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19 protocols using gv141 vector

1

Silencing SURF4 and BIRC3 Genes Using siRNA and shRNA

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Small-interfering RNAs (siRNAs) against SURF4 and BIRC3, along with RNAi negative controls, were purchased from Genepharma (Shanghai, China). Transfection were performed on cells with the siRNAs (50 nM) using Lipofectamine™ RNAiMAX (ThermoFisher, Waltham, MA, USA) according to the manufacturer's protocol. The siRNA sequences are listed in the Table 1.
The full-length open reading frames with FLAG tag of human BIRC3 (NM_182962) were digested by XhoI and Kpnl, then ligated into GV141 vector (GENECHEM, Shanghai, China). DNA sequencing was applied to verify sequences of all the constructs. The primer sequences are listed in the Table 1. Cells were transfected with plasmid using X-treme GENE HP DNA transfection reagent (Roche, Basel, Switzerland) according to the manufacturer's protocol.
The short-hairpin RNAs (shRNA) for SURF4 oligonucleotides were cloned into hU6-MCS-CMV-puromycin lentivirus expression vectors (GENECHEM, Shanghai, China) between the AgeI and EcoRI sites and then transfected into cells according to instructions. After 72 hours of transfection, the cells were selected using 2 μg/mL puromycin for 4 days. All construct sequences were confirmed using DNA sequencing. The shRNA oligonucleotides are listed in Table 1.
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2

Plasmid Construction for SETDB1 and MCT1 Studies

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The Flag‐SETDB1 and Flag‐SETDB1 H1224K plasmids have been described previously[21]. The plasmid HA‐MCT1 was purchased from GENECHEM, and the DNAs of MCT11‐443 and MCT1444‐500 were cloned into the GV141 vector (GENECHEM). Subsequently, the MCT1 mutants (K462R, K473R, K479R) were generated from the HA‐MCT1 plasmid by a site‐directed mutagenesis kit (C214‐01; Vazyme). The genes of MCT4, P62, Nix, NDP52, Tollip, OPTN, TAX1BP1 were inserted into pcDNA3.1(+) vector. The lentiviral plasmids pLVX‐MCT1‐puro and pLVX‐SETDB1‐neo were constructed by cloning MCT1 and SETDB1 genes into the pLVX‐puro/neo vector. The lentiviral plasmids pLV2‐U6‐SETDB1‐puro or pLV2‐U6‐MCT1‐puro were constructed by inserting the SETDB1 shRNA or the MCT1 shRNA into the pLV2‐U6‐puro vector. The shRNA sequences against human SETDB1 were: 5′‐GCTCAGATGATAACTTCTGTA‐3′, 5′‐AGTTAGAGACATGGGTAATAC‐3′, the sequences against mouse SETDB1 were: 5′‐GAGACTTCATAGAGGAATATA‐3′, 5′‐AAGCAGTTCTCAAGATCTACA‐3′, and the sequence against mouse MCT1 3′UTR was 5′‐GCTTTGTCAGACATTGTTACT‐3′.
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3

Modulating miR-21-3p expression

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Gain and loss of function of miR-21-3p were accomplished by transfecting miRNA mimics and inhibitors, respectively. Mimic- (mimic-NC) and inhibitor- (in-NC) negative controls were purchased from Ribobio. The complementary strand of miR-21-3p served as an inhibitor of miR-21-3p and competed for binding sites between miR-21-3p and target genes, but would not decrease the expression levels of miRNAs. The final concentration of these reagents was 50 nM. The SMAD7 expression vector (P-SMAD7) was constructed using a GV141 vector (GeneChem, China) with plasmids-NC (P-NC) serving as an experimental control. All transfection experiments were performed using Lipofectamine 2000 (Invitrogen, USA) according to manufacturer guidelines.
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4

