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102 protocols using plvx puro

1

Lentiviral Overexpression of Mouse and Human GPx2

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The open reading frame of mouse GPx2 (GenScript NM_030677.2) was subcloned by PCR into Xho1/BamH1 restriction sites of lentiviral expression vector pLVX-puro (Clontech), using 5’ region primer: 5’-TAT CTC GAG GCC ACC ATG GCT TAC ATT GCC AAG TCG-3’ and 3’ region primer: 5’-TAT GGA TCC CTA GAT GGC AAC TTT GAG GAG CCG-3’, and the open reading frame of human GPx2 (GenScript NM_002083.4) was subcloned by PCR into Xho1/BamH1 restriction sites of lentiviral expression vector pLVX-puro (Clontech), using 5’ region primer: 5’-CCC CTC GAG ATG GCT TTC ATT GCC AAG TCC TTC TAT GAC-3’ and 3’ region primer: 5’-CCC GGA TCC CTA TAT GGC AAC TTT AAG GAG GCG CTT GAT-3’. Recombinant lentiviruses expressing mGPx2 and hGPx2 were packaged in 293 T cells and expressed in PyMT2 and JIMT1 respectively as described below.
The third generation lentiviral transfer plasmid pXPR_dCas9-VPR_sgRNA was cloned from pXPR_dCas9-VP64-Blast (Addgene plasmid #61425) [19 (link)]. For mouse GPx2 sgRNA design, two custom anti-sense DNA oligonucleotides (CTTTGTTCAGTGGCAGTAAG, TTGTTCAAACAGTTCACAGG) were annealed and ligated into pXPR_dCas9-VPR_sgRNA. Non-targeting pXPR_dCas9-VPR with no GPx2-sgRNA inserted recognition sequence was used as a control. Lentiviral construct for dCas9-VPR-sgRNA and virus particles was prepared by Memorial Sloan Kettering Cancer Center, New York.
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2

Overexpression of TRIM48 in Glioma Cells

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The designed primers of human TRIM48 gene (AF521869.1) were: 5′-CGGAATTCATGAATTCTGGAATCTCGCAAG-3′ (forward) and 5′-CGGGATCCAGGAGAATACAGAAAAAGATAGG-3′(reverse), which was inserted into Plasmid pLVX-Puro (Clontech), and 2000 ng/ml of pLVX-Puro-TRIM48 was transfected into U87MG and U138MG using Lipofectamine 2000. pLVX-Puro without TRIM48 expression was used as a control vector.
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3

Plasmid Constructs for Cell Biology

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PPP1R12A (NM_002480) and PPP1CB (NM_002709) were inserted into pIRESpuro3-FLAc (FL denotes FLAG epitope; Ac denotes Aequorea coerulescens green fluorescent protein 1 (AcGFP))43 (link). To create siRNA-resistant alleles, the PPP1R12A sequence TTCCATTTCT was changed to CAGCATCAGC, and the PPP1CB sequence TGGTGTTTC was changed to CGGCGTGAG by introducing synonymous mutations. The resulting plasmids are named pIRESpuro3-PPP1R12Ar-FLAc and pIRESpuro3-PPP1CBr-FLAc, respectively. Rat LAP2β (amino acids 244-453) was inserted into pIRESpuro3-AcFL44 (link) to obtain pIRESpuro3-AcFL-LAP2β. SEC61B (NM_006808.2) was inserted into pIRESpuro3-AcFL to obtain pIRESpuro3-AcFL-SEC61B. pIRESpuro3-AcGFP-NES was constructed by fusing the sequence encoding the nuclear export signal (NES) of HIV-1 Rev (amino acids PLQLPPLQRLTLN) to AcGFP. pIRESneo3-mCherry-NLS was constructed by fusing the sequence encoding the nuclear localization signal (NLS) of SV40 large T antigen (amino acids GGPKKKRKV) to mCherry. pLVXpuro-MRLC-EGFP WT, TASA (T18A S19A) and TDSD (T18D S19D) were constructed by inserting rat MRLC (MYL12B NP_059039.2)-EGFP with or without the indicated point mutations into pLVXpuro (Takara, Clontech).
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4

