAPRICORN scientific) supplemented with 10% heat-inactivated fetal bovine serum, 10 μg/mL human recombinant Zn-insulin, and antibiotics: penicillin (100 U/ml), streptomycin (100 μg/ml) and gentamicin at a final concentration of 50 μg/ml. Cells were grown at 37°C in humidified incubator containing 5% CO2 in air and were sub-cultured at 90% confluence.
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6

Culturing Breast Cancer Cell Lines

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MDA-MB-231 and MCF-7 cells were grown as adherent monolayers in low glucose (1.0 g/L) Dulbecco's modified Eagle's medium (DMEM) with stable L-glutamine and sodium pyruvate (from Capricorn Scientific GmbH) supplemented with 10% heat-inactivated fetal bovine serum, 10 μg/mL human recombinant Zn insulin, and antibiotics: penicillin (100 U/mL), streptomycin (100 μg/mL), and gentamicin at a final concentration of 50 μg/mL. Cells were grown at 37°C in a humidified incubator containing 5% CO2 in air and were subcultured at 2-3-day intervals.
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7

Cell Culture Protocols for Skin Cell Lines

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The human fibroblast cell line CCD-1137Sk (ATCC® CRL-2703™) was cultured in Iscove’s Modified Dulbecco’s Medium (IMDM), with L-Glutamine, supplemented with 10% fetal bovine serum (Sigma), and 1% Penicillin Streptomycin (Capricorn). The human keratinocyte cell line HaCaT (CLS order no. 300493) and the human malignant melanoma cell line SK-MEL-28 (CLS order no. 300337) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) High Glucose (4.5 g/l), with L-Glutamine, with Sodium Pyruvate (Capricorn) supplemented with 10% fetal bovine serum, and 1% Penicillin Streptomycin. Cells were maintained at 37 °C in 5% CO2. Cell lines were obtained in 2016 and repeatedly authenticated by phenotypic analysis, including expression of collagen IV for CCD-1137Sk, establishment of a CK10/CK14 gradient in 3D for HaCaT, and high proliferation rate for SK-MEL-28. Mycoplasma tests using the MycoAlert™ Mycoplasma Detection Kit (Lonza) were routinely performed to ensure mycoplasma-free cell cultures.
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8

Establishment of BRAFV600E-Mutant Cell Lines

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Human colon carcinoma cell line RKO and human melanoma cell line A375 both harbouring the BRAFV600E mutation were purchased from the American Type Culture Collection (Manassas, VA, USA). Both RKO and vemurafenib-resistant RKO cells were maintained in Eagle’s Minimum Essential Medium (Capricorn Scientific, Ebsdorfergrund, Germany) supplemented with 10% fetal bovine serum (Capricorn Scientific, Germany), 2 mM L-glutamine (Capricorn Scientific, Germany), penicillin (100 U/mL) (Capricorn Scientific, Germany) and streptomycin (100 µg/mL) (Capricorn Scientific, Germany) in humified atmosphere with 5% CO2 at 37 °C. Melanoma cell line A375 and its vemurafenib-resistant counterpart were maintained in Dulbecco’s Modified Eagle Medium (Capricorn Scientific, Germany) supplemented with 10% fetal bovine serum (Capricorn Scientific, Germany), 2 mM L-glutamine (Capricorn Scientific, Germany), penicillin (100 U/mL) (Capricorn Scientific, Germany), streptomycin (100 µg/mL) (Capricorn Scientific, Germany) and 1 mM sodium pyruvate (Capricorn Scientific, Germany) in humified atmosphere with 5% CO2 at 37 °C.
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9

Viability of DUV-Irradiated HaCaT Cells

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HaCaT cells, a spontaneously immortalized human keratinocyte line, were cultured in Dulbecco’s Modified Eagle Medium—high glucose (4.5 g/L) with L-glutamine and with sodium pyruvate (Capricorn) supplemented with 10% fetal bovine serum. HaCaT cells (4.0 × 105/dish) were seeded in 35 mm dishes and cultured at 37 °C in 5% CO2 for 24 h. The cells were then washed twice with PBS, after which we immediately irradiated the cells with DUV-LED light. Two milliliters of fresh medium was added, and the mixture was cultured for 24 h. Then, the cells were harvested, and cell viability was evaluated by trypan blue dye exclusion assay. The number of viable cells was counted, and the survival rate was expressed as a percentage of the non-irradiated control. The experiment was performed three times, and the average percentage of surviving HaCaT cells was evaluated.
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