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11 protocols using a 485

1

Evaluating A-485 Efficacy in NSG Mice

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Here, 2 × 106 CDS1 cells were resuspended in 100 uL of 1X PBS prior to bilateral subcutaneous injection in the subcutaneous suprascapular region of NSG mice. The experiment included a cohort of eleven mice, which were allocated between the control-treated (n = 6) or the drug-treated (n = 5) group to normalize their size before starting the treatment. A-485 (MedChemExpress, Cat# HY-107455, Monmouth Junction, NJ, USA) was prepared daily and administered intraperitoneally at a dose of 50 mg/kg twice daily. When the first tumors started to be visible, mice were treated with either 50 mg/kg of A-485 or solvent for 15 days. All mice were monitored daily for signs of distress and were weighed three times a week. Tumor size was measured three times a week with a caliper, and tumor volume was calculated according to the following equation: (length × width2)/2 = tumor volume [mm3]. Control-treated mice received the solvent used for oral administration. Mice were sacrificed, as described above, the day after the last dose of A-485.
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2

Cell Line Cultivation and Treatment Protocol

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Jurkat, CEM, C8166/45, MT-2, SLB-1, and ATL-2 cells were cultured in Isocove’s modified Dulbecco medium (IMDM). Primary CD4+ lymphocytes, TL-Om1, and HTLV-1-immortalized lymphocyte cell lines [47 (link)] were cultured in Roswell Park Memorial Institute (RPMI) medium. HeLa and HeLa-HBZ clonal cell lines [48 (link)], CHO-LFA-1 clones [38 (link)], and HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM). All cells were supplemented with 10% FBS or 10% FetalPlex (GeminiBio) and 2 mM L-glutamine, 100 U/mL penicillin, and 50 μg/mL streptomycin. Jurkat pminLuc-viral CRE cells [38 (link)] and Jurkat-HBZ cells [38 (link)] were supplemented with 1.5 mg/mL of G418. HeLa and CHO clones were supplemented with 0.5 mg/mL of G418. Primary lymphocytes and lymphocyte cell lines were cultured with IL-2. Primary lymphocytes were activated in culture wells coated with anti-CD3 and anti-CD28 antibodies. Where indicated, cells were treated with 10 μM A485 (MedChem Express) or DMSO for 3 h.
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3

Primary Mouse Hepatocyte Isolation and Treatment

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Primary mouse hepatocytes were isolated from C57BL/6 mice by a two-step perfusion technique as described17 (link). Cells were treated with 100 μM 8-Bromoadenosine 3′,5′-cyclic monophosphate (8-Br-cAMP, Sigma), 3 μM A-485 (MedChemExpress), 10 μM MG132 (Beyotime Biotechnology), or 10 μg/ml cycloheximide (CHX, Sigma).
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4

Inhibitors Modulate NF-κB and IRF Activation

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HCT116-Dual cells were treated with DMSO or inhibitors (500 nM). After a 48-h incubation, NF-κB activation was determined using QUANTI-Blue (InvivoGen; cat #rep-qbs), a secreted alkaline phosphatase detection reagent, by reading the OD at 655 nm. IRF activation was determined by measuring the relative light units in a luminometer using QUANTI-Luc (InvivoGen; cat #rep-qlc1).
The inhibitors of ABT-263/cat #S1001, AZD2014/cat #S2783, ABT737/cat #S1002, irinotecan HCl trihydrate/cat #S2217, RO-3306/cat #S7747, AZD5363/cat #S8019, BKM120/cat #S2247, azacitidine/cat #S1782, GSK343/cat #S7164, crizotinib/cat #S1068, EPZ5676/cat #S7062, GSK2118436/cat #S2807, AZD8055/cat #S1555, BMN673/cat #S7048, GSKJ4 HCl/cat #S7070, JQ1/cat #S7110, AZD7762/cat #S1532, AZD6244/cat #S1008, LY3214996/cat #S8534, GSK1120212/cat #S2673, AZD1775/cat #S1525, and milciclib/cat #S2751 were purchased from Selleck Chemicals. The milciclib/cat #HY-10424, gefitinib/cat #HY-50895, UNC1215/cat #HY-15649, cisplatin/cat #HY-17394, vorinostat/cat #HY-10221, and A-485/cat #HY-10745 were from MedChemExpress.
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5

