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38 protocols using rpe 1

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Cell Culture Protocols for Various Cell Lines

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A431 (CRL-1555), EA.hy926 (CRL-2922), A498 (HTB-44) and CFPAC-1 (CRL-1918), Jurkat (TIB-152) and RPE-1 (CRL-4000) cells were obtained from the ATCC. They were grown in DMEM (A431, EA.hy926, A498 and CFPAC-1), RPMI medium (Jurkat) or DMEM F12 (RPE-1), supplemented with 10% FBS, and were maintained at 37 °C in a humidified atmosphere of 95% air/5% CO2. Mycoplasma testing was regularly performed.
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2

Evaluating Cytotoxicity of PBCA in Cell Lines

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The human cell lines RPE-1, U2OS and HEK293 were obtained from ATCC, Manassas, VA, USA and cultured in DMEM/F12 (RPE-1) or DMEM (U2OS and HEK293) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin (herein referred to as complete medium, CM) (all from Sigma-Aldrich, St. Louis, MO, USA) at 37 °C and 5% CO2. The cells have been authenticated and regularly tested for mycoplasma contamination. Depending on the assay, cells were seeded one or two days prior to the experiments. Cells were starved for amino acids by incubation in Earle’s balanced salt solution (EBSS, #24010043, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% dialyzed FBS (EBSS/FBS, dialysis tube cutoff 3.5 kDa). For studies using inhibitors or antioxidants, the cells were pre-treated for either 1.5 h (BIRB 796 and U0126, both 10 µM), 1 h (NAC, 3 mM; GSH, 10 mM), or 30 min (SB203580, SB202190 and JNK-IN-8, 3 µM; PF-3644022, 2.5 µM) before addition of PBCA. To assess cell viability after PBCA treatment, cellular ATP was measured as an indicator of metabolically active cells using CellTiter-Glo® Luminescent Cell Viability Assay (#G7571, Promega, Madison, WI, USA). Luminescence was measured by a Synergy2 plate reader (BioTek Instruments Inc., Winooski, VT, USA).
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Cell Culture Practices and Mycoplasma Screening

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Human HEK293, U2OS, RPE-1, and HeLa cells were obtained from ATCC. All cell lines were cultured in DMEM containing 10% FBS and 5% Penicillin/Streptomycin. All cell lines were regularly screened for mycoplasma using a MycoAlert™ Mycoplasma Detection Kit.
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4

Characterization of Glioma Stem Cell Lines

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The CB660, GliNS2, and GNS 144 cell lines were all obtained directly from the lab of S. Pollard in 2010 where these cell lines were previously characterized (19 (link)). The GNS 179 cell line was also obtained directly from S. Pollard in 2011 where this cell line was previously characterized (19 (link)). For determining the frequency of anaphase errors and chromosome copy numbers by FISH, GNS 179 cells ranged in passage number from 26–31 (early) and 47–51 (late). GliNS2 cells ranged in passage number from 25–35 (early) and 50 (late). GNS 144 cells ranged in passage number from 39–42 (early) and 61–76 (late). CB660 cells ranged in passage number from 39–44 in these experiments. The PDX cells were obtained directly from the lab of J. Rich in 2014 where these cells were previously validated and characterized (2 (link),30 ,48 (link),49 (link)). The GNS and PDX cell lines were previously characterized and no further authentication was performed for this study. RPE-1 (CRL-4000) and U2OS (HTB-96) cells were obtained from ATCC. For further details on the isolation of single cell GNS 144 clones, GNS cell astrocyte differentiation, and the construction of the stable GNS 179 cell lines, please see supplemental methods.
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5

ADAMTS9 Mutant Characterization in Cell Lines

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Human embryonic kidney 293 (HEK293, CRL-1573) and hTERT retinal pigment epithelial-1 (RPE1, CRL-4000) cells were obtained from ATCC. HEK293 cells were cultured in high glucose DMEM with 10% FBS and penicillin (50 IU/mL)/streptomycin (50 μg/mL), while RPE1 cells were cultured in DMEM/F12 with 10% FBS and penicillin (50 IU/mL)/streptomycin (50 μg/mL). HEK293 cells were transfected with plasmids containing C-terminal V5-tagged wild type (WT) or mutant ADAMTS9 using the Lipofectamine PLUS reagent (Invitrogen) according to the manufacturer’s instructions. RPE1 cells were transfected with cDNA constructs containing C-terminal V5-tagged WT or mutant ADAMTS9 using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. To examine the pathogenicity of ADAMTS9 mutations identified in this study, IMR90 (6.25*104 cells) were transfected with cDNA constructs containing C-terminal V5-tagged WT or mutant ADAMTS9 (10 μg) using electroporation (NEPA21, Nepa gene) according to the manufacturer’s instructions. Single iPSC colony was picked and analyzed for further differentiation steps.
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6

