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Nov 1, 2011 (Vol. 31, No. 19)

Cutting-Edge Approaches and Applications for RNAi

Powerful Tool's Exquisite Specificity Fuels Its Utility Across a Broad Range of Research Channels

  • Reconstructing Bases

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    Professor Peter Beal’s lab at the University of California-Davis has developed new RNA bases to reduce immune stimulation by siRNAs and miRNA mimics. A) The cPentG nucleoside analog bears a cyclopentane modification of guanosine. When cPentG base pairs with cytidine (C), the cyclopentane projects into the duplex RNA minor groove. B) Model of a mimic of miR122 with two minor groove cyclopentane modifications that eliminate cytokine production in human peripheral blood mononuclear cells while maintaining knockdown of native miR122 targets.

    Most approaches to improve on short interfering RNAs (siRNAs) have focused on the ribose moiety of nucleotides. A largely unexplored but potentially significant route to modulate siRNA properties is the base itself, suggested Peter A. Beal, Ph.D., professor of chemistry, University of California-Davis.

    “Modifying nucleobases within a sequence can exert profound effects on the chemical, biological, and physical properties and interactions of oligonucleotides. Immune stimulation mediated by RNA oligonucleotides harboring certain sequence motifs, such as GU-rich regions, is a significant hurdle to the development of safe and effective RNAi therapeutics.

    “We addressed this challenge in a series of studies in which we employed novel nucleobases in an oligonucleotide mimic of microRNA-122 (miR-122). Because it is already known that modification of the ribose 2´-position can reduce immunostimulation, we constructed our study to also include these modifications for comparison.”

    Dr. Beal and colleagues utilized analogues of adenosine and guanosine that contained cyclopentyl and propyl minor-groove projections. “siRNAs have an A-form helix structure that contains both a major groove and so-called minor groove. The latter is the site of binding for many RNA-interacting proteins. We synthesized guanosine analogs with base modifications that affected the minor groove. Further, we substituted these analogs at different positions within reported immunostimulatory motifs. To test for RNAi activity, we measured the knockdown of two native miR-122 targets (Necap2 and Slc7a1).”

    The results were unanticipated. “To our surprise, we found single nucleotide positions throughout the guide strand of an miRNA-122 mimic acted as immunostimulatory hot spots of activity that did not correspond with putative motifs (e.g., GU-rich regions). We believe these hot spots are locations where RNA and Toll-like receptors interact. Thus, modification of nucleobases at specific positions can control immunostimulatory properties of siRNAs in ways not predicted with traditional immunostimulatory motifs.”

  • Promoter Impact

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    The Thermo Scientific SMARTvector 2.0 system utilizes lentiviral vectors to stably deliver and express gene-silencing reagents capable of entering the RNAi pathway. The figures illustrate the general process by which the lentivirus transduces the cell (1). Upon binding the cell, the viral genome is delivered into the cytoplasm and is reverse-transcribed (i.e., RNA to DNA) (2). The DNA intermediate is imported into the host cell nucleus (3) where it is stably integrated into the host genome (4). The silencing construct is then constitutively expressed and processed into shRNAs that enter the RNAi pathway to effect knockdown (5). With each cellular division, the integrated virus is replicated and passed on to the daughter cells, thus ensuring continued expression of the targeting sequence throughout the population.

    Successful RNAi-mediated knock-down requires efficient delivery of the payload. Traditional methods (e.g., lipid-based reagents) may not work well for certain cell types such as neurons and hematopoietic cells. Viral vectors offer an alternative system for delivery.

    “Viral biology can be engineered to deliver genetic material into cells very effectively and modulate gene expression for both short- and long-term functional studies,” explained Devin Leake, Ph.D., global director of R&D genomics, Thermo Fisher Scientific.

    According to Dr. Leake, a viral vector system needs to address three key parameters. “It must be able to effectively deliver genomic content, have a very broad tropism, and allow for the long-term expression of that content. This requires the careful design of the short hairpin RNA (shRNA), the vector backbone, and choosing the best promoter for the particular cell type utilized.”

    In creating the Thermo Scientific SMARTvector2.0® Lentiviral shRNA platform, the company designed a microRNA-adapted expression scaffold to maximize accurate processing of the silencing sequence while minimizing the potential for off-target effects.

    “We rigorously tested a panel of miRNAs and selected one that could consistently and efficiently be processed by the endogenous RNAi-silencing machinery. It is also necessary to have rationally designed highly functional gene targeting sequences. The SMARTvector2.0 algorithm selects optimal shRNA targeting sequences and includes seed-based filters to reduce toxicity.”

    Another important feature of a lentiviral vector system is the promoter. Although the company initially included the promoter from cytomegalovirus (CMV), it will soon be releasing an a-la-carte series of promoters that investigators may choose.

    “The CMV promoter may be too weak in some cell types. There is no universally optimal promoter, so we have developed a series of SMARTvector backbones with the option of seven different promoters, called the Thermo Scientific SMARTchoice system, which will provide researchers with greater flexibility and more choices for successful RNAi experiments.”

    Thermo Fisher Scientific custom-builds the lentiviral system using the requested promoter and the appropriate sequence for the client’s target of interest. It plans to release the system in the first quarter of 2012.

  • RSV miRNA Tactics

    Respiratory syncytial virus (RSV) infects many children by the age of 2 and causes >100,000 hospitalizations each year in the U.S. It also strikes the elderly resulting in more than 14,000 deaths. Currently there is no safe and effective vaccine against RSV. Further, antiviral drugs are limited. Clinical trials are currently being conducted using RNAi therapeutically against RSV. Additionally use of a humanized mAb (palivizumab) against another RSV protein provides an option for treating infants at risk.

    Ralph A. Tripp, Ph.D., Georgia Research Alliance chair and professor of infectious diseases, is investigating how RSV modulates human miRNAs. “Studies are showing that many viruses like RSV dysregulate host miRNAs to alter host defenses, and that this process can be attributed to specific virally encoded proteins that assist infectious processes. Because single miRNAs are predicted to regulate multiple genes and affect hundreds of processes, a goal of my lab is to determine how RSV infection influences global gene expression in respiratory epithelial cells.”

    Dr. Tripp’s group infected cultured cells with RSV and RSV mutant viruses deficient in single genes and utilized miRNA reporter assays to assess cellular dysfunctions. Next they employed computational algorithms to predict miRNA target genes and found and validated sets of genes targeted by the miRNAs.

    “Our studies demonstrated that in epithelial cells, RSV infection induced five specific miRNAs and repressed two. The RSV-specific proteins modulated miRNAs that affected cell cycle and chemokine genes, and suppressed cytokine signaling genes that control antiviral cytokine responses.”

    These findings may translate into improved therapeutics eventually. “We’ve spent over 35 years trying to produce a vaccine against RSV. Now that we better understand how it controls host immune responses, we have the opportunity to create a new vaccine using miRNAs to create a more robust immune response to RSV. Additionally, development of miRNA agonists or inhibitors could also be envisioned for inhibiting an active RSV infection. Understanding the mechanisms used by RSV to control the host’s response to infection will allow us to develop improved intervention strategies that are safe and effective.”

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