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28 protocols using staurosporine

1

MAPK Pathway Inhibition in Macrophages

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For the MAPK pathway inhibition combination of 5 μM SB203580 (Cayman Chemical) and 5 μM PD98059 (Merck Millipore), which target p38 and MEK1, respectively, was used. Inhibitors were added to macrophages 30–60 min before the infection.
Staurosporine (LC Laboratories; 5 μM) or C646 (Merck; 10 μM) were added at the start of infection.
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2

Evaluating Drug Combination Cytotoxicity

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Dasatinib, erlotinib and paclitaxel (LC Laboratories) were dissolved in water-free DMSO. For the determination of relative cell viability, 10 μM and 1 μM or serial dilutions of the three drugs were screened in quadruplicates. In brief, 8000 cells per well were seeded in 96-well plates 24 h prior to the addition of the individual compounds. For the co-treatment experiments, either siRNA transfection was carried out as described, or cells were pretreated with 100 nM ketoconazole for 2 h and then treated in the presence of ketoconazole. After incubation for 48 h or 7 days, cell viability was assessed using CellTiterBlue (Promega) following manufacturer’s instructions. Vehicle (DMSO) was used as negative control. Treatment with 20 μM staurosporine (LC Laboratories) was used as positive control. Responses were normalized to DMSO- and staurosporine- treated controls. Relative cell viability curves were plotted using Graph Pad Prism 6.0b software.
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3

Routine Cultivation and Genetic Analysis of N. crassa

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Routine cultivation of N. crassa was performed on Vogel’s minimal medium with 2% sucrose (plus 1.5% agar for solid medium). Asexual spores were obtained by growing strains in glass tubes with slanted medium for one week until full sporulation was evident. Mutant strains were obtained from the Fungal Genetics Stock Center [7 (link)]. The genomic sequence of NCU09974 in the acr-3 mutant was obtained using a routine sequencing methodology [12 (link)]. Radial growth and spot assays were conducted as previously described [10 (link)]. Staurosporine was obtained from LC Laboratories and acriflavine and malachite green from Sigma-Aldrich. For quantitative real-time PCR experiments (qRT-PCR), asexual spores at a concentration of 106 cells/mL were grown at 26 °C in liquid VMM for 7 h; RNA was then isolated using the ZR Fungal/Bacterial RNA MicroPrep kit (Zymo Research), used for cDNA preparation using the SuperScript First-Strand Synthesis System kit (Life Technologies) and the relative expression of abc-3 in different strains using actin (NCU04173) as the reference gene was obtained using the 2−ΔΔCt calculation method from mixes containing previously described primers [13 (link)] and SYBR Green (Bio-Rad) that were analyzed in a Corbett Research Rotor-Gene 6000 thermocycler. Statistical analysis of qRT-PCR results was conducted on Prism 6 software (Graphpad).
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4

Quantifying NP Subcellular Localization in HT1080 Cells

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To quantify
subcellular localization of NPs in HT1080 cells, Rab7a-RFP and Lamp1-RFP
fusion constructs were expressed using a commercial baculovirus platform
(CellLight BacMam 2.0, Invitrogen), following manufacturing guidelines.
Pharmacological modulation of NP uptake was performed using the following:
staurosporine (1 μM; LC laboratories), latrunculin B (1 μM;
Tocris), cytochalasin D (1 μM; Sigma), chloroquine (50 μM;
Sigma), and ethylisopropyl amiloride EIPA (100 μM; Tocris).
Cells were rinsed in fresh media immediately prior to imaging; only
adherent cells were quantified. chloroquine dose–response measurements
were normalized to the C16proDOX control (rather than the
chloroquine-free control), in order to compare relative effects on
the potency of Pd-mediated C16proDOX activation itself.
50 μM chloroquine alone caused a 15–30% decrease in cell
viability.
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5

Assessing Compound Toxicity and Migration in A375 Melanoma

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The following compounds were tested for toxicity with the CellTiterGlo assay after a 4-day treatment in A375 melanoma cells and used at the maximal nontoxic dose in the transwell assay: Integrin inhibitor (Echistatin, 100 nM, R&D Systems), FAK inhibitor (PF562271 besylate, 500 nM, Cayman Chemicals), SRC inhibitor (Dasatinib, 10 nM, LC Laboratories), RAC1/CDC42 inhibitor (MBQ-167, 50 nM, Selleckchem), Wnt inhibitor (XAV939, 1 μM, Cayman Chemicals), JNK inhibitor (SP600125, 1 μM, LC Laboratories), ROCK inhibitor (RKI-1447, 500 nM, Cayman Chemicals), PKC inhibitor (Staurosporine, 1 nM, LC Laboratories), AMPKa inhibitor (Dorsomorphin, 1 μM, LC Laboratories), integrin inhibitor (SB273005, 100 nM, Selleckchem), FAK inhibitor (GSK2256098, 1 μM, Cayman Chemicals) and SRC inhibitor (Bosutinib, 100 nM, LC Laboratories). Echistatin was resuspended in water. All other compounds were dissolved in DMSO.
In addition, CD49f (Integrin alpha 6) monoclonal antibody (GoH3) (14-0495-85, eBioscience) was used at 40 μg ml−1 to block integrin α6β4.
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6