Serum Starvation and Growth Factor Stimulation

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Human fetal lung fibroblast cell line IMR90 was obtained from the American Type Culture Collection (ATCC) (#CCL-186) and maintained at 37°C in DMEM (#10-013-CV, Corning) supplemented with 10% fetal bovine serum (FBS) (#S11150, Atlanta Biologicals). hTERT-immortalized human retina pigmented epithelial cell line RPE1 was originally obtained from ATCC (#CRL-4000) and maintained at 37°C in Dulbecco’s modified Eagle’s medium (DMEM)/F12 with GlutaMAX (#10565018, Thermo Fisher Scientific) supplemented with 10% FBS and hygromycin B (0.01 mg/ml). Cells were serum-starved by removing medium, rinsing cells with base medium (no FBS or hygromycin B), and incubating at 37°C in base medium for 22 to 26 hours. All cell lines were routinely tested for mycoplasma contamination.
For EGF stimulation experiments, recombinant human EGF (#PRD236-50, R&D Systems) was reconstituted in 1× PBS and added to cell culture medium to a final concentration of 750 pM for 30 min unless otherwise stated. For PDGF stimulation experiments, recombinant human PDGF (#1159-SB-025, R&D Systems) was reconstituted in HCl and added to cell culture medium to a final concentration of 7.143 μM PDGF and 4 μM HCl for 30 min.
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7

Cell Line Maintenance and Synchronization

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HeLa (American Type Culture Collection (ATCC), CCL-2) and HEK293T (ATCC, ACS-4500) cell lines were maintained in low-glucose and high-glucose DMEM supplemented with 10% fetal bovine serum (Invitrogen), respectively. The hTERT-immortalized retinal pigment epithelial cell line, RPE1, was purchased from ATCC (CRL-4000) and maintained in F12 medium with fetal bovine serum in the presence of hygromycin B. The HeLa cells stably expressing RSF1 shRNA targeting 3′-untranslated region of RSF1 gene was established by infection of the lentiviral vector containing RSF1 shRNA, followed by clonal selection in the presence of puromycin (1 μg ml−1) according to the manufacture's protocol (Sigma-Aldrich). To obtain cells synchronized at prometaphase, cells were treated with 100 ng ml−1 of paclitaxel (Sigma-Aldrich) or 100 nM of nocodazole (Sigma-Aldrich) for 12–16 h and collected by gentle shake-off.
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8

Sensitizing RPE-1 cells to apoptosis

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Human retinal pigment epithelial cells transformed with telomerase (RPE-1) (ATCC) were cultured in Dulbecco's Modified Eagle Medium (DMEM) containing 1 g/L glucose supplemented with penicillin, streptomycin, 1X non-essential amino acid cocktail (Life Technologies), and 10% Fetal Bovine Serum (Life Technologies). For siRNA-transfections, 30,000–35,000 cells/mL were seeded overnight. Cells received 10 nM siRNA diluted in serum-free DMEM and combined with 0.3% Interferin transfection reagent (PolyPlus). For apoptosis sensitization, cells received 1 nM Bcl-XL siRNA. Cells were harvested 2–3 days post-transfection.
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9

Immortalized Human Cell Lines for DSB Study

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The hTERT‐immortalized human fibroblast cell line OUMS‐36T‐3F (obtained from Japanese Collection of Research Bioresources Cell Bank, hereafter referred to as OUMS), the hTERT‐immortalized human retinal pigment epithelial cell line RPE1 (obtained from ATCC), and HEK293T cells (obtained from ATCC) were maintained in Dulbecco's modified Eagle's medium (FUJIFILM Wako Pure Chemical) containing 10% (v/v) fetal bovine serum (Biosera) and penicillin–streptomycin‐glutamine (Thermo Fisher Scientific). Cells were confirmed to be mycoplasma‐free using 4′6‐diamidino‐2‐phenylindole (DAPI) (DAPI Fluoromount‐G, SouthernBiotech). ADR (FUJIFILM Wako Pure Chemical) for DSB‐generation, doxycycline (DOX) (Merck) for inducing shRNA against 53BP1, 1,6‐hexanediol (1,6‐HD) (Sigma‐Aldrich) for inhibition of phase separation, and Sorbitol (Sigma‐Aldrich) for inhibition of phase separation were used at the concentrations indicated in the figure legends.
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10

Cell Culture Protocols for HeLa and RPE1 Lines

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HeLa cells (CCL-2) and RPE1 (CRL-4000) were obtained from the ATCC. All cells were grown at 37°C in a humidified environment with 5% CO2. The unmodified cell lines were grown in DMEM (#15-017-CM; Corning) containing 10% FCS (#82013-586; Hyclone), 250 µg/l Amphotericin B (#82026-728; VWR), 50 U/ml penicillin, and 50 µg/ml streptomycin (#15140122; Thermo Fisher Scientific). Doxycycline-inducible Hec1 knockout HeLa cells (gift of Iain Cheeseman, Massachusetts Institute of Technology, Cambridge, MA) were grown in media containing 10% tetracycline-free FBS (#1005807; Denville Scientific), the same antibiotics as for unmodified cells, 500 µg/ml G418 (#ant-gn-5; Invivogen), and 5 µg/ml puromycin (#A1113803; Thermo Fisher Scientific). HeLa Cyclin B1-GFP cells were grown in media containing 4 μg/ml blasticidin (# ant-bl-05; Invivogen). HeLa Cyclin A2-GFP cells (Alfonso-Pérez et al., 2019 (link)) were grown in media containing 9 μg/ml blasticidin (gifts of Francis Barr, University of Oxford, Oxford, UK). Cells were verified to be free of mycoplasma by frequent staining of plated cells with DAPI. No contamination was observed.
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