Optimal design and validation of antiviral siRNA for targeting HIV-1

Naito, Yukiko; Nohtomi, Kyoko; Onogi, Toshinari; Uenishi, Rie; Ui-Tei, Kumiko; Saigo, Kaoru; Takebe, Yutaka

doi:10.1186/1742-4690-4-80

Cited by 53 publications

(52 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The sequences for sense and antisense strands are provided in Table S1 in the supplemental material. Sequences for si5983-27/29D were obtained from a published sequence called tat/rev siRNA (site I [tat/rev] 27 mer) (10) and the nonsense siRNA, siNS-25D/27, was adapted from a previous nonsense siRNA called siControl (41). All shRNAs were expressed from the human RNase P H1 promoter in the vector psiRNA-hH1GFPzeo (InvivoGen, San Diego, CA).…”

Section: Methodsmentioning

confidence: 99%

Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats

Scarborough

Adams

Daher³

et al. 2015

Antimicrob Agents Chemother

View full text Add to dashboard Cite

We have previously identified a target site in HIV-1 RNA that was particularly accessible to a ribozyme and a short hairpin RNA (shRNA). To design small interfering RNAs (siRNAs) targeting this site, we evaluated the effects of siRNAs with different lengths on HIV-1 production. The potency and efficacy of these siRNAs were dependent on the length of their intended sense strand with trends for symmetrical and asymmetrical formats that were similar. Although a typical canonical format with a 21-nucleotide (nt) sense strand was effective at inhibiting HIV-1 production, Dicer substrate siRNAs (dsiRNAs) with the longest lengths (27 to 29 nucleotides) were the most effective. Induction of double-stranded RNA immune responses and effects on cell viability were not detected in cells transfected with different siRNAs, suggesting that the differences observed were not related to indirect effects on HIV-1 production. For the corresponding shRNA designs, a different trend in potency and efficacy against HIV-1 production was observed, with the most effective shRNAs having stem lengths from 20 to 27 bp. Our results highlight the importance of evaluating different designs to identify the best siRNA and shRNA formats for any particular target site and provide a set of highly effective molecules for further development as drug and gene therapies for HIV-1 infection.

show abstract

Section: Methodsmentioning

confidence: 99%

Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats

Scarborough

Adams

Daher³

et al. 2015

Antimicrob Agents Chemother

View full text Add to dashboard Cite

show abstract

“…RNAi, directed to viral and/or host RNA sequences, has been employed to inhibit HIV-1 replication (3)(4)(5)(6). These approaches are effective over the short term; however, over longer durations, they have elicited either a high rate of escape mutation when viral sequences are targeted or cytotoxicity when cellular genes are chronically suppressed (7)(8)(9)(10).…”

mentioning

confidence: 99%

A Genome-wide Short Hairpin RNA Screening of Jurkat T-cells for Human Proteins Contributing to Productive HIV-1 Replication

Yeung

Houzet

Yedavalli

et al. 2009

Journal of Biological Chemistry

230

262

View full text Add to dashboard Cite

Short interfering RNAs (siRNAs) have been used to inhibit HIV-1 replication. The durable inhibition of HIV-1 replication by RNA interference has been impeded, however, by a high mutation rate when viral sequences are targeted and by cytotoxicity when cellular genes are knocked down. To identify cellular proteins that contribute to HIV-1 replication that can be chronically silenced without significant cytotoxicity, we employed a shRNA library that targets 54,509 human transcripts. We used this library to select a comprehensive population of Jurkat T-cell clones, each expressing a single discrete shRNA. The Jurkat clones were then infected with HIV-1. Clones that survived viral infection represent moieties silenced for a human mRNA needed for virus replication, but whose chronic knockdown did not cause cytotoxicity. Overall, 252 individual Jurkat mRNAs were identified. Twenty-two of these mRNAs were secondarily verified for their contributions to HIV-1 replication. Five mRNAs, NRF1, STXBP2, NCOA3, PRDM2, and EXOSC5, were studied for their effect on steps of the HIV-1 life cycle. We discuss the similarities and differences between our shRNA findings for HIV-1 using a spreading infection assay in human Jurkat T-cells and results from other investigators who used siRNAbased screenings in HeLa or 293T cells.

show abstract

“…Human immunodeficiency virus (HIV) was one of the first targets for therapeutic application of RNAi. The virus has been targeted by either synthetic siRNA or promoter-expressed short hairpin RNA (shRNA), which are processed by Dicer into siRNAs [9]. However, for HIV and other viruses [10], the use of a single siRNA often results in the emergence of RNAi-escape mutants [11].…”

Section: Targeting Relevant Genes or Genome Regions: Hiv Case Reportmentioning

confidence: 99%

RNAi and small interfering RNAs in human disease therapeutic applications

Lares

Rossi

Ouellet

2010

Trends in Biotechnology

253

173

View full text Add to dashboard Cite

Small interfering RNAs (siRNAs) have shown to effectively down-regulate gene expression in human cells, giving them potential to eradicate disease. Prospects for clinical applications are discussed in this review, along with an overview of recent history and our current understanding of siRNAs used for therapeutic application in human diseases, such as cancer and viral infections. Over recent years, progress has been made in lipids, ligands, nanoparticles, polymers and viral vectors as delivery agents and for gene-based expression of siRNA to enhance the efficacy and specificity of these methods while at the same time reducing toxicity. It has become apparent that given the recent advances in chemistry and delivery, RNAi will soon prove to be an important and widely used therapeutic modality.

show abstract

Optimal design and validation of antiviral siRNA for targeting HIV-1

Cited by 53 publications

References 19 publications

Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats

Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats

A Genome-wide Short Hairpin RNA Screening of Jurkat T-cells for Human Proteins Contributing to Productive HIV-1 Replication

RNAi and small interfering RNAs in human disease therapeutic applications

Contact Info

Product

Resources

About