Quantifying Apoptosis in B16 Cells and BMDCs

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The B16 cells and the BMDCs were cultivated for 24 h with appropriate concentrations of the different active compounds. BMDCs were gated as CD11c+ cells using a CD11c-PE tagged antibody (MCA 1369, AbD serotec). Translocation of the phosphatidylserine residues of the B16 cells and CD11c+ BMDCs were measured by incubating 106 cells with 5 μl of annexin V-fluorescein (ImmunoTools GmbH, Oldenburg, Germany) and 5μl of 7-Amino-actinomycin D (7-AAD) (eBioscience, Germany) in a scheduled buffer for 15 min. The cells were analyzed by flow cytometry on FACS Canto II (BD Biosciences, Heidelberg, Germany) using a FACS DIVA device. The DMSO treated cells were used as a negative control, and the cells treated with 500 nM staurosporine (LC Laboratories, Woburn, USA) were used for the compensations as a positive control. Flow Jo soft (7.6.5) was used for the data analysis and presentation.
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7

Diverse Compound Network Analysis

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The reference compound set selected for standard compound network were chosen to represent diverse scaffolds from natural products or natural product derivatives. Daunomycin (7), roxithromycin (5), erythromycin (4), puromycin (8), novobiocin (10), and cycloheximide were obtained from Sigma-Aldrich. Ursolic acid, betulinic acid, and oleanolic acid were purchased from Extrasynthese SA. Chloramphenicol (1) was obtained from Calbiochem. Azithromycin (3) and rifamycin S were purchased from TCI. Thiamphenicol (2) was acquired from Spectrum Chemicals, and actinomycin D was purchased from RPI. Mupirocin (9) was purchased from AppliChem. Epirubicin (6) was purchased from MP Biomedicals LLC, and staurosporine was purchased from LC Laboratories.
Parameters used for this study are displayed in Table S2. The resulting networks were exported in graphML format and processed in Gephi for visualization using the Force Atlas 2 algorithm with default parameters except; spacing = 10, dissuade hubs = True, prevent overlap = True.
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8

Comprehensive Cellular Apoptosis Evaluation

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DMSO (dimethylsulfoxide) was purchased from Fisher Scientific. Staurosporine was purchased from LC Laboratories, while etoposide, phenol/chloroform/isoamyl alcohol mixture, and RNase A were purchased from Sigma-Aldrich® Canada. Ethidium bromide was purchased from Fluka. β-Hederin was purchased from ChemFaces. Acridine orange and Image-iT™ TMRM Reagent were purchased from Molecular Probes® Webinars, ThermoFisher Scientific. Caspase-Glo® 9, Caspase-Glo® 8, Caspase-Glo® 3/7 were purchased from Promega. Dihydrorhodamine 123 was purchased from Cayman Chemical. 28-O-α-l-Rhamnopyranosylbetulin 3β-O-α-l-rhamnopyranoside (Bi-L-RhamBet) was synthesized following protocols presented in our previous study [10 (link)]. Bi-L-RhamBet was further purified by preparative HPLC.
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9

Diverse Chemical Reagents for Research

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Antimycin A (#A8674), carbonyl cyanide m-chlorophenyl hydrazone (CCCP, #C2759), chloramphenicol (#C0378-5G), clotrimazol (#C6019), lonidamine (#L4900), paclitaxel (#T7402), potassium cyanide (#60178), rotenone (#45656), sodium azide (NaN3, #S200), thenoyltrifluoroacetone (TTFA, #88300), tigecycline (#220620097) and vinblastine (VBL, #V1377) were purchased from Sigma (Munich, Germany), cycloheximide (#8682.1) from Roth (Karlsruhe, Germany), N-(2-Quinolyl)valyl-aspartyl-(2,6-difluorophenoxy)methyl ketone (QVD, #S7311) from Selleckchem (Houston, TX, USA), oligomycin A (#O532970) from Toronto Research Chemicals (Toronto, Canada), etoposide (#1043) from Biovision and staurosporine (STS, #9300) from LC Laboratories (Woburn, MA, USA). All other substances for which a manufacturer is not explicitly specified were obtained from Carl Roth.
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10

Ferroptosis and Necroptosis Modulation

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Erastin (cat. no. E7781), ferrostatin‐1 (Fer‐1; cat. no. SML0583), propargylglycine (cat. no. P7888), and liproxstatin‐1 (cat. no. SML1414) were purchased from Sigma‐Aldrich. (1S,3R)‐RSL3 (cat. no. HY‐100218A) and necrostatin‐1 stable (Nec‐1s; cat. no. HY‐14622) were purchased from MedChem Express (Monmouth Junction, NJ, USA), and staurosporine was from LC Laboratories (Woburn, MA, USA) (cat. no. S‐9300). Rabbit antibody against poly(ADP‐ribose) polymerase (PARP) was from Cell Signaling Technology (Danvers, MA, USA; cat. no. 9532), antibody against actin was from Santa Cruz Biotechnology (Dallas, TX, USA; cat. no. sc‐1616‐R), and secondary antibody against rabbit IgG was from LI‐COR Biotechnology (Lincoln, NE, USA; cat. no. 925‐68071).
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