Functional shRNA expression system with reduced off-target effects

Author(s):  
Yuki Naito ◽  
Kenji Nishi ◽  
Aya Juni ◽  
Kumiko Ui-Tei
2011 ◽  
Vol 16 (10) ◽  
pp. 1247-1253 ◽  
Author(s):  
Bryan D. Marks ◽  
Stephen A. Fakhoury ◽  
William J. Frazee ◽  
Hildegard C. Eliason ◽  
Steven M. Riddle

Developing molecularly targeted therapeutics with minimal off-target effects is facilitated by an understanding of compound selectivity. However, for HDAC inhibitors, a clear understanding of specificity has been challenging. In particular, it has been suggested that use of nonspecific substrates and the presence of multiple HDAC activities in enzyme preparations may complicate interpretation of inhibitor experiments. To overcome these and other potential limitations of activity-based HDAC assays, the authors have developed an assay format based on measurement of the binding affinity of inhibitors rather than measurement of enzyme activity. One advantage of this format is that it does not require use of a substrate and thus ameliorates concerns about lack of specificity of existing substrates. This assay is based on an Alexa Fluor® 647-labeled HDAC inhibitor or “tracer,” which binds with a high affinity to Class I and Class IIb HDACs. Unlike activity assays, which can be affected by the presence of residual untagged endogenous HDACs from the host expression system, the signal in this format is dependent on the presence of an epitope tag on the specific HDAC of interest. The authors demonstrate the utility of this method by determining the potencies of commonly used inhibitors for six human HDACs.


2017 ◽  
Author(s):  
James M. Burke ◽  
Rodney P. Kincaid ◽  
Francesca Aloisio ◽  
Nicole Welch ◽  
Christopher S. Sullivan

AbstractShort hairpin RNAs (shRNAs) are effective in generating stable repression of gene expression. RNA polymerase III (RNAP III) type III promoters (U6 or H1) are typically used to drive shRNA expression. While useful for some knockdown applications, the robust expression of U6/H1-driven shRNAs can induce toxicity and generate heterogeneous small RNAs with undesirable off-target effects. Additionally, the U6 and H1 promoters encompass the majority of the ∼270 base pairs (bp) of vector space required for shRNA expression. This can limit the efficacy and/or number of delivery vector options, particularly when delivery of multiple gene/shRNA combinations is required. Here, we develop a compact shRNA (cshRNA) expression system based on retroviral microRNA (miRNA) gene architecture that uses RNAP III type II promoters. We demonstrate that cshRNAs coded from as little as 100 bps of total coding space can precisely generate small interfering RNAs (siRNAs) that are active in the RNA-induced silencing complex (RISC). We provide an algorithm with a user-friendly interface to design cshRNAs for desired target genes. This cshRNA expression system reduces the coding space required for shRNA expression by greater than two-fold as compared to the U6/H1 promoters, which may facilitate therapeutic RNAi applications where delivery vector space is limiting.


2007 ◽  
Vol 51 (1) ◽  
pp. 57-58
Author(s):  
N. Inoue ◽  
A. Shionoya ◽  
N. Ogawa ◽  
A. Matsuda

Plasmid ◽  
2009 ◽  
Vol 62 (1) ◽  
pp. 50-55 ◽  
Author(s):  
James R. Gilbert ◽  
Christopher S. Adams ◽  
Irving M. Shapiro ◽  
Noreen J. Hickok

2020 ◽  
Author(s):  
Célia Souque ◽  
José A. Escudero ◽  
R.Craig MacLean

AbstractMobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to ‘evolve on demand’ in response to antibiotic pressure. To test this hypothesis, we inserted a custom three cassette integron into P. aeruginosa, and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.


2021 ◽  
Author(s):  
Abtin Behmardi ◽  
Touraj Farazmandfar

Abstract Gene therapy can be an option to overcoming the side effects of chemotherapy and preventing the development of drug-resistant HIV viruses in HIV-infected patients. The need to develop a safe and efficient vector for gene transfer is always necessary and an appropriate option might be adenovirus (Ad). the use of Ad vectors in the gene delivery applications is limited due to the semi-specific tropism. A strategy to overcome this tropism limitation may be the modification of fiber protein domain involved in the viral binding to cells. Therefore, we designed an Ad5 vector with a specific tropism to CD4+ cells containing an expression system limited to HIV-infected cells. We replaced the knob region of Ad5 fiber protein with the extracellular region of HIV-1 envelope. We also used a specific Tat-inducible promoter to express two anti-HIV-1 shRNAs. Tropism of recombinant Ad5 was assayed by comparison of shRNA expression level in CEM and PBMC cells (as CD4+ cells) and HEK293 cells (as CD4- cells). HIV-1 inhibition was assayed by determination of p24 antigen in the HIV-infected CEM cells transduced with the recombinant Ad5 vector. Our results showed that shRNA expression was significantly higher in CEM and PBMC cells than HEK293 cells when were transduced with recombinant Ad5 vector. This new Ad5 vector also inhibited HIV-1 proliferation in a Tat-inducible manner. Our new recombinant Ad5 vector has a specific tropism to CD4-positive cells that can effectively suppress the HIV-1 replication.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2455-2455
Author(s):  
Frida Ponthan ◽  
Hesta McNeill ◽  
Lars Buechler ◽  
Vasily Grinev ◽  
Josef Vormoor ◽  
...  

