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7 protocols using mscv pig

1

BDH1 Gene Cloning and Expression

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The CDS of BDH1, encoding the human BDH1 gene, was amplified through PCR using primers 5′-TATAGCTAGCATGCTGGCCACCCG-3′ and 5′-TATAACCGGTTCAGCGGATGTAGATCAT-3′, and then cloned into pLJM1-EGFP lentiviral vector (Addgene, 19319). The CDS of mouse Bdh1 gene was amplified through PCR using primers 5′-TATACTCGAGATGCTAGCTGCC-3′ and 5′- TATAGAATTCTCAGTGTATGTAGATCTTGT-3’, and then ligated into a retroviral vector, namely MSCV-PIG (Addgene, 105594).
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2

Cloning of Tumor Suppressor Genes

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TSG cDNAs (see Supplementary Table S10) were cloned, by PCR (using primers listed in Supplementary Table S9) followed by restriction enzyme digestion, into MSCV PIG (Puro-IRES-GFP) (Addgene plasmid 18751). For some genes, a 3xFlag tag sequence was incorporated into the primers for cloning in-frame with the target gene. For further details, please refer to the Supplementary Methods.
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3

Retroviral Expression of XBP1 and UFBP1

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cDNA from mouse XBP1u, XBP1s, and human Ufbp1, and its mutant Ufbp1K267R were cloned into retrovirus vector MSCV-PIG (Addgene, cat# #18751) and/or MSCV-Thy1.1 (Addgene, cat# 17442). Retroviruses were prepared using Plat-E packaging cell line (Cell Biolabs, Inc, cat # RV-101). Viral supernatants were concentrated by centrifugation at 10,000 × g at 4 °C overnight. LPS-stimulated B cells were infected with retrovirus by centrifugation at 700 × g for 30 min in the presence of 4 µg/ml polybrene. Two days after infection, cells were analyzed as indicated in figure legends.
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4

Constructing LentiCRISPR-v2 and MSCV-P11 Vectors

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LentiCRISPR-v2 plasmid was a gift from Dr. Feng Zhang of Broad Institute of MIT and Harvard. LentiCRISPRv2-p11-gRNA was constructed as described previously 45 (link), 46 (link). Briefly, P11-gRNAs were designed according to CRISPR Design Tool (http://crispr.mit.edu/) and synthesized with BsmBI sticky end, then annealed and inserted into the BsmBI (Fermentas, Vilnius, Lithuania) digested lentiCRISPR-v2 plasmid. For constructing lentiviral vector MSCV- P11, the P11 coding sequence was amplified using wild-type MEF cDNA as the template, and then digested with XhoI and EcoRI (Fermentas), and cloned into MSCV PIG(18751, Addgene, Cambridge, USA). Primer sequences are described below (restriction enzyme recognition sites shown underlined):
F(5'-3'): AATCTCGAGATGCCATCCCAAATGGAGCAC; R(5'-3'): AATGAATTCCTACTTCTTCCCCTTCTGCT.
Cas9 expression vector (pST1374-N-NLS-flag-linkerCas9) for in vitro transcription (44758) and PUC57-sgRNA expression vector (51132) were obtained from Addgene. P11-gRNAs were designed according to CRISPR Design Tool (http://crispr.mit.edu/). Synthesized oligos for gRNA expression were denatured at 95 °C for 5 minutes and annealed at room temperature, then cloned into linearized PUC57-sgRNA expression vector.
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5

Retroviral Overexpression of MYC Mutant

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Mouse MycT58A cDNA was cloned into MSCV-Puro-IRES-GFP (MSCV-PIG) (Addgene cat# 21654) (Mayr and Bartel, 2009 (link)) plasmid for retroviral overexpression of MYC in vitro. MSCV-PIG-MYCT58A plasmid was confirmed by direct sequencing. For generation of high-titer virus, HEK-293T cells were transfected with a three-plasmid system including: MSCV-PIG (Addgene cat# 21654) with an empty vector or Myc T58A insert, pCMV-VSVG (Stewart et al., 2003 (link)), (Addgene cat# 8454), and pCMV delta R8.2 (Stewart et al., 2003 (link)) (Addgene cat# 8455). Viruses were harvested at 48 and 72 h post-transfection, concentrated by ultracentrifugation (24,000 x g for 1.45 h), and stored at −80°C until use. MYCT58A was overexpressed in human cell lines (H889, H1963) or RPR2 primary cells through retroviral spinoculation. Spinoculation was performed at 37°C, 900 x g, for 75 min. During spinoculation, 0.5-1 million cells per well of a 6-well plate were cultured with 2 mL RPMI, 25 μL HEPES buffer (Thermo Fisher cat# 15630080), 8 μg/mL polybrene (Santa Cruz cat# sc-134220), and 25 μL retroviral MSCV-PIG or MSCV-PIG-MYCT58A with titer >106 infectious units/mL. Cells were selected 48 h after spinoculation with puromycin at a concentration of 1 μg/mL (H889) or 0.5 μg/mL (H1963, RPR2) until uninfected control cells were dead.
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6

Stable Transfection of sPD-1 in PC3 Cells

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The HPV16-associated cervical cancer cell line, CaSki, and a HPV-negative epithelial cell line, PC3, were obtained from the China Center for Type Culture Collection (Wuhan, China). Cells were cultured in RPMI-1640 medium (Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) supplemented with 10% newborn calf serum (NBCS; Gibco; Thermo Fisher Scientific, Inc.) and 1% penicillin/streptomycin (North China Pharmaceutical Co., Ltd., Hebei, China) at 37°C in 5% CO2. Purified plasmids MSCVPIG (Addgene, Cambridge, MA, USA) and MSCVPIG-sPD-1 (constructed in the lab) were stably transfected into PC3 cells (1×105/ml) using Lipofectamine 2000 (Invitrogen; Thermo Fisher Scientific, Inc.) according to the manufacturer's instructions. After 2 weeks, positive clones were selected based on their resistance to G418 (800 mg/ml; North China Pharmaceutical Co., Ltd.), which were analyzed by reverse transcription-polymerase chain reaction (RT-PCR), flow cytometry and western blot analysis.
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7

Retroviral Transduction of Mouse TET2

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Cell lines were infected with retroviral vectors (pMSCV-PIG) containing either empty vector (EV) or a mouse TET2 full-length cDNA. pcDNA3-Tet2 (#60939) and MSCV PIG (Puro-IRES GFP) (#18751) were obtained from Addgene. Mm TET2 cDNA was subcloned from pcDNA3-Tet2 using SnaBI/NotI restriction sites, into adapted pMSCV-PIG (Puro-IRES-GFP) plasmid using HpaI/NotI restriction sites. Adapted pMSCV-PIG plasmid vector was modified with destroyed second EcoRI site and introduced NotI site and was a gift from Dr. Honglin Li, Augusta University. pMSCV-PIG-MmTET2 clone was verified via DNA sequencing. Briefly, Phoenix-Ampho cells were transfected using Lipofectamine 2000 (Invitrogen) with pMSCV-PIG plasmid. Virus particles were collected for spinoculation at 2400 rpm for 2 h at 32 °C. Upon selection of positive cells with 2–4 µg of puromycin, cDNA expression was detected using RT-qPCR for TET2.
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