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6 protocols using alpelisib byl719

1

Derivation and Characterization of OCI Cell Lines

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The derivation of OCI-C1p, OCI-C4p, OCI-C5x, and OCI-P5x cells was previously described (16 (link)). OCI-cells were cultured in OCMI-L, a specific growth medium developed for these cells (US Biological, Cat # 506390). The OCI cells are available from the Ince laboratory. The passage number of OCI cells at the time of each experiment was from 40 to 60. TOV21G cells were obtained from ATCC and cultured in 1:1 of Medium 199 (Gibco®) and MCDB105 (Cell Application Inc.) with 15% fetal bovine serum (FBS). RMG1 cells were obtained from JCRB cell bank and maintained in RPMI with 20% FBS. Dicer-substrate small interfering RNAs (dsiRNAs) targeting BRD2, BRD3, BRD4 as well as negative control dsiRNA were purchased from Integrated DNA Technologies. AllStars Hs Cell Death Control siRNA was purchased from QIAGEN. JQ1 (13 (link)), CP203 (13 (link), 17 (link)), CPI0610 (18 (link)), Alpelisib (BYL719) (19 (link)) and MK2206 (20 (link)) were purchased from Selleckchem.
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2

Investigating Protein Signaling Pathways

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Lapatinib (Selleck Chemicals, #S2111), alpelisib (BYL719, Selleck Chemicals, #S2814) and cobimetinib (GDC‐0973, Selleck Chemicals, #S8041) were dissolved in DMSO (Sigma, #D2650) for in vitro studies and in 0.5% CMC‐Na (Selleck Chemicals, #S6703) for in vivo studies. The primary antibodies used for western blotting included those against p‐HER2‐Tyr1221/1222 (Abcam, #ab131102, 1:500), HER2 (CST, #2242, 1:1000), pIGF‐1R (CST, #3021, 1:500), IGF‐1R (CST, #9750, 1:500), p‐AKT‐Ser473 (CST, #4060, 1:1000), p‐AKT‐Thr308 (CST, #13038, 1:1000), AKT (CST, #4691, 1:1000), p‐ERK‐Tyr202/204 (CST, #4370, 1:1000), ERK (CST, #4695, 1:1000), p‐MEK‐Ser217/221 (CST, #9154, 1:1000), MEK (CST, #9126, 1:1000), p‐S6‐Ser240/244 (CST, #5364, 1:1000), S6 (CST, #2217, 1:1000), HA‐tag (CST, #3724, 1:1000), p110α (CST, #4249, 1:1000) and vinculin (CST, #13901, 1:2000), and HRP‐conjugated goat‐anti‐rabbit secondary antibody (Invitrogen, #31460, 1:5000). Exposure time of each band depends on the saturation degree of chemiluminescent, generally no more than 1 min.
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3

PI3K Pathway Drug Response Assay

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To test the effect of drug treatment on protein and phosphoprotein levels, cell lines were dosed with drugs focused on the PI3K pathway including buparlisib (BKM-120, Selleck Chemicals), alpelisib (BYL-719, Selleck chemicals), IPI-549 (Selleck Chemicals), sirolimus (rapamycin, Selleck Chemicals), and ipatasertib (GDC-0068, Selleck Chemicals). To determine dosing for imaging-based experiments, all drugs were screened against each cell line to determine IC50 values via conventional cell viability assay (MTT). Treatments were administered at 80% of the IC50 dosing overnight prior to fixation for cell line treatments (Fig. 5b, Supplementary Fig. 10).
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4

Characterization of B-ALL Cell Lines

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E2A-PBX1+ B-ALL cell lines RCH-ACV and 697, as well as E2A-PBX1- B-ALL cell lines REH and SEM were obtained from DSMZ (Braunschweig, Germany) in 2013, and were authenticated in 2020 in DSMZ. They were monitored to exclude mycoplasma contamination regularly. Culturing of human cells was performed as previously described [7 (link)]. RPMI-1640, IMDM, DMEM, and Opti-MEM mediums were obtained from Thermo Fisher (Waltham, MA, USA). Torin-1, everolimus (RAD001), ipatasertib (GDC-0068), alpelisib (BYL719), capivasertib (AZD5363) and idelalisib (CAL-101) were from Selleck Chemicals (Houston, TX, USA). FBS was from Sigma-Aldrich (St. Louis, WIS, USA).
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5

Cytoskeletal Dynamics and Cellular Signaling

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Anti–VE-cadherin (F-8) was from Santa Cruz Biotechnology. Anti-CD31 (89C2) was from Cell Signaling Technologies. 4′,6-Diamidino-2-phenylindole (DAPI), rhodamine phalloidin (1 mg/ml), Alexa Fluor 647 phalloidin (1 mg/ml), and Alexa Fluor–conjugated secondary antibodies were from Life Technologies. For antibody concentrations, see the “Immunofluorescence” and “Western blot and small GTPase activity assays” sections below. Rapamycin, alpelisib (BYL719), Y-27362 2HCl, trametinib (GSK1120212), batimastat (BB-94), EHT1864 2HCl, and PF-3758309 were from Selleckchem.
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6

PI3K Inhibitor Assay Protocol

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Copanlisib, idelalisib (CAL101), AZD8186, alpelisib (BYL719) and duvelisib (IPI145) were purchased from Selleck Chemicals (Houston, TX). Inhibitors were prepared in sterile DMSO (final concentration <0.1%) and stored at −80 °C in small aliquots. Primary antibodies to Akt, mTOR, 4E-BP1, S6K, p-Akt-Ser473, p-Akt-Thr308, p-mTOR, p-PRAS40, p-4E-BP1, p-S6, p-GSK, cleaved caspase-3, cleaved-PARP, and PI3K-α were purchased from Cell Signaling Technology (Danvers, MA). Antibodies to PI3K-δ, Ki67, and α-Tubulin were obtained from Santa Cruz Biotechnology (Dallas, TX), Abcam (Cambridge, MA), and Sigma-Aldrich (St. Louis, MO), respectively. RPMI-1640 and Dulbecco’s Modified Eagle’s Medium (DMEM) were purchased from American Type Culture Collection (ATCC, Manassas, VA). Fetal bovine serum and tissue culture supplements were obtained from Atlanta Biologicals (Flowery Branch, GA) and Life Technologies (Houston, TX), respectively. Additional reagents include RIPA buffer (Sigma-Aldrich) and enhanced chemiluminescence (ECL) detection reagent (Millipore).
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