Lentiviral Overexpression and Knockdown of CCNG1 and Notch3

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The full lengths of CCNG1 (Table 1) were synthesized by Biosune (Shanghai, China) and inserted into Sgf1/MIu1 sites of a PLenti‐C‐Myc/DDKvector (OriGene, 10069). PLenti‐C‐Myc/DDK vector was designated as the mock control. The vector pCMV‐p53mt135 (631922) was bought from Conetech, USA.
Plasmid GV141‐NICD3 (Notch3 intracellular domain plasmid; amino acids 1663 to 2312) was constructed by cloning the NICD3‐coding region (NM_000435‐P1) to GV141 vector (Genechem, CON106). GV141 null vector was designated as the mock control. PCR primers used for amplification of the full‐length cDNAs are shown in Table 1. Ultimately, shRNAs were used to knockdown CCNG1 and Notch3 pathways. Empty pLKO.1 vectors (Addgene, 10878) were used as controls (shRNA sequences displayed in Table 2).
For stable infection, Lentivirus expressing CCNG1 and Plko.1‐shRNA (CCNG1, Notch3, P53 proteins), packaged with psPAX2 (Addgene, 12260) and pMD2G (Addgene, 12259), were produced in HEK293T cells with Lipofectamine 2000 (Invitrogen, 11668019) according to a protocol (Appendix S1). After transfection by Lentivirus for 24 hours, the cells were selected in medium containing 2 μg/mL puromycin (Merck Millipore; Burlington, MA, USA) for two weeks. Stable expression cells were obtained and expanded for further studies.
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5

Cloning and Mutagenesis of Human FSHR

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Wild‐type human FSHR cDNA (NM_000145) was synthesized (General Biotech) and cloned into the GV141 vector (Genechem) to create the fusion protein expression vector pFSHR‐3Flag. The sequences encoding p.Ile61Asn and p.Pro688Thr were amplified from the pFSHR‐3Flag vector using a high‐fidelity DNA polymerase (New England Biolabs). The following oligonucleotides were employed for mutagenesis: FSHR/ p.Ile61Asn P1, 5ʹ‐TGTCCTCACCAAGCTTCGAGTCAACCAAAAAGGTGCATTTTCAGGATTTGGG‐3ʹ; FSHR/ p.Ile61Asn P2, 5ʹ‐CCCAAATCCTGAAAATGCACCTTTTTGGTTGACTCGAAGCTTGGTGAGGACA‐3ʹ; FSHR/ p.Pro688Thr P1: 5ʹ‐CAGCTCCCAGAGTCACCAATGGTTCCACTTACATAC‐3ʹ; and FSHR/ p.Pro688Thr P2: 5ʹ‐GTATGTAAGTGGAACCATTGGTGACTCTGGGAGCTG‐3ʹ. These constructs were transiently transfected into HEK‐293T cells using Lipofectamine® 2000 (Invitrogen). Expression was verified by Western blotting.
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6

FZD2 Silencing and Overexpression

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siRNAs targeting FZD2 were designed and synthesized by Ribobio (Guangzhou, China). For the silencing of FZD2, siRNAs were transfected into SK-BR-3 and MDA-MB-231 cells in accordance with the instruction manual for Lipofectamine 3000 (#L3000015, Invitrogen, Carlsbad, CA, USA). The full-length cDNA sequence of FZD2 was amplified and inserted into GV141 vector (Genechem, China) for overexpressing FZD2. The levels of FZD2 mRNA and protein were separately checked by qRT-PCR and western blot. Sequences for all siRNAs are as follows:
si-FZD2-1CATCCTATCTCAGCTACAA
si-FZD2-2CCATCATGCCCAACCTTCT
si-FZD2-3CCCGATGGTTCCATGTTCT
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7

Modulation of miR-92b-3p in HUVEC

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Transient transfections of negative controls, miR‐92b‐3p mimics, and inhibitor were performed by FECT according to the protocols. The reagents were all purchased from Ribobio Co. miR‐92b‐3p overexpression lentiviruses and lentiviral construct expressing luciferase were purchased from Genechem and used in the experiments. For inhibition, siRNAs against SOX4 were synthesized by Genepharma and transfected by DharmaFECT transfection reagents (T‐2001‐03, Thermo). The SOX4 overexpression plasmids were constructed with the GV141 vector by GeneChem and transfected into HUVECs using X‐tremeGENE HP DNA transfection reagent (43940400, Roche). Exosomes were transfected with miR‐92b‐3p inhibitor using Exo‐Fect Reagent (EXFT10A‐1, SBI).
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8