Engineered RBCs Expressing Chimpanzee CMAH

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Neu5Gc was expressed on the surface of modified human erythrocytes by expressing chimpanzee CMAH in ex-vivo-cultured red blood cells (cRBCs)26 (link). Briefly, differentiation and proliferation of bone marrow-derived CD34+ hematopoietic stem cells (Lonza) were achieved in Iscove’s Modified Dulbecco-based medium (Biochrom) supplemented with 5% solvent/detergent virus-inactivated human plasma (Octaplas, Octapharma), stem cell factor (R&D Systems), hydrocortisone (Invitrogen), IL-3 (R&D Systems), and erythropoietin (Amgen) according to a published protocol48 (link) with the following modifications. Cells were transduced on day 7 with lentivirus harbouring either the chimpanzee (Pan troglodytes) CMAH cDNA sequence in pLVX-Puro (Clontech) or the empty vector, pLVX-Puro. The CMAH insert was codon-optimized for human expression and synthesized with a C-terminal tobacco etch virus (TEV) cleavage site and FLAG-c-myc tags (GeneArt). Transductants were selected on 2 mg ml−1 puromycin (Sigma–Aldrich). Drug selection was maintained until day 13 when cells were co-cultured on a murine MS-5 stromal cell layer. Cells were replated on MS-5 stroma on day 18 and harvested on day 20 or 21. Cells were stored at 4 °C in incomplete RPMI (RPMI-1640 [Sigma–Aldrich] supplemented with 25 mM HEPES and 50 mg l−1 hypoxanthine) until binding and flow cytometry assays.
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5

Overexpression of Human NLRP3 in Cells

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The full-length human NLRP3 was cloned into pLVX-puro (Clontech, Palo Alto, CA, USA), then pLVX-NLRP3 (oeNLRP3) and pLVX-puro (vector control) were propagated in 293T cells along with packaging plasmids psPAX2 and pMD2.G.
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6

SUMO1 Overexpression and Silencing in HTEC Cells

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Human SUMO1 cDNA was cloned into the lentiviral core plasmid pLVX-Puro (Clontech, Palo Alto, CA, USA) to construct the recombinant plasmid pLVX-Puro-SUMO1. The SUMO1 targeting siRNA sequences (targeting sequence: siSUMO1-1 (238-256): 5'-GCAGTGAGATTCACTTCAA-3'; siSUMO1-2 (395-413): 5'-GGAAGAAGATGTGATTGAA-3'; siSUMO1-3 (727-745): 5'-GGCTTGTGGTGATAAATAA-3' were cloned into lentiviral core plasmid PLKO.1 (Addgene, Cambridge, MA, USA) to construct the recombinant plasmid PLKO.1-shARHGAP18. HTEC cells were pre-cultured in serum-free medium and co-transfected with liposome-mediated recombinant plasmid pLVX-Puro-SUMO1 and packaging plasmids psPAX2 and pMD2G.
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7

SUMO1 Overexpression and Silencing in HTEC Cells

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Human SUMO1 cDNA was cloned into the lentiviral core plasmid pLVX-Puro (Clontech, Palo Alto, CA, USA) to construct the recombinant plasmid pLVX-Puro-SUMO1. The SUMO1 targeting siRNA sequences (targeting sequence: siSUMO1-1 (238-256): 5'-GCAGTGAGATTCACTTCAA-3'; siSUMO1-2 (395-413): 5'-GGAAGAAGATGTGATTGAA-3'; siSUMO1-3 (727-745): 5'-GGCTTGTGGTGATAAATAA-3' were cloned into lentiviral core plasmid PLKO.1 (Addgene, Cambridge, MA, USA) to construct the recombinant plasmid PLKO.1-shARHGAP18. HTEC cells were pre-cultured in serum-free medium and co-transfected with liposome-mediated recombinant plasmid pLVX-Puro-SUMO1 and packaging plasmids psPAX2 and pMD2G.
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8