Detailed Antibody and Inhibitor Protocol

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Antibodies: For immunoblotting, immunofluorescence and immunohistochemistry were anti-PRRX1 (Sigma, HPA051084), β actin (Sigma, A2228), H4K20me3 (Abcam, ab9053), The antibodies used for ChIP were anti-H3K27ac (Diagenode, C15410196) and anti-PRRX1 (Sigma, HPA051084). Full list with catalog numbers available in Table S2. Inhibitors were obtained from Selleckchem: Galunisertib, LY2157299 cat#S2230, Xav939 cat#S1180, LGK-974 cat#S7143, Vismodegib (GDC-0449) cat#S1082, Sonidegib (Erismodegib, NVP-LDE225) cat#S2151, NVP-BHG712 cat#S2202, BGJ398 (NVP-BGJ398) cat#S2183, Vorinostat (SAHA, MK0683) cat#S1047, Tretinoin cat#S1653, MK-8617 cat#S8443, Ruxolitinib, INC018424 cat#S1378, A-1155463 cat#S7800, ML324 cat#S7296, GSK J1 cat#S7581, Verteporfin cat#S1786 and MedChem Express: A-485 cat#HY-107455.
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6

HAdV-5 Infection Assay in HBTECs

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HBTECs (catalog number FC-0035, lot number 02196; Lifeline Cell Technology) were grown at 37°C in a BronchiaLife medium complete kit (LL-0023; Lifeline Cell Technology) in a 5% CO2 incubator until they reached confluence. Cells were then incubated 3 days more without addition of fresh medium and were infected for 12 hr with the indicated HAdV-5 mutants in the conditioned medium. A-485 (MedChemExpress) was added to a final concentration of 10 µM, or the same volume of DMSO (dimethyl sulfoxide) vehicle was added, and cells were incubated for an additional 2 hr.
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7

Isolation and Culture of Islet Cells

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Islets of Langerhans were isolated from 8-week-old male Sprague-Dawley rats, C57BL/6 mice or db/db mice by using collagenase digestion and separated by density gradient centrifugation. Freshly isolated rat islets were cultured in RPMI 1640 medium containing 5.6 mM glucose and 5% fetal bovine serum (FBS) at 37 °C and 5% CO2 for 2–3 h. For RNA-Seq and ChIP-Seq sample preparation, incubated islets were transferred into 6-well plates and cultured in RPMI 1640 medium containing 5.6 mM glucose and 0.25% bovine serum albumin (BSA) in the presence or absence of 3 μM A-485 (MedChemExpress, New Jersey, USA) for 16 h or 6 h.
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8

Culturing and Characterizing Glioblastoma Cell Lines

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Parental U87MG were obtained and cultured as described previously (51 (link),52 (link)). PDX sphere lines were cultured in DMEM/F12 medium supplemented with B27 (GIBCO/Life Technologies) and 20 ng/ mL human recombinant EGF, 20 ng/mL bFGF. GSC11 was provided by Frederick Lang (M.D. Anderson Cancer Center); TS576 was provided by Cameron Brennan (Memorial Sloan Kettering Cancer Center). All cells were incubated at 37°C, 5% CO2, and 100% relative humidity in low-attachment flasks. PDX cell lines were dissociated with Accutase (Stemcell Technologies). GSK620 and A-485 were purchased from MedChem Express. ABBV-744 was provided by Andrew Shiau (UCSD). The near-infrared fluorescent protein iRFP720 cDNA construct was from (53 (link)). pLV-IκB-SR vector was a gift from Inder Verma (Salk Institute). The pGL4.32[luc2P/ NFκB-RE/Hygro] vector for NF-κB luciferase reporter assays was purchased from Promega. shRNA constructs targeting BRD2 were purchased from Sigma (Mission shRNA).
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9

Pharmacological Inhibitors for Cellular Assays

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A-485, Cycloheximide (CHX), MG-132 and CCS1477 were purchased from MedChemExpress Monmouth Junction, NJ, USA).
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10

Insulin Uptake in Mice Muscles

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Paired soleus and EDL muscles from 13-week-old female mice were placed into a preincubation solution including 0.2% DMSO or 50 μM A-485 (MedChem Express LLC, HY-107455; DMSO final concentration also 0.2%) for 1 hour. Subsequently, muscles were transferred into an incubation solution that included [3H]2DOG and [14C]mannitol for 30 minutes, with muscles from one side being exposed to insulin (0.36 nM) and the contralateral side exposed to no insulin (Basal). During this 30-minute period, muscles continued to be incubated with DMSO or A-485 (Supplemental Figure 6A).
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