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To identify novel regulators of transcription factors, we developed an approach to screen arrayed lentiviral or retroviral RNAi libraries using a dual-luciferase-based transcriptional reporter assay. This approach offers a quick and relatively inexpensive way to screen hundreds of candidates in a single experiment.
Transcription factors can alter the expression of numerous target genes that influence a variety of downstream processes making them good targets for anti-cancer therapies. However, directly targeting transcription factors is often difficult and can cause adverse side effects if the transcription factor is necessary in one or more adult tissues. Identifying upstream regulators that aberrantly activate transcription factors in cancer cells offers a more feasible alternative, particularly if these proteins are easy to drug. Here, we describe a protocol that can be used to combine arrayed medium-scale lentiviral libraries and a dual-luciferase-based transcriptional reporter assay to identify novel regulators of transcription factors in cancer cells. Our approach offers a quick, easy, and inexpensive way to test hundreds of genes in a single experiment. To demonstrate the use of this approach, we performed a screen of an arrayed lentiviral RNAi library containing several regulators of Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ), two transcriptional co-activators that are the downstream effectors of the Hippo pathway. However, this approach could be modified to screen for regulators of virtually any transcription factor or co-factor and could also be used to screen CRISPR/CAS9, cDNA, or ORF libraries.
The purpose of this assay is to use viral libraries to identify regulators of transcription factors in a relatively quick and inexpensive manner. Aberrant transcriptional activity is associated with cancer and metastasis1,2,3,4,5,6, so targeting transcription factors in cancer cells is a promising therapeutic approach. However, transcription factors are often difficult to target pharmacologically7 and many are required for normal cellular function in adult tissues8,9,10. Targeting the cancer-associated pathways that aberrantly activate transcription factors to drive disease is a more feasible approach with the potential to have less severe side effects. The commercial availability of arrayed lentiviral and retroviral RNAi, CRISPR/CAS9, cDNA, or ORF libraries allows researchers to test the importance of numerous genes in a single experiment. However, a reliable readout for altered transcriptional activity is required.
Here, we describe the use of a dual-luciferase-based transcriptional reporter assay and arrayed lentiviral libraries to identify proteins that regulate transcription factors in cancer cells. In this assay, shRNAs that target cancer-associated genes are delivered to mammalian cancer cells via lentiviral transduction and cells are selected for stable integration using puromycin. The cells are next transfected with a reporter construct that expresses firefly luciferase driven by a promoter specific to the transcription factor that is being investigated and a control construct that expresses Renilla luciferase from a constitutively active promoter that is not responsive to the transcription factor being investigated. We demonstrate this approach with a proof-of-concept screen for regulators of YAP and TAZ, the critical downstream effectors of the Hippo pathway8,10,11. Abnormal activity of YAP and TAZ promotes several steps of the metastatic cascade11 and is observed in many cancers11,12,13. However, how YAP and TAZ become aberrantly activated in some cancer cells is not yet fully understood. YAP and TAZ do not bind DNA, but instead are recruited to promoters by other transcription factors. Members of the TEA domain (TEAD) family of transcription factors are the major binding partners for YAP and TAZ, and are critical for most YAP and TAZ-dependent functions. Our reporter construct expresses firefly luciferase from a YAP/TAZ-TEAD-responsive promoter and previous studies have demonstrated that it faithfully detects changes in YAP-TEAD and TAZ-TEAD transcriptional activity2,14,15.
Our approach is rapid, medium-throughput, and does not require screening facilities, automated robots, or deep sequencing of pooled libraries. The costs are relatively low and there are numerous commercially available libraries to choose from. The required equipment and reagents are also relatively standard in most laboratories. It can be used to screen for regulators of virtually any transcription factor if a luciferase-based reporter exists or is generated. We use this approach to screen shRNAs in cancer cells, but any cell line that can be transfected with reasonable efficiency could be used with any type of arrayed library.
NOTE: A schematic summary of this protocol is shown in Figure 1.
1. Lentiviral vector library preparation
NOTE: The demonstrated screen used an arrayed shRNA library purchased as glycerol stocks in 96-well plates, but libraries can also be assembled manually based on a list of candidates. Appropriate controls should be considered and included in any library. This includes a non-targeting control shRNA (shNTC), a control shRNA targeting the transcription factor being investigated, and if possible, an shRNA targeting firefly luciferase.
2. Packaging of the arrayed lentiviral library
NOTE: All work involving lentivirus, including packaging, infection, and subsequent culturing of infected cells should strictly follow the institutional biosafety rules and regulations.
3. Infection of the cells for the screen
NOTE: Human melanoma cells (A375) were used to demonstrate this approach, but this method can be applied to any adherent cells that infect with lentivirus. However, cell culture and plating conditions should be optimized for each cell line (see Discussion).
4. Seeding cells for transfection of dual-luciferase reporter
NOTE: A test transfection should be done to determine the optimal seeding density for each new cell line.
5. Transfection of dual-luciferase reporter
6. Quantification of dual-luciferase activity
Our YAP/TAZ-TEAD reporter construct (pGL3-5xMCAT (SV)-492,14,15) contains a minimal SV-49 promoter with 5 repeats of the canonical TEAD binding element (MCAT)15 driving the firefly luciferase gene (Figure 1). It is co-transfected into cells along with the PRL-TK control vector (Promega), which expresses Renilla luciferase from the con...
In this study, we demonstrate an approach for medium-throughput screening of arrayed viral libraries in combination with a dual-luciferase-based transcriptional reporter assay that can be used to identify and test novel regulators of transcription factors. It is critical to characterize and optimize the reporter system for each cell line prior to any screen. Experiments should be done to confirm that the reporter is responsive to altered activity of the transcription factor being investigated and the magnitude of change ...
The authors have nothing to disclose.
We would like to thank Emily Norton and Mikaelan Cucciarre-Stuligross for assisting in the preparation of shRNA vectors. This work was supported in part by a Susan G. Komen Career Catalyst Grant that awarded to J.M.L. (#CCR17477184).
Name | Company | Catalog Number | Comments |
2.0 ml 96-well deep well polypropylene plate | USA Scientific | 1896-2000 | For bacterial mini-prep |
Trypsin - 2.50% | Gibco | 15090-046 | Component of trypsin-EDTA |
96 well flat bottom white assay plate | Corning | 3922 | For dual-luciferase assay |
Ampicillin - 100 mg/ml | Sigma-Aldrich | 45-10835242001-EA | For bacterial mini-prep |
Bacto-tryptone - powder | Sigma-Aldrich | 95039 | Component of LB broth |
Dual-luciferase reporter assay system, which include LAR II reagent (reagent A), Stop & Glo substrate (reagent B substrate) and Stop & Glo buffer (reagent B buffer) - Kit | Promega | E1960 | For dual-luciferase assay |
Dulbecco's phosphate buffered saline w/o calcium, magnesium and phenol red - 9.6 g/L | Himedia | TS1006 | For PBS |
EDTA - 0.5 M | VWR | 97061-406 | Component of trypsin-EDTA |
Ethanol - 100% | Pharmco-AAPER | 111000200 | For bacterial mini-prep |
Foetal Bovine Serum - 100% | VWR | 97068-085 | Component of complete growth media |
Hexadimethrine bromide (Polybrene) - 8 mg/ml | Sigma-Aldrich | 45-H9268 | For virus infection |
HyClone DMEM/High glucose - 4 mM L-Glutamine; 4500 mg/L glucose; sodium pyruvate | GE Healthcare life sciences | SH30243.01 | Component of complete growth media |
I3-P/i3 Multi-Mode Microplate/EA | Molecular devices | For dual-luciferase assay | |
L-Glutamine - 200 mM | Gibco | 25030-081 | Component of complete growth media |
Lipofectamine 3000 (Transfection Reagent 2) - 100% | Life technologies | L3000008 | For transfections |
Molecular Biology Water - 100% | VWR | 02-0201-0500 | For dilution of shRNA vector for virus packaging |
NaCl - powder | BDH | BDH9286 | Component of LB broth |
NanoDrop One Microvolume UV-Vis Spectrophotometer | Thermo scientific | For measuring vector DNA concentration | |
Opti-MEM (Transfection Buffer) - 100% | Gibco | 31985-062 | For transfections |
Penicillin Streptomycin - 10,000 Unit/ml (Penicillin); 10,000 µg/ml (Streptomycin) | Gibco | 15140-122 | Component of complete growth media |
PureLink Quick Plasmid Miniprep Kit - Kit | Thermo Fisher Scientific | K210010 | For bacterial mini-prep |
Puromycin - 2.5 mg/ml | Sigma-Aldrich | 45-P7255 | For antibiotic selection after infection |
TC20 automated cell counter | Bio-Rad | For cell counting | |
X-tremeGENE 9 DNA transfection reagent (Transfection Reagent 1) - 100% | Roche | 6365787001 | For virus packaging |
Yeast extract - powder | VWR | J850 | Component of LB broth |
P3000 (Transfection Reagent 3) - 100% | Life technologies | L3000008 | For transfections |
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