1
|
Reporter Gene Assays Using Viral Functional Genomics Libraries. Methods Mol Biol 2018. [PMID: 29671267 DOI: 10.1007/978-1-4939-7724-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
While transfectable libraries are the workhorse for many screening cores, there is one obvious area where these reagents are not useful-hard to transfect cell lines and primary cells. One solution to this problem is the use of virus to introduce genomic reagents. This strategy is more commonplace now than ever before with libraries covering cDNAs, shDNAs, miRNAs, and guide RNAs readily available. Maintenance and use of these libraries are more challenging than the transient transfection approach due to the viral production step, and the infrastructure necessary to generate them. The following pages will delve into the details for working with arrayed well formats for both lentiviral and retroviral libraries.
Collapse
|
2
|
Aguiar S, van der Gaag B, Cortese FAB. RNAi mechanisms in Huntington's disease therapy: siRNA versus shRNA. Transl Neurodegener 2017; 6:30. [PMID: 29209494 PMCID: PMC5702971 DOI: 10.1186/s40035-017-0101-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/30/2017] [Indexed: 12/19/2022] Open
Abstract
Huntington's Disease (HD) is a genetically dominant trinucleotide repeat disorder resulting from CAG repeats within the Huntingtin (HTT) gene exceeding a normal range (> 36 CAGs). Symptoms of the disease manifest in middle age and include chorea, dystonia, and cognitive decline. Typical latency from diagnosis to death is 20 years. There are currently no disease-modifying therapies available to HD patients. RNAi is a potentially curative therapy for HD. A popular line of research employs siRNA or antisense oligonucleotides (ASO) to knock down mutant Huntingtin mRNA (mHTT). Unfortunately, this modality requires repeated dosing, commonly exhibit off target effects (OTEs), and exert renal and hepatic toxicity. In contrast, a single AAV-mediated short-hairpin RNA (shRNA) dose can last years with low toxicity. In addition, we highlight research indicating that shRNA elicits fewer OTEs than siRNA when tested head-to-head. Despite this promise, shRNA therapy has been held back by difficulties controlling expression (oversaturating cells with toxic levels of RNA construct). In this review, we compare RNAi modalities for HD and propose novel methods of optimizing shRNA expression and on-target fidelity.
Collapse
Affiliation(s)
- Sebastian Aguiar
- Molecular Neuroscience Laboratory, Swammerdam Institute for Life Sciences (SILS-CNS), University of Amsterdam, Amsterdam, Netherlands
- Fulbright Program, US Department of State (IIE), New York City, NY USA
| | - Bram van der Gaag
- Molecular Neuroscience Laboratory, Swammerdam Institute for Life Sciences (SILS-CNS), University of Amsterdam, Amsterdam, Netherlands
- Department of Neurobiology, Care Sciences and Society, Karolinska Institute, Stockholm, Sweden
| | - Francesco Albert Bosco Cortese
- Biogerontology Research Foundation (BGRF), Oxford, UK
- Department of Biomedical and Molecular Sciences, Queen’s University School of Medicine, Queen’s University, Kingston, Canada
| |
Collapse
|
3
|
Weng Y, Shi Y, Xia X, Zhou W, Wang H, Wang C. A multi-shRNA vector enhances the silencing efficiency of exogenous and endogenous genes in human cells. Oncol Lett 2017; 13:1553-1562. [PMID: 28454290 PMCID: PMC5403481 DOI: 10.3892/ol.2017.5672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/27/2016] [Indexed: 01/10/2023] Open
Abstract
RNA interference (RNAi) is a powerful technology for suppressing gene function. In most studies, small interfering RNAs (siRNAs) consist of one short hairpin RNA (shRNA) and, therefore, are often unable to achieve loss-of-function of their target genes. In the current study, an RNAi vector containing three shRNAs under the control of three RNA polymerase III U6 promoters was constructed. RNAi vectors containing one or two shRNAs were generated for comparisons. A pilot study targeting exogenously expressed DsRed in the HEK293 cell line revealed promising effects and a high selectivity for the multi-shRNA RNAi vector. Akt2 is constitutively expressed in cultured SKOV3 human ovarian cancer cells, and the multi-shRNA RNAi vector showed a strong efficiency for downregulating the expression of Akt2 in these cells, with no apparent interferon response. In addition, the Akt2-3shRNA vector, containing three shRNAs targeting Akt2, showed the best effect of all the shRNA vectors in reversing paclitaxel-induced resistance in SKOV3 cells. This study developed a widely applicable resource for enhancing the efficiency of gene silencing and a novel technique for performing complex loss-of-function screens in mammalian cells.
