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36 protocols using ve 822

1

Evaluating Synthetic Lethality in CRC

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The IC50 value was evaluated using an MTT assay. CRC cells, both with and without NRIP3 expression, were seeded into 96-well plates at a density of 2000 cells/well. The cells were treated by 0.1 μM cisplatin (#S1166; Selleck, Houston, TX) combination with 0, 0.2, 0.4, 0.8, 1.6, 3.2, 6.4, 12.8, and 25.6 μM VE-822 (#S7102; Selleck) or 0, 1, 2, 4, 8, 16, 32, 64, and 128 μM AZD0156 (#S8375; Selleck) for 48 hours. For synthetic lethality analysis, NRIP3 unexpressed DLD1, RKO, and HCT116 cells were treated with 0.2 μM VE-822/combined with 50 nM NVP-BEZ235 (#S1009; Selleck) or treated with 0.5 μM AZD0156/combined with 50 nM NVP-BEZ235 under 0.1 μM cisplatin treatment for DNA damage. Each experiment was repeated 3 times.
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2

Inhibitors for DNA Damage Response Pathways

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Compound B (RUVBL1 inhibitor) and Compound C (Compound B control) were synthesized by Daiichi-Sankyo. VE-822 (ATR inhibitor) was purchased from Selleckchem (catalog # S7102). LY2603618 (CHEK1 inhibitor) was purchased ApexBio (catalog # A8638). Puromycin was purchased from InvivoGen (catalog #ant-pr-1). Geneticin (G418) was purchased from ThermoFisher Scientific (catalog # 11811031). Doxycycline was purchased from MilliporeSigma (catalog # D9891).
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3

Acute Lymphoblastic Leukemia Cell Lines and Samples

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RS4;11, REH, MUTZ-5, 697, SEM, KOPN-8 and NALM-6 cell lines were purchased from German Collection of Microorganisms and Cell Cultures (DSMZ). Informed consent was obtained in accordance with the institutional review board guidelines for the patient samples and normal bone marrow samples used in this study. Patient samples were layered on a Ficoll-Hypaque density gradient centrifugation and enriched blasts were stored in liquid nitrogen until further use. The diagnosis of ALL was based on morphology and flow cytometric analysis on immunophenotype. Cytogenetic was determined by standard procedures. Cell lines and patient samples used in this study are listed in supplementary table 1 and 2. CX-5461 was purchased from Xcess Biosciences; VE-822 and KU-60019 from Selleck Chemicals; Caffeine and Nocodazole from Sigma-Aldrich.
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4

Targeted Gene Silencing with siRNA and Molecular Compounds

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The siRNAs targeting human genes were obtained from Invitrogen and JTSBIO Co., Ltd. The target sequences were listed in Table S1. Antibodies used in this manuscript were listed in Table S2. Small molecular compound caffeine was obtained from sigma; KU55933, VE‐822, NMN, and MDL‐800 were obtained from Selleck; etoposide and Doxycycline (Dox) were obtained from sigma.
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5

Cell Culture and Inhibitor Assay

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HEK293T (CRL-3216), HCT116 (CCL-247) and U2OS (HTB-96) cell lines were purchased from ATCC and cultured in Dulbecco’s Modified Eagle’s Medium or McCoy’s 5A supplemented with 10% fetal bovine serum (FBS) at 37 °C in 5% (v/v) CO2.The following inhibitors were used: VE-822 (Selleckchem: s7102), NU7441 (selleckchem:S2638), and KU55933 (abcam: ab120637).
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6

DNA Damage Response Pathway Analysis

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Cells were treated with inhibitors: pladienolide B (EMD Millipore), E7107 (H3 Biomedicine), ATR inhibitors (VE-821, VE-822, SelleckChem; AZ-20), ATMi (KU55933, SelleckChem). Antibodies used in this study include AQR (A302–547A-T, Bethyl), pChk2 (2661, Cell Signaling), Flag (F7425, Sigma), GAPDH, (ABS16, Millipore), GFP (A11122, ThermoFisher Scientific), γH2AX (9718S, Cell Signaling), Ku70 (GTX70271, Genetex), PCNA (sc-56, Santa Cruz Biotechnology), pRPA (A300–246A, Bethyl), U2AF1 (ab197591, abcam), and S9.6 (Protein A purified from hybridoma S9.6 by Antibodies Incorporated).
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7

Enzymatic Synthesis of ω-Pentadecalactone

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ω-Pentadecalactone (PDL), poly(ethylene glycol) methyl ether (Mn = 2000 Da, MeO-PEG2K-OH), and Novozym 435 catalyst (Candida antarctica lipase B or CALB supported on acrylic resin) were obtained from Sigma-Aldrich Chemical. The enzyme catalyst was dried at 40 °C under 2.0 mmHg overnight prior to use. p-Dioxanone (DO) was acquired from Leap Labchem Scientific Co. in China. Aceonitrile and dimethylsulfoxide were obtained from J.T. Baker (Avantor Performance Materials, Central Valley, PA, USA). VE822 was obtained from Selleck (Houston, TX, USA). DiI dye was purchased from Thermo Fisher Scientific (Waltham, MA, USA). RG2 cells were purchased from ATCC (Manassas, VA). Normal Human Astrocytes were obtained from Tim Chan at Memorial Sloan Kettering Cancer Center. All cells were cultured in 5% CO2 and air humidified in a 37 °C incubator. Each cell line was cultured up to passage number 20.
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8

Small Molecule Inhibitor Preparation

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All reagents were obtained from Sigma Aldrich if not otherwise specified. Synthetic oligonucleotides were obtained from Eurofins (Eurofins MWG Operon, Huntsville, AL, USA) and purified by HPLC. All small molecule inhibitors used were dissolved in dimethyl sulfoxide at 10 mM (Fisher Scientific, Watham, MA, USA) and stored at −20 °C until further use: AZD6738 (Astra Zeneca, London, UK), KU60019 (Selleck Chemicals LLC, Munich, Germany), AZ20 (Tocris, Bristol, UK), VE822 (Selleck Chemicals LLC), AZD7762 (Selleck Chemicals LLC).
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9

Inhibitor Screening for DNA Damage Response

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Cells were treated with inhibitors PARPi (olaparib, ABT-888), ATRi (VE-821, VE-822, AZ20), ATMi (KU55933), Chk1i (MK-8776/SCH900776), DNA-PKi (NU7026), and Wee1i (MK-1775), all from SelleckChem, except AZ20 (custom-made).
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10

Combinatorial Potentiation of ATR Inhibition

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Cells were seeded at 500 cells per well in a 96 well plate and then treated with purified 2XMBP-scFv proteins, a small molecule inhibitor of ATR (VE-822, Selleckchem #S7102), or both the purified 2XMBP-scFvs and ATR inhibitor. For the combination of the purified 2XMBP-scFvs and ATR inhibitor, cells were pre-treated with the purified 2XMBP-scFvs for 24 hours and then the ATR inhibitor was added. Cells were treated for five days before cell viability was assessed via the CellTiter-Glo Luminescent Cell Viability Assay (Promega) according to the manufacturer’s instructions. Experiments were performed at least two times for biological replicates. Statistical significance was determined using the unpaired t test (GraphPad Prism). Synergism was calculated using the CompuSyn software (ComboSyn, Inc.).
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