Abstract Abstract 2455 Background: MLL/AF4 and AML1/MTG8 are fusion genes most frequently found in infant acute lymphoblastic leukaemia (ALL) and acute myeloid leukaemia (AML), respectively. We have previously shown that transient siRNA mediated knock-down of MLL/AF4 and AML/MTG8 impairs proliferation and clonogenicity in vitro and causes a significant increase in median survival in a xeno-transplantation model. Aims: We investigated the role of MLL/AF4 and AML1/MTG8 in leukaemic maintenance and progression of established disease in vivo. We used an inducible lentiviral shRNA expression system to determine the effects of knockdown of MLL/AF4 in the t(4;11)-positive SEM cell line and of AML1/MTG8 in the t(8;21)-positive human leukaemic cell line Kasumi-1. In addition, to allow in vivo imaging SEM and Kasumi-1 cells were labelled with luciferase. Methods: shRNA cassettes specifically targeting the MLL/AF4 and the AML1/MTG8 fusions were cloned into the pTRIPZ vector where shRNA expression and RFP expression are both induced by doxycycline. Luciferase labelled SEM and Kasumi-1 cells were transduced with lentiviral particles, selected with puromycin and transduction efficiency was determined by quantification of RFP positive cells using flow cytometry. Experiments were initiated when more than 65% of the cell populations expressed RFP. Knockdown and expression of known targets of the fusion genes were verified at both the RNA and protein level by qPCR and western blotting, respectively. Cell growth was monitored by cell counts. Immunodeficient NSG mice were given doxycycline in the diet (625ppm) from two days prior to intrafemoral transplantations with 106 luciferase labelled SEM and Kasumi cells transduced with pTRIPZshAML1/MTG8 or pTRIPZshMLL/AF4. The food was changed every other day and disease progression was monitored using in vivo bioluminescence imaging. Results: Upon induction of shRNA expression in vitro Kasumi-1 cells transduced with pTRIPZshAML1/MTG8 showed decreased expression of AML1/MTG8 at protein and RNA levels, which correlated with impaired proliferation. Furthermore, the AML1/MTG8 knockdown resulted in decreased CD34 expression and increased levels of IGFBP7 and PRG2. Induction of shMLL/AF4 expression in SEM cells resulted in decreased expression levels of MLL/AF4 with concomitant decreased expression of HOXA7. However, the number of RFP positive SEM pTRIPZshMLL/AF4 cells decreased over time. When we investigated the in vivo consequences of fusion-gene knockdown in transplanted NSG mice we found no significant differences in overall survival. Notably, mice transplanted with pTRIPZshAML1/MTG8-transduced Kasumi-1 cells showed a lower grade of disseminated disease compared to mice transplanted with pTRIPZshMLL/AF4-transduced Kasumi-1 cells. Furthermore, tumours from these mice had significantly lower RNA and protein levels of AML1/MTG8 (p<0.05). We could not verify knockdown of MLL/AF4 in tumour cells harvested from mice transplanted with SEM pTRIPZshMLL/AF4. Interestingly, these cells showed a complete loss of RFP expression compared to SEM transduced with pTRIPZshAML1/MTG8 (p<0.05). Conclusions: Knockdown of MLL/AF4 and AML1/MTG8 in vitro using an inducible shRNA system led to decreased proliferation and affected genes associated with differentiation. However, the effects were delayed compared to transient siRNA knockdown. In vivo optical imaging is a useful tool to monitor leukaemic progression in vivo. The technique gives information about location and degree of disease dissemination in addition to the overall survival. The loss of RFP expression particularly in SEM pTRIPZshMLL/AF4 cells both in vitro and in vivo highlights the significance of MLL/AF4 in leukaemic maintenance. Further in vitro and in vivo experiments are currently ongoing with knockdown of AML1/MTG8 and MLL/AF4 in alternative cell lines and primary patient-derived material. Disclosures: No relevant conflicts of interest to declare.


2007 ◽  
Vol 35 (7) ◽  
pp. e54 ◽  
Author(s):  
Jost Seibler ◽  
Andre Kleinridders ◽  
Birgit Küter-Luks ◽  
Sandra Niehaves ◽  
Jens C. Brüning ◽  
...  

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Célia Souque ◽  
José Antonio Escudero ◽  
R Craig MacLean

Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to ‘evolve on demand’ in response to antibiotic pressure. To test this hypothesis, we inserted a custom three-cassette integron into Pseudomonas aeruginosa and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.


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