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61 protocols using calcusyn 2

1

Anti-Proliferative Assay of Compounds

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Cells were seeded in 96-well plates for 24 h/37°C at a density of 5,000 (MCF-7), 10,000 (HL-60), 2,000 (HCT116) and 10,000 (3T3 and H9c2) cells/well. For 3T3 and H9c2 cells, the medium was changed to serum- and pyruvate-free DMEM 24 h prior to the experiments. Anti-proliferative and cytotoxicity effects of the compounds were studied at different concentrations after incubations for 72 h/37°C. Viabilities of cells were determined using MTT assays (Sigma-Aldrich, Germany) according to the manufacturer's instructions on a Tecan Infinite 200M plate reader (Tecan, Austria). The proliferation/viability of treated groups was expressed as a percentage of the untreated controls (100%). The half maximal inhibitory concentrations resulting in a 50% reduction of cellular proliferation/viability (IC50) as compared to the untreated control value, were calculated using CalcuSyn 2.0 software (Biosoft, U.K.).
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2

Cytotoxicity and Cytoprotective Assays

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In this study, the statistical software SigmaStat for Windows 3.5 (SPSS, CA, USA) was used. Data are presented as mean ± S.D. (standard deviation). Statistical significance was assessed using one-way or two-way ANOVA with a Bonferroni post hoc test (comparisons of multiple groups against corresponding controls). Results were considered to be statistically significant when p < 0.05. The biological half-lives of tested compounds (t1/2 values); the concentrations of compounds inducing 50 % loss of cellular viability (TC50 values); and the concentrations leading to 50 % protection of cellular viability from toxicity induced by CA (EC50 values) were calculated using the CalcuSyn 2.0 software (Biosoft, U.K.). The graphs were created using GraphPad Prism 6.04 for Windows (GraphPad Software, CA, U.S.A.).
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3

Analyzing Compound Toxicity and Protection

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In this study, the statistical software SigmaStat for Windows 3.5 (SPSS, U.S.A.) was used. Data are presented as mean ± SD (standard deviation). Statistical significance was determined using ANOVA with a Bonferroni post hoc test (comparisons of multiple groups against a corresponding control). Results were considered to be statistically significant when p < 0.05. The concentrations of tested compounds inducing 50% toxicity / viability decrease (median toxic concentration; TC50) and the concentration leading to 50% protection from toxicity induced by H2O2 (median effective concentration; EC50) were calculated using CalcuSyn 2.0 software (Biosoft, U.K.). The graphs were created using GraphPad Prism 5.04 for Windows.
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4

Growth Inhibition Isobologram Analysis

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All data are presented as means ± SEM. Significance of differences between experimental variables was determined by Tukey's test. Statistical analyses were performed with KyPlot. A P-value of <0.05 was considered to indicate a statistically significant result. Isobologram analysis of growth inhibition was performed with CalcuSyn 2.0 software (Biosoft) as previously described (23 (link)).
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5

Evaluating Drug Cytotoxicity and Synergy

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Drug toxicity was determined as previously described (16 (link)). Briefly, cells were seeded in 96-well plates (3,000 cells/well) in triplicate and were treated with a range of concentrations of the indicated drugs, as depicted in Fig. 1, at 37°C for 72 h. Controls were treated with vehicle (either PBS or DMSO). Drug toxicity was assessed after staining with MTT (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China) by measuring the production of formazan, which is directly proportional to the number of viable cells. Briefly, to each well of a 96-well plate containing 100 µl medium, 10 µl MTT solution (5 mg/ml MTT in PBS) was added and incubated at 37°C for 2 h. Solubilization of formazan was achieved following the addition of 100 µl solubilization solution [40% dimethylformadide v/v in 2% glacial acetic acid v/v, to which 16% sodium dodecyl sulphate (pH 4.7) had been added w/v] and reading optical density at 570 nm. For drug combination experiments, a combination index (CI) was calculated using CalcuSyn 2.0 software (Biosoft, Cambridge, UK) based on the Chou and Talalay method (17 (link)). CI values between 0.1 and 0.9 refer to different grades of synergism, values between 0.9 and 1.1 refer to additive effects, whereas values >1.1 refer to antagonistic effects.
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6