Cloning and Characterization of EIF1AX Variants

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The cDNAs of the EIF1AX splice variants (c’spl and t’spl)
were cloned by PCR amplification from parental
EIF1AX-A113splice mutant human thyroid cell line HTH83. The
full-length cDNAs of human wild type EIF1AX and the EIF1AX splice variants
(c’spl and t’spl) were cloned into pLVX-puro and the dox-inducible
pLVX-Tight-puro vectors (Clonetech). EIF1AX N-terminal tail (NTT) mutants were
generated from pLVX-puro-EIF1AX-WT by site-directed mutagenesis (Strategene
protocol). The EIF1AX c’spl cDNA was cloned into the pLVX-puro vector or
the pLVX-Tight-puro vector. Bicistronic expression constructs for EIF1AX-WT and
the two EIF1AX splice variants were generated by sequential cloning into
pLVX-Tight-puro, as schematically shown in Supplementary Fig. S2C. The PCR
primers used to amplify EIF1AX-WT, to generate NTT mutants by site-directed
mutagenesis, or to amplify the specific splice variants in cell lines harboring
endogenous EIF1AX mutations are shown in Supplementary Table S5. The TCRS
and the TCRSΔuORF vector systems were provided by Dr. Cor
Calkhoven (ERIBA, Groningen, NL). The targeting plasmid ColA1-TRE (ColA-CHC
system for cDNA expression) used to clone the EIF1AX-c’spl cDNA was
provided by Dr. Luke Dow (Weill Cornell College of Medicine, NY). All constructs
were sequence-verified.
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9

Investigating miR-200c Regulation of Pin1 3'UTR

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Total RNA was isolated from miRNeasy kit (Qiagen) and reversely transcribed by miScript PCR starter kit. Qiagen's miScript PCR system was used to detect miR-200c and miR-15a transcription. MiR-200c was cloned into pLVX-puro (Clonetech) for inducible expression. Cells were exposed to doxycline at final concentration of 4 μg/ml to induce miR-200c expression.
In vitro microRNA binding assay was performed as described (23 (link)). In short, Bluescript plasmid containing the Pin1 3' UTR was used as template in PCR. Forward primer located at the vector. Reverse primer is from the DNA sequence of miR-200c. The parameters for the PCR reaction were: one cycle at 95°C for 5 min; 35 cycles at 95°C for 1 min, 37°C for 1 min, 72°C for 1 min; and a final elongation step at 72°C for 10 min. The PCR products were then visualized with a 1.5% agarose gel stained with ethidium bromide.
For the reporter assay of Pin1 3'UTR by miR-200c, wildtype and mutant Pin1 3'UTR was cloned into a luciferase construct psiCHECK2 (Promega). Cells were harvested and luciferase activity was measured using the Dual-Luciferase Reporter Assay System (Promega).
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10

Lentiviral Transduction of Mammalian Cells

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Viral particles were produced using Lenti-X 293T cells. Briefly, 3x106 Lenti-X-293T cells were seeded one day before transfection. For the transfection assays, Lipofectamine® 3000 (Invitrogen; Thermo Fisher Scientific, Inc.) was used according to the manufacturer's protocol and utilizing a mix of Lenti-X HT packaging systems (4 µg) and 1 µg of one of the following lentiviral vectors, pLVX-Puro (Takara Bio, Inc.) or the pLVX-EF1alpha-SARS-CoV-2-ORF3a-2xStrep-IRES-Puro vector (cat no. 141383; Addgene, Inc.) (43 (link)). After 48 h, to eliminate detached cells and cell detritus, the medium containing the viral particles was filtered through a 0.45-µm polyethersulfone membrane (Merck KGaA). The titer of viral particles was tested using Lenti-X GoStix (Takara Bio, Inc.). The medium containing the viral particles was aliquoted and stored at -80˚C until use. For the transduction assays, 1x106 target cells were seeded one day before transduction. The target cells were transduced with 200 µl medium containing lentiviral particles (~1x106 Inclusion-Forming Units). To obtain stable cell lines, after 72 h of transduction, the cells were incubated with 0.5 µg/ml puromycin for 3 weeks. The medium containing puromycin was replaced every three days; stable cells were cultured under normal conditions without puromycin. Cells were always cultivated or treated at 37˚C in a 5% CO2 atmosphere.
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