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33 protocols using ribociclib

1

Melanoma Cell Lines and Compounds

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Melanoma cell lines YUSEEP, YUHIMO, YUWERA, and YUCRATE were obtained from Ruth Halaban (Yale University) in 2020. Melanoma cell lines WM4235, WM4324, WM9, 1205Lu, WM989, WM983B, WM4380 and WM4258, as well as the PDX model WM4223 were obtained from Meenhard Herlyn (Wistar Institute) in 2020. All patient samples were collected under institutional review board (IRB) approval [34 (link)]. Cell lines were tested for Mycoplasma biannually and authenticated using short-tandem repeat fingerprinting. All cell lines are cultured in RPMI-1640 (Corning,10-040-CM) supplemented with 5% fetal bovine serum (FBS; Cytiva, SH30109.03) in the presence of 5% CO2 at 37 °C. Commercially purchased compounds include palbociclib (SelleckChem, S1116), ribociclib (SelleckChem, S7440), abemaciclib (Apex Biotechnology, A1794), trametinib (SelleckChem, S2673), AZD6244 (SelleckChem, S1008) and VX-11e (SelleckChem, S7709).
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2

Drug Sensitivity in 3D Cultures

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Palbociclib, ribociclib, abemaciclib, oxaliplatin, cisplatin, and actinomycin D were purchased from Selleck Chemicals (Houston, TX, USA). Phenanthriplatin was generously provided by Professor Stephen J Lippard of the Department of Chemistry, Massachusetts Institute of Technology, Boston, MA, USA. Drug testing in resistant cell lines and 3-demensional (3D) spheroids was performed as previously described (10 (link)).
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3

Cell Line Characterization and Inhibitor Screening

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LNCaP cell line was obtained from ATCC, the v-Src PEC and the NeuT-PEC cell lines were previously described (18 (link)). Original cells were expanded and stored in the liquid nitrogen at early passage. During the experiments, the morphology of all cell lines was checked under phase contrast microscope routinely. For LNCaP cell line, proliferation and AR abundance in response to DHT stimulation were tested by MTT assay and Western-blot. For v-Src-PEC and NeuT-PEC cell lines, the proliferation in response to Src kinase inhibitor or NeuT inhibitor was tested. V-Src or NeuT expression in these cells was checked by Western-blot for verification. All of the newly revived cells were treated with BM-cyclins (Roche) and the mycoplasma contamination was determined with Hoechst 33258 staining under high magnification fluorescent microscope routinely. DNA transfection and luciferase assays were performed as previously described (1 (link),18 (link)). The CBF-Luc and -3,400 cyclin D1-Luc reporter plasmids were previously described (19 (link),20 (link)). The Src kinase inhibitor PP1 (4-amino-5-(4-methylphenyl)-7-(t-butel)pyrazolo-d-3-4-pyrimidine (Calbio Chem) and Dasatinib (BMS-354825, Selleckchem), the CDK inhibitor Abemaciclib (MedChem Express), Palbociclib (Sigma-Aldrich), Ribociclib (Selleckchem) and the EGFR inhibitor Canertinib (Selleckchem) were used at the indicated doses.
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4

Cell Cycle Regulators Profiling

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Palbociclib (S1116), abemaciclib (S7158), and ribociclib (S7440) were purchased from Selleck Chemicals. CR-1–31-B and silvestrol were synthesized as described previously (26 (link), 27 (link)). Antibodies against HSP90 (H-114), Cyclin D1 (M20), Cyclin D3 (DCS28), Cyclin A2 (BF683), Cyclin E1 (HE12), Cyclin E2 (A-9), CDK2 (D-12), CDK4 (DCS-35), CDK6 (C-21), p16 (C-20), p21 (H164), and p27 (C-19) were purchased from Santa Cruz Biotechnology; p-RB (S795) and Cyclin D2 (D52F9) were purchased from Cell Signaling Technology; RB (554136) was purchased from BD Pharmingen; and eIF4A1 (ab31217) was purchased from Abcam.
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5