Apoptosis Assay for Cancer Cells

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Cancer, NK, or T cells were treated with different compounds or dimethyl sulfoxide (DMSO) as indicated in the figures and figure legends. DMSO served as the drug vehicle, and its final concentration was no more than 0.1%. After treatment, cells were collected, stained with annexin V and DAPI, and analyzed by flow cytometry. Briefly, 10X annexin V binding buffer (100 mM HEPES, 40 mM KCl, 1.4 M NaCl, 7,5 mM MgCl2, 25 mM CaCl2, pH 7.4) with fluorochrome-conjugated annexin V and 20 µM/mL DAPI was added and incubated at RT for 15 min. Next, the plates were placed on ice and analyzed immediately with BD Fortessa flow cytometer. To determine absolute cell number, CountBright Absolute Counting Beads (Life Technologies) were also added. Data were analyzed by BD FACSDiva™ Software (BD Biosciences) and Flowjo software v10 (Flowjo). Calcusyn 2.0 software (Biosoft) was used to calculate combination index and whether there is a synergy, based on the number of live cells (i.e., AnxV/DAPI). The percentage of specific apoptosis was calculated as follows: 100 × (experimental apoptosis % – spontaneous apoptosis %)/(100 % – spontaneous apoptosis %).
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7

Statistical Analysis of Combined Drug Effects

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Statistical significance in assays with identical cell lines was assessed with Student’s t test (two-tailed). GraphPad Prism 6.02 (GraphPad Software) was used for all statistical analyses. The Calcusyn 2.0 software (Biosoft, Cambridge, UK) was used to analyse combined drug effects and produce the isobolograms normalized to the IC50 of each inhibitor.
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8

Statistical Analysis of Experimental Data

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SigmaStat for Windows 3.5 (Systat Software, San Jose, CA, USA) statistical software package was utilized to analyze results. The data are expressed as the mean ± SD of a given number of experiments. Statistical significance was determined using a one-way ANOVA with a Bonferroni post-hoc test or Student’s t-test. The results were considered to be statistically significant when p < 0.05. The IC50 values were calculated using CalcuSyn 2.0 software (Biosoft, Cambridge, UK). Cell cycle analysis was evaluated using MultiCycle AV Software (Phoenix Flow Systems, San Diego, CA, USA).
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9

Quantifying Cell Death by Flow Cytometry

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Exponentially growing cells were treated with different compounds or dimethyl sulfoxide (DMSO) as indicated in the figures and figure legends. DMSO served as the drug vehicle, and its final concentration was no more than 0.1%. After treatment, cells were collected, stained with annexin V (AnnV) and propidium iodide (PI; Sigma-Aldrich, St Louis, MO, USA), and analyzed by flow cytometry. Briefly, cells were washed twice by centrifugation (1,000 g, 5 min) with 2 mL AnnV binding buffer (ABB; 10 mM HEPES, 140 mM NaCl, and 5 mM CaCl2 at pH 7.4). After washing, cells were resuspended in 0.1 mL ABB containing fluorochrome-conjugated AnnV and incubated in darkness at room temperature for 15 min. The cells were washed again with 2 mL ABB and then resuspended in 0.3 mL ABB. PI was added at a final concentration of 1 μg/mL before analysis by a Gallios flow cytometer (Beckman Coulter, Indianapolis, IN, USA). To determine absolute cell number, CountBright Absolute Counting Beads (Life Technologies, Carlsbad, CA, USA) were also added. Data were analyzed by Kaluza software version 1.3 (Beckman Coulter). Calcusyn 2.0 software (Biosoft, Great Shelford, UK) was used to calculate IC50 values and combination index, based on the absolute number of live cells (i.e., AnnV/PI). AnnV-FITC and AnnV-APC were purchased from BD Biosciences (San Jose, CA, USA).
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10

Evaluating Synergistic Drug Combinations

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RL95-2 (8 × 103) and HEC-1-A (5 × 103) cells were seeded into 96-well plates and incubated in their respective media. The next day, they were exposed to the indicated drugs in fresh DMEM/F12 or McCoy’s 5A medium for the indicated periods. MTT solution (0.5 mg/mL in phosphate-buffered saline (PBS)) was then added to each well, and the cells were incubated for 4 h at 37 °C. After removing the supernatants, we added dimethyl sulfoxide (DMSO; 100 μL) to dissolve the precipitate, and the absorbances at 570 nm and 650 nm were then measured using an enzyme-linked immunosorbent assay plate reader (Multiskan EX, Thermo Fisher Scientific). The relative metabolic activity was calculated on the basis of the absorbance ratio between cells cultured with the indicated drugs and the untreated controls, which were assigned a value of 100. A combination index (CI) was also calculated using CalcuSyn 2.0 software (Biosoft, Cambridge, United Kingdom) to produce an isobologram where a CI < 1 indicates a synergistic combination effect and a CI > 1 indicates an antagonistic combination effect [60 (link)].
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