Transcriptional Regulation by p53 and SMAD3

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Plasmids encoding p53 in the GV141 vector were purchased from GeneChem (Shanghai, China). Both WT and mutant SMAD3 genes were synthesized by chemical methods and cloned downstream of the luciferase gene in GV238 luciferase vectors that were obtained from GeneChem (Shanghai, China). These plasmids and a Renilla luciferase plasmid (GeneChem, Shanghai, China), which was used as a normalization control, were cotransfected into cells using Lipofectamine 3000 (Invitrogen, Shanghai, China). 293T cells (8 × 103 per well) were seeded in 96-well plates the day before transfection, and the cells were cotransfected with 1.25 μg of GV238-SMAD3 and 0.75 μg of p53 DNA when they reached 70%–90% confluence. In total, 50 ng of the expression plasmid (Renilla) was cotransfected as a transfection efficiency control. After 24 h, the cells were harvested, washed three times with PBS, and lysed in 20 μL of passive lysis buffer (PLB) according to the manufacturer’s instructions (Promega, Madison, WI, USA). Cell debris was removed by centrifugation, and the supernatant was used for a luciferase assay read with SpectraMax single-mode microplate readers (Molecular Devices, Sunnyvale, CA, USA).
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9

Investigating miR-148b-3p Regulation of KIT

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miR-148b-3p mimics, miR-148b-3p inhibitor, mimic control and inhibitor control were obtained RiboBio Co. (Guangzhou, Guangdong, China). KIT-coding sequences without the 3′-UTR were cloned into the GV141 vector by GeneChem (Shanghai, China) (called pGV141-KIT). The psiCHECK-2 vector (C8021) was purchased from Promega (Madison, WI, USA). The psiCHECK-2-KIT-wt, psiCHECK-2-KIT-mut-1378, and psiCHECK-2-KIT-mut-1639 were constructed by Bios Biological (Wuhan, Hubei, China). miR-148b-3p agomir and miR agomir NC were generated by GenePharma Co., Ltd. (Shanghai, China). Lipofectamine 3000 (L3000015, Invitrogen, Grand Island, NY, USA) was used to transfect cells with the desired genes or plasmids.
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10

Molecular Cloning of Human Protein Constructs

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The molecular clone protocol was done according to the previous study35 (link). The full-length of human HSP90AA1 (NM_001017963.3), hHNRNPK (NM_002140.5), and hPPARγ (NM_015869.5) open reading frames were amplified and connected with flag label (hHSP90AA1-Flag, hHNRNPK-Flag and hPPARγ-Flag) and then inserted into GV141 vector (GeneChem, Shanghai, China). The primer sequences of hHSP90AA1 were as follows: forward: 3′-ACGGGCCCTCTAGACTCGAGCGCCACCATGCCCCCGTGTTCGGGCGGGGACGGC-5′, reverse: 3′-AGTCACTTAAGCTTGGTACCGAGTCTACTTCTTCCATGCGTGATGTGTC-5′; hHNRNPK, forward: 3′-ACGGGCCCTCTAGACTCGAGCGCCACCATGGAAACTGAACAGCCAGAAG-5′, reverse: 3′-AGTCACTTAAGCTTGGTACCGAGAATCCTTCAACATCTGCATACTGCTTCACACTG-5′; hPPARγ, forward: 3′-ACGGGCCCTCTAGACTCGAGCGCCACCATGGGTGAAACTCTGGGAGATTC-5′, reverse: 3′-AGTCACTTAAGCTTGGTACCGAGTACAAGTCCTTGTAGATCTCCTGC-5′. The product was cut with XhoI/KpnI (New England BioLabs, Inc., Ipswich, MA, USA). The full-length of hHSP90AA1 was inserted into GV314 vector and used to construct the Lentiviral hHSP90AA1 (LV-hHSP90AA1) plasmid.
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