Modulating Cell Cycle Progression in T Cells

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All cell cycle inhibitors were titrated on CFSE labeled CD8 T cells to identify a dose that inhibited proliferation by approximately 50%. Mouse and human CD8 T cells showed similar responses to each drug; therefore, the same concentrations were used for both species. Palbociclib (PD 0332991, Sigma product #PZ0383) was used at 500nM. Abemaciclib (LY2835219, obtained from Eli Lilly Pharmaceuticals) was used at 100 nM. Ribociclib (LEE011, Selleckchem product #S7440) was used at 200 nM. CDK1/2i (RO-3306, Selleckchem product #S7747) was used at 4.5 μM. Aurora kinase inhibitor (MLN-8054, Selleckchem product #S1100) was used at 1 μM. Polo-like kinase inhibitor (GSK-461364, Selleckchem product #S2193) was used at 0.15 μM. CDK7i (YKL-5124) was developed by Nathanael Gray’s lab as reported (53 (link)) and used at 100 nM. CDK4/6 degrader (BJS 2–162) was developed by Nathanael Gray’s lab as reported (32 (link)) and used at 2 μM.
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6

Cell Cycle Analysis of Ribociclib Treatment

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Hey1 and COV362 cells were grown in 6-well plates in triplicate and treated for 72 hours with 0, 250 nM, 1 uM, or 3 uM Ribociclib (initially purchased from Selleckchem, later generously provided by Novartis) for three days. Cells were then harvested, fixed dropwise in 70% ethanol, and incubated with 0.1 ug/mL RNAse for 1h at 37° F. 1 ug/mL propidium iodide was added and then cells were run on the BD Accuri C6 flow cytometer (Becton Dickinson) and analyzed with FlowJo Version 10. 10,000 events were used for each sample.
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7

Cell Cycle Regulation via CDK Inhibitors

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Palbociclib, Abemaciclib, Ribociclib, and Roscovatin were from Selleckchem. CDK2i III was from Millipore. NaCl, Neocarzinostatin, and hydrogen peroxide were from Sigma-Aldrich. Tunicamycin was from Cayman Chemical. Oligomycin A and Antimycin A were from Abcam, TGF-β1 and Rabbit anti-phospho-Rb (Ser807/811) (#8516) were from Cell Signaling Technology.
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8

Melanoma Cell Lines and Compounds

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Melanoma cell lines YUSEEP, YUHIMO, YUWERA, and YUCRATE were obtained from Ruth Halaban (Yale University) in 2020. Melanoma cell lines WM4235, WM4324, WM9, 1205Lu, WM989, WM983B, WM4380 and WM4258, as well as the PDX model WM4223 were obtained from Meenhard Herlyn (Wistar Institute) in 2020. All patient samples were collected under institutional review board (IRB) approval (31 (link)). Cell lines were tested for Mycoplasma biannually and authenticated using short-tandem repeat fingerprinting. All cell lines are cultured in RPMI-1640 (Corning,10–040-CM) supplemented with 5% fetal bovine serum (FBS; Cytiva, SH30109.03) in the presence of 5% CO2 at 37°C. Commercially purchased compounds include palbociclib (SelleckChem, S1116), ribociclib (SelleckChem, S7440), abemaciclib (Apex Biotechnology, A1794), trametinib (SelleckChem, S2673), AZD6244 (SelleckChem, S1008) and VX-11e (SelleckChem, S7709).
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9

Evaluating Anti-Cancer Compound Potency

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Abemaciclib (S5716), ribociclib (S7740), and lenvatinib (S1164) were purchased from Selleckchem (Houston, TX). All drugs were dissolved in DMSO. DMSO concentration never exceeded 0.1% (v/v); equal amounts of the solvent were added to control cells.
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10

Anticancer Drug Compound Acquisition

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33-Azido-3-deoxythymidine (zidovudine, AZT), nevirapine (NVP), 1-beta-D-Arabinofuranosylcytosine (AraC), 9-beta-D-Arabinofuranosyl-2-fluoroadenine (fludarabine), 2-Amino-9-beta-D-arabinofuranosyl-6-methoxy-9H-purine (nelarabine), 2-Chloro-2′-deoxyadenosine (cladribine), 2-chloro-9-(2-Deoxy-2-fluoro-beta-D-arabinofuranosyl)adenine (clofarabine), 2′,2′-Difluorodeoxycytidine (gemcitabine), 5-Fluoro-2-desoxyuridine (floxuridine), 5-Fluoropyrimidine-2,4-dione (fluorouracil), pemetrexed and 4′-N-benzoylstaurosporine (midostaurin) were purchased from Sigma-Aldrich (Madrid, Spain). Palbociclib, ribociclib and abemaciclib were purchased from Selleckchem (Munich, Germany). 4-amino-10-methylfolic acid (methotrexate) was purchased from Eurodiagnosticos SL (Madrid, Spain).
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