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6 protocols using ppackh1

1

Quantifying ARHGAP24 Isoform Transcripts

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Lentivirus particles were produced by transfection of HEK-293 T cells with pCDH-EF1-MCS-IRES-GFP and UPF3B expressing derivatives together with helper plasmid mix pPACKH1 (System Biosciences). After 2 days, virus-containing supernatants were collected and applied to neural stem cells and after a further 24 h, differentiation was induced. Total RNA was prepared using a Purelink RNA kit with DNAse treatment (Life Technologies). cDNA synthesis was done using Superscript II reverse transcriptase (Life Technologies) and oligo-dT primers (Promega). Quantitative PCR (qPCR) reactions to detect Gapdh, Arhgap24 and Atf4 mRNAs were performed using a LightCycler 480 qPCR system with Universal ProbeLibrary assays (Roche) (Additional file 1: Table S1). ARHGAP24 isoform 1 (Swiss-Prot:Q5U2Z7) encoding transcripts were identified by blast search. The qPCR assay specifically detects the region encoding the ARHGAP24 isoform 1 N-terminal PH domain represented by Arhgap24 mRNAs GenBank:CB582621 and GenBank:CB609913. A second Arhgap24 assay detects transcripts encoding ARHGAP24 isoform 1, the shorter isoform encoding GenBank:NP_001012032 and predicted transcripts encoding related isoforms lacking the PH domain.
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2

CCND2 Mutation Analysis via Lentiviral Transduction

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The open reading frame of wild-type CCND2 and CCND2 harboring the Thr280Ala mutation were cloned into an HIV-based lentiviral dual promoter vector (pCDH-CMV-MCS-EF1-copGFP+Puro cDNA; System Biosciences, Palo Alto, CA) for stable expression. The mutation was introduced using a 1-basepair mismatch reverse primer. Primer sequences were as follows: CCND2 clone F, gcgtgctagcatggagctgctgtgccacgag; CCND2 clone R, gcgtgaattcctcacaggtcgatatcccgcacgtctgtagggttg; CCND2 mutR, cagcaaccctacagacgtgcgggatatcgacctgtgaggat (System Biosciences). The lentiviral construct (45μg) was transfected into HEK-293TN cells using 45μl pPACKH1 and 55μl PureFection (System Biosciences). The supernatant containing the pseudoviral particles was collected after 48 and 72 hours, and the virus was precipitated at 4°C overnight using 5X PEG-IT virus precipitation solution (System Biosciences). Two hundred microliters of Phosphate Buffered Saline (PBS) and 25μM Hepes Buffer were used for resuspension of the pelleted virus. We infected 200,000 cells in triplicate with 20 IU of virus using 5μl Transdux Infection Reagent (System Biosciences). RNA was harvested after 72 hours, and CCND2 overexpression was confirmed at the RNA and protein level.
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3

Lentiviral Vector Production and Titration

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Lentiviral vector constructs were packaged into lentivirus using pPACKH1 (SBI, Cat# LV500A-1) as previously reported [36 (link), 41 ]. 293TN cells were transfected with lenti-vector and pPACK-H1, lentivirus packaging mix. 48 and 72 h post transfection, cell culture media containing Lentivirus was collected at and concentrated using PEG-it (SBI, Cat# LV810A-1). The viral pellet was suspended in sterile PBS and tittered using the Global Ultra-Rapid Tattering kit (SBI, Cat# LV961A-1). These concentrated lentiviruses were used to infect the 293TN cells.
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4

Derivation and Labeling of NZB and B6 ESCs

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NZB morula-blastocyst stage embryos were cultured 24 hours in KSOM medium. The zona pellucida was removed with acidic Tyrode’s solution (Sigma-Aldrich) and blastocysts were individually plated onto mitomycin C (Sigma-Aldrich) treated mouse embryonic fibroblast (mEF) feeder layers in ES derivation medium: KODMEM (Invitrogen) containing 1mM L-glutamine, 100 units/mL penicillin, 100 μg/mL streptomycin, 100 μM β-mercaptoethanol (Sigma), 100 μM nonessential amino acids (Invitrogen), 1,000 units/mL LIF (Millipore), 10% FBS and 10% KSR (Invitrogen). ICM outgrowth colony was collected and dispersed into single cells using 0.15% trypsin solution (Sigma-Aldrich) before replating onto fresh mEF in ES medium containing 1 μM PD0325901 (Axon) and 3 μM CHIR99021 (Axon).
To induce fluorescent marker uniformly expressed under the control of the Ubiquitin-C promoter in NZB ES cell lines, Ubc-Td-tomato coding sequence was cloned into lentiviral vector with pPACKH1 (SBI) and Purfection (SBI) (Shibuya et al., 2003 (link); Yamaguchi et al., 2012 (link)). The presence of Ubc-Td-tomato expression was examined by fluorescence under 568 nm light and confirmed by FACS sorting purification (BD AriaII). GFP labeled B6 ESC line carrying mtDNA mutations, were generated using PolG mutator mice and B6 Ubc-GFP mice (Jackson laboratory) as recently described (Ma et al., 2020 (link)).
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5

Reprogramming Somatic Cells to iPSCs

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Lentiviral vectors carrying Oct4, Sox2, C-myc, Klf4 and RTTA genes (Addgene) were transfected with pPACKH1 (SBI) and PureFection (SBI) in 293T cells. Supernatants were collected every 24 hours during 3 days starting 24 hours after transfection and filtration through a 0.45 um pore size cellulose acetate filter. Cells (1 x 105) per well were plated in 6-well culture dishes containing DMEM/F12 medium with 10% FBS one day before transduction. Cultured cells were transduced with filtered supernatants containing viral vector. Three days after transduction, cells were re-plated onto 100-mm dishes containing feeder layers of mitomycin C inactivated mouse embryonic fibroblasts (mEFs) with mouse ES cell media: KODMEM (Invitrogen) supplemented with 20% KSR, 1 mM L-glutamine, 0.1 mM nonessential amino acids (NAA), 0.1 mM β-mercaptoethanol (Sigma), penicillin-streptomycin and 1,000 units/ml LIF (Millipore). Doxycycline was added at a final concentration of 2 μg/ml and medium was changed every day. Colonies appeared 3–4 weeks after transduction and 10 colonies with typical mouse pluripotent stem cell morphology were randomly picked up and propagated for each iPSC line.
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6

Tetracycline-Inducible Viral Vector Transduction

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The best-performing shRNA cassette from the RNAiONE screen was cloned into the tetracycline (TET)-inducible all-inone vector pLVi(3G)-MCS-Puro. For TET-inducible rescue of the cancer gene of interest (GOIc) the coding region of GOIc silent was correspondingly cloned into pLVi(3G)-MCS-Neo. For the resulting vectors, cloning success was verified by restriction analysis and DNA sequencing. LV, HIV-based, VSVG-pseudotyped, self-inactivating transduction particles were produced by co-transfection of HEK293TN cells with the expression vectors and the third-generation LV packaging plasmid mix pPACKH1 (SBI, Mountain View, CA) following the instructions given by the manufacturer. Transfection reagent lipofectamine 2000 was used. Viral genomic titers were determined using the LentiX qRT-PCR kit (Clontech, Mountain View, CA). For subsequent cell transductions, infectious titers were calculated by assuming a ratio of genomic-to-infectious titer of 100:1.
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