Collapse
Affiliation(s)
- Yanjie Weng
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Ying Shi
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xi Xia
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China.,Department of Gynecology and Obstetrics, Affiliated Shenzhen Nanshan Hospital, Guangdong Medical College, Shenzhen, Guangdong 518052, P.R. China
| | - Wenjuan Zhou
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Hongyan Wang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Changyu Wang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| |
Collapse
|
4
|
Zhang X, Chibli H, Mielke R, Nadeau J. Ultrasmall Gold−Doxorubicin Conjugates Rapidly Kill Apoptosis-Resistant Cancer Cells. Bioconjug Chem 2010; 22:235-43. [DOI: 10.1021/bc100374p] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Xuan Zhang
- Department of Biomedical Engineering, McGill University, 3775 University Street, Montreal,
Quebec, Canada H3A 2B4
| | - Hicham Chibli
- Department of Biomedical Engineering, McGill University, 3775 University Street, Montreal,
Quebec, Canada H3A 2B4
| | - Randall Mielke
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
91109, United States
| | - Jay Nadeau
- Department of Biomedical Engineering, McGill University, 3775 University Street, Montreal,
Quebec, Canada H3A 2B4
| |
Collapse
|
5
|
Klinghoffer RA, Magnus J, Schelter J, Mehaffey M, Coleman C, Cleary MA. Reduced seed region-based off-target activity with lentivirus-mediated RNAi. RNA (NEW YORK, N.Y.) 2010; 16:879-884. [PMID: 20348445 PMCID: PMC2856882 DOI: 10.1261/rna.1977810] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Accepted: 02/01/2010] [Indexed: 05/29/2023]
Abstract
Along with silencing intended target genes, transfected siRNAs regulate numerous unintended transcripts through a mechanism in which the equivalent of a microRNA-like seed region in the siRNA recognizes complementary sequences in transcript 3' UTRs. Amelioration of this off-target silencing would lead to more accurate interpretation of RNA interference (RNAi) experiments and thus greatly enhance their value. We tested whether lentivirus-mediated delivery of shRNA is prone to the sequence-based off-target activity prevalent in siRNA experiments. We compared target gene silencing and overall impact on global gene expression caused by multiple sequences delivered as both transfected siRNAs and lentivirus vector-expressed shRNAs. At equivalent levels of target gene silencing, signatures induced by shRNAs were significantly smaller than those induced by cognate siRNAs and arose less frequently from seed region activity. Interestingly, the low level of seed region-based off-target activity exhibited by shRNAs resulted in down-regulation of transcripts that were largely distinct from those regulated by siRNAs. On the basis of these observations, we recommend lentivirus-mediated RNAi for pathway profiling experiments that measure whole genome transcriptional readouts as well as for large-scale screens when resources for extensive follow up are limited.
Collapse
|
6
|
Klinghoffer RA, Frazier J, Annis J, Berndt JD, Roberts BS, Arthur WT, Lacson R, Zhang XD, Ferrer M, Moon RT, Cleary MA. A lentivirus-mediated genetic screen identifies dihydrofolate reductase (DHFR) as a modulator of beta-catenin/GSK3 signaling. PLoS One 2009; 4:e6892. [PMID: 19727391 PMCID: PMC2731218 DOI: 10.1371/journal.pone.0006892] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 08/06/2009] [Indexed: 11/18/2022] Open
Abstract
The multi-protein beta-catenin destruction complex tightly regulates beta-catenin protein levels by shuttling beta-catenin to the proteasome. Glycogen synthase kinase 3beta (GSK3beta), a key serine/threonine kinase in the destruction complex, is responsible for several phosphorylation events that mark beta-catenin for ubiquitination and subsequent degradation. Because modulation of both beta-catenin and GSK3beta activity may have important implications for treating disease, a complete understanding of the mechanisms that regulate the beta-catenin/GSK3beta interaction is warranted. We screened an arrayed lentivirus library expressing small hairpin RNAs (shRNAs) targeting 5,201 human druggable genes for silencing events that activate a beta-catenin pathway reporter (BAR) in synergy with 6-bromoindirubin-3'oxime (BIO), a specific inhibitor of GSK3beta. Top screen hits included shRNAs targeting dihydrofolate reductase (DHFR), the target of the anti-inflammatory compound methotrexate. Exposure of cells to BIO plus methotrexate resulted in potent synergistic activation of BAR activity, reduction of beta-catenin phosphorylation at GSK3-specific sites, and accumulation of nuclear beta-catenin. Furthermore, the observed synergy correlated with inhibitory phosphorylation of GSK3beta and was neutralized upon inhibition of phosphatidyl inositol 3-kinase (PI3K). Linking these observations to inflammation, we also observed synergistic inhibition of lipopolysaccharide (LPS)-induced production of pro-inflammatory cytokines (TNFalpha, IL-6, and IL-12), and increased production of the anti-inflammatory cytokine IL-10 in peripheral blood mononuclear cells exposed to GSK3 inhibitors and methotrexate. Our data establish DHFR as a novel modulator of beta-catenin and GSK3 signaling and raise several implications for clinical use of combined methotrexate and GSK3 inhibitors as treatment for inflammatory disease.
